diff --git a/.cache.tar.xz b/.cache.tar.xz index 7188532c0d..10245ec8f5 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 77bf777c99..d8142977b7 100644 --- a/public/components.json +++ b/public/components.json @@ -21,52 +21,65 @@ "doi": "10.1093/bioinformatics/btp347", "licence": [ "GPL v2-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "scaffold": { - "type": "file", - "description": "Fasta file containing scaffold", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "file", - "description": "List containing abacas output files\n[ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',\n'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',\n'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',\n'test.abacas.tab', 'test.abacas.unused.contigs.out',\n'test.abacas.MULTIFASTA.fa' ]\n", - "pattern": "*.{abacas}*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:abacas" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "scaffold": { + "type": "file", + "description": "Fasta file containing scaffold", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.abacas*": { + "type": "file", + "description": "List containing abacas output files\n[ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',\n'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',\n'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',\n'test.abacas.tab', 'test.abacas.unused.contigs.out',\n'test.abacas.MULTIFASTA.fa' ]\n", + "pattern": "*.{abacas}*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106,52 +119,65 @@ "tool_dev_url": "https://github.com/tseemann/abricate", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "FASTA, GenBank or EMBL formatted file", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" - } - }, - { - "databasedir": { - "type": "directory", - "description": "Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb`", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "report": { - "type": "file", - "description": "Tab-delimited report of results", - "pattern": "*.{txt}" - } + ], + "identifier": "biotools:ABRicate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "FASTA, GenBank or EMBL formatted file", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" + } + } + ], + [ + { + "databasedir": { + "type": "directory", + "description": "Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb`", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited report of results", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -189,45 +215,56 @@ "tool_dev_url": "https://github.com/tseemann/abricate", "licence": [ "GPL v2" - ] + ], + "identifier": "biotools:ABRicate" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reports": { - "type": "file", - "description": "FASTA, GenBank or EMBL formatted file", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reports": { + "type": "file", + "description": "FASTA, GenBank or EMBL formatted file", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited report of aggregated results", + "pattern": "*.{txt}" + } + } + ] }, { - "report": { - "type": "file", - "description": "Tab-delimited report of aggregated results", - "pattern": "*.{txt}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -260,67 +297,129 @@ "doi": "10.1038/s41467-022-35713-4", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembled contigs in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "matches": { - "type": "file", - "description": "Tab-delimited file, with a row per sequence, and columns representing functional drug classes", - "pattern": "*.summary_matches.txt" - } - }, - { - "partials": { - "type": "file", - "description": "Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes", - "pattern": "*.summary_partials.txt" - } - }, - { - "virulence": { - "type": "string", - "description": "Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification", - "pattern": "*.summary_virulence.txt" - } - }, - { - "txt": { - "type": "string", - "description": "Tab-delimited file, combining non-empty summary files", - "pattern": "*.abritamr.txt" - } - }, - { - "out": { - "type": "string", - "description": "raw output from AMRFinder plus (per sequence)", - "pattern": "*.amrfinder.txt" - } + ], + "identifier": "biotools:abritamr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembled contigs in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + } + } + ] + ], + "output": [ + { + "matches": [ + { + "meta": { + "type": "file", + "description": "Tab-delimited file, with a row per sequence, and columns representing functional drug classes", + "pattern": "*.summary_matches.txt" + } + }, + { + "${prefix}.summary_matches.txt": { + "type": "file", + "description": "Tab-delimited file, with a row per sequence, and columns representing functional drug classes", + "pattern": "*.summary_matches.txt" + } + } + ] + }, + { + "partials": [ + { + "meta": { + "type": "file", + "description": "Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes", + "pattern": "*.summary_partials.txt" + } + }, + { + "${prefix}.summary_partials.txt": { + "type": "file", + "description": "Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes", + "pattern": "*.summary_partials.txt" + } + } + ] + }, + { + "virulence": [ + { + "meta": { + "type": "string", + "description": "Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification", + "pattern": "*.summary_virulence.txt" + } + }, + { + "${prefix}.summary_virulence.txt": { + "type": "string", + "description": "Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification", + "pattern": "*.summary_virulence.txt" + } + } + ] + }, + { + "out": [ + { + "meta": { + "type": "string", + "description": "raw output from AMRFinder plus (per sequence)", + "pattern": "*.amrfinder.txt" + } + }, + { + "${prefix}.amrfinder.out": { + "type": "string", + "description": "raw output from AMRFinder plus (per sequence)", + "pattern": "*.amrfinder.txt" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "string", + "description": "Tab-delimited file, combining non-empty summary files", + "pattern": "*.abritamr.txt" + } + }, + { + "${prefix}.abritamr.txt": { + "type": "string", + "description": "Tab-delimited file, combining non-empty summary files", + "pattern": "*.abritamr.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -352,87 +451,173 @@ "documentation": "https://adapterremoval.readthedocs.io", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" - } - }, - { - "adapterlist": { - "type": "file", - "description": "Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args." - } - } - ], - "output": [ - { - "singles_truncated": { - "type": "file", - "description": "Adapter trimmed FastQ files of either single-end reads, or singleton\n'orphaned' reads from merging of paired-end data (i.e., one of the pair\nwas lost due to filtering thresholds).\n", - "pattern": "*.truncated.fastq.gz" - } - }, - { - "discarded": { - "type": "file", - "description": "Adapter trimmed FastQ files of reads that did not pass filtering\nthresholds.\n", - "pattern": "*.discarded.fastq.gz" - } - }, - { - "paired_truncated": { - "type": "file", - "description": "Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge\nwith their respective R{1,2} pair due to long templates. The respective pair\nis stored in 'pair{1,2}_truncated'.\n", - "pattern": "*.pair{1,2}.truncated.fastq.gz" - } - }, - { - "collapsed": { - "type": "file", - "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair but were not trimmed.\n", - "pattern": "*.collapsed.fastq.gz" - } - }, - { - "collapsed_truncated": { - "type": "file", - "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair and were trimmed of adapter due to sufficient overlap.\n", - "pattern": "*.collapsed.truncated.fastq.gz" - } - }, - { - "paired_interleaved": { - "type": "file", - "description": "Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads\n", - "pattern": "*.paired.fastq.gz" - } - }, - { - "settings": { - "type": "file", - "description": "AdapterRemoval log file", - "pattern": "*.settings" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:adapterremoval" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" + } + } + ], + [ + { + "adapterlist": { + "type": "file", + "description": "Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args." + } + } + ] + ], + "output": [ + { + "singles_truncated": [ + { + "meta": { + "type": "file", + "description": "Adapter trimmed FastQ files of either single-end reads, or singleton\n'orphaned' reads from merging of paired-end data (i.e., one of the pair\nwas lost due to filtering thresholds).\n", + "pattern": "*.truncated.fastq.gz" + } + }, + { + "${prefix}.truncated.fastq.gz": { + "type": "file", + "description": "Adapter trimmed FastQ files of either single-end reads, or singleton\n'orphaned' reads from merging of paired-end data (i.e., one of the pair\nwas lost due to filtering thresholds).\n", + "pattern": "*.truncated.fastq.gz" + } + } + ] + }, + { + "discarded": [ + { + "meta": { + "type": "file", + "description": "Adapter trimmed FastQ files of reads that did not pass filtering\nthresholds.\n", + "pattern": "*.discarded.fastq.gz" + } + }, + { + "${prefix}.discarded.fastq.gz": { + "type": "file", + "description": "Adapter trimmed FastQ files of reads that did not pass filtering\nthresholds.\n", + "pattern": "*.discarded.fastq.gz" + } + } + ] + }, + { + "paired_truncated": [ + { + "meta": { + "type": "file", + "description": "Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge\nwith their respective R{1,2} pair due to long templates. The respective pair\nis stored in 'pair{1,2}_truncated'.\n", + "pattern": "*.pair{1,2}.truncated.fastq.gz" + } + }, + { + "${prefix}.pair{1,2}.truncated.fastq.gz": { + "type": "file", + "description": "Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge\nwith their respective R{1,2} pair due to long templates. The respective pair\nis stored in 'pair{1,2}_truncated'.\n", + "pattern": "*.pair{1,2}.truncated.fastq.gz" + } + } + ] + }, + { + "collapsed": [ + { + "meta": { + "type": "file", + "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair but were not trimmed.\n", + "pattern": "*.collapsed.fastq.gz" + } + }, + { + "${prefix}.collapsed.fastq.gz": { + "type": "file", + "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair but were not trimmed.\n", + "pattern": "*.collapsed.fastq.gz" + } + } + ] + }, + { + "collapsed_truncated": [ + { + "meta": { + "type": "file", + "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair and were trimmed of adapter due to sufficient overlap.\n", + "pattern": "*.collapsed.truncated.fastq.gz" + } + }, + { + "${prefix}.collapsed.truncated.fastq.gz": { + "type": "file", + "description": "Collapsed FastQ of paired-end reads that successfully merged with their\nrespective R1 pair and were trimmed of adapter due to sufficient overlap.\n", + "pattern": "*.collapsed.truncated.fastq.gz" + } + } + ] + }, + { + "paired_interleaved": [ + { + "meta": { + "type": "file", + "description": "Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads\n", + "pattern": "*.paired.fastq.gz" + } + }, + { + "${prefix}.paired.fastq.gz": { + "type": "file", + "description": "Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads\n", + "pattern": "*.paired.fastq.gz" + } + } + ] + }, + { + "settings": [ + { + "meta": { + "type": "file", + "description": "AdapterRemoval log file", + "pattern": "*.settings" + } + }, + { + "*.settings": { + "type": "file", + "description": "AdapterRemoval log file", + "pattern": "*.settings" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -476,45 +661,56 @@ "doi": "10.1186/s13059-016-0918-z", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file from AdapterRemoval2", - "pattern": "*.{fq.gz,fastq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file from AdapterRemoval2", + "pattern": "*.{fq.gz,fastq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fixed_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fq.gz": { + "type": "file", + "description": "FASTQ file with fixed read prefixes for DeDup", + "pattern": "*.{fq.gz}" + } + } + ] }, { - "fixed_fastq": { - "type": "file", - "description": "FASTQ file with fixed read prefixes for DeDup", - "pattern": "*.{fq.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -548,73 +744,96 @@ "doi": "10.1101/gr.094052.109", "licence": [ "Free for Academic Use" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed_ped_geno": { - "type": "file", - "description": "One of PLINK \".bed\" file or PLINK \".ped\" or EIGENSTRAT \".geno\" file. If you provide \".bed\" then you need to provide \".bim\" and \"fam\" files. If you provide \".ped\" or \".geno\" then you need to provide a \".map\" file and an empty channel.", - "pattern": "*.{bed}" - } - }, - { - "bim_map": { - "type": "file", - "description": "Mandatory accompanying file. One of PLINK \".bim\" file or PLINK \".map\" file. Provide \".bim\" if \".bed\" is the input. Provide \".map\" if \".ped\" or \".geno\" is the input.", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK \".fam\" file. Mandatory if you provide \".bed\" as input. Replace with an empty channel if input is \".ped\" or \".geno\".", - "pattern": "*.{fam}" - } - }, - { - "K": { - "type": "integer", - "description": "Belief of the number of ancestral populations.", - "pattern": "{*}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "ancestry_fractions": { - "type": "file", - "description": "Space-delimited files containing ancestry fractions. The output filenames have the number of populations (K) that was assumed for the analysis.", - "pattern": "*.{Q}" - } - }, - { - "allele_frequencies": { - "type": "file", - "description": "Space-delimited files containing the allele frequencies of the inferred ancestral populations. The output filenames have the number of populations (K) that was assumed for the analysis.", - "pattern": "*.{P}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed_ped_geno": { + "type": "file", + "description": "One of PLINK \".bed\" file or PLINK \".ped\" or EIGENSTRAT \".geno\" file. If you provide \".bed\" then you need to provide \".bim\" and \"fam\" files. If you provide \".ped\" or \".geno\" then you need to provide a \".map\" file and an empty channel.", + "pattern": "*.{bed}" + } + }, + { + "bim_map": { + "type": "file", + "description": "Mandatory accompanying file. One of PLINK \".bim\" file or PLINK \".map\" file. Provide \".bim\" if \".bed\" is the input. Provide \".map\" if \".ped\" or \".geno\" is the input.", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK \".fam\" file. Mandatory if you provide \".bed\" as input. Replace with an empty channel if input is \".ped\" or \".geno\".", + "pattern": "*.{fam}" + } + } + ], + [ + { + "K": { + "type": "integer", + "description": "Belief of the number of ancestral populations.", + "pattern": "{*}" + } + } + ] + ], + "output": [ + { + "ancestry_fractions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Q": { + "type": "file", + "description": "Space-delimited files containing ancestry fractions. The output filenames have the number of populations (K) that was assumed for the analysis.", + "pattern": "*.{Q}" + } + } + ] + }, + { + "allele_frequencies": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.P": { + "type": "file", + "description": "Space-delimited files containing the allele frequencies of the inferred ancestral populations. The output filenames have the number of populations (K) that was assumed for the analysis.", + "pattern": "*.{P}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -649,71 +868,110 @@ "doi": "10.1093/bioinformatics/btg405", "licence": [ "LGPL >=2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata and CEL file names\n" - } - }, - { - "celfiles_dir": { - "type": "list", - "description": "Path to a directory containing CEL files", - "pattern": "*.{CEL,CEL.gz}" - } - }, - { - "description": { - "type": "file", - "description": "Optional description file in MIAME format\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "expression": { - "type": "file", - "description": "TSV-format intensity matrix", - "pattern": "matrix.tsv" - } - }, - { - "annotation": { - "type": "file", - "description": "TSV-format annotation table", - "pattern": "*.annotation.tsv" - } - }, - { - "rds": { - "type": "file", - "description": "Serialised ExpressionSet object", - "pattern": "*.rds" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:affy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata and CEL file names\n" + } + }, + { + "celfiles_dir": { + "type": "list", + "description": "Path to a directory containing CEL files", + "pattern": "*.{CEL,CEL.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "description": { + "type": "file", + "description": "Optional description file in MIAME format\n" + } + } + ] + ], + "output": [ + { + "rds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.rds": { + "type": "file", + "description": "Serialised ExpressionSet object", + "pattern": "*.rds" + } + } + ] + }, + { + "expression": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*matrix.tsv": { + "type": "file", + "description": "TSV-format intensity matrix", + "pattern": "matrix.tsv" + } + } + ] + }, + { + "annotation": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.annotation.tsv": { + "type": "file", + "description": "TSV-format annotation table", + "pattern": "*.annotation.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -753,46 +1011,75 @@ "doi": "10.5281/zenodo.3552717", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}" - } - } - ], - "output": [ - { - "output_gtf": { - "type": "file", - "description": "Annotation file in GTF format", - "pattern": "*.{gtf}" - } - }, - { - "log": { - "type": "file", - "description": "Log file of the conversion process", - "pattern": "*.{log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}" + } + } + ] + ], + "output": [ + { + "output_gtf": [ + { + "meta": { + "type": "file", + "description": "Annotation file in GTF format", + "pattern": "*.{gtf}" + } + }, + { + "*.agat.gtf": { + "type": "file", + "description": "Annotation file in GTF format", + "pattern": "*.{gtf}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log file of the conversion process", + "pattern": "*.{log}" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of the conversion process", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -828,39 +1115,57 @@ "doi": "10.5281/zenodo.3552717", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:AGAT" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}" + } } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}" - } - } + ] ], "output": [ { - "tsv": { - "type": "file", - "description": "Annotation file in TSV format", - "pattern": "*.{gtf}" - } + "tsv": [ + { + "meta": { + "type": "file", + "description": "Annotation file in TSV format", + "pattern": "*.{gtf}" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Annotation file in TSV format", + "pattern": "*.{gtf}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -900,46 +1205,75 @@ "doi": "10.5281/zenodo.3552717", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gxf": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}" - } - } - ], - "output": [ - { - "output_gff": { - "type": "file", - "description": "Cleaned annotation file in GFF3 format", - "pattern": "*.{gff}" - } - }, - { - "log": { - "type": "file", - "description": "Log file of the conversion process", - "pattern": "*.{log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gxf": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}" + } + } + ] + ], + "output": [ + { + "output_gff": [ + { + "meta": { + "type": "file", + "description": "Cleaned annotation file in GFF3 format", + "pattern": "*.{gff}" + } + }, + { + "*.agat.gff": { + "type": "file", + "description": "Cleaned annotation file in GFF3 format", + "pattern": "*.{gff}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log file of the conversion process", + "pattern": "*.{log}" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of the conversion process", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -971,46 +1305,66 @@ "tool_dev_url": "https://github.com/NBISweden/AGAT", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Input gtf/gff file", - "pattern": "*.{gff,gff3,gtf}" - } - }, - { - "config": { - "type": "file", - "description": "Optional input agat config file", - "pattern": "*.{yaml,yml}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gff": { - "type": "file", - "description": "Output gff3 file with introns", - "pattern": "*.gff" - } + ], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Input gtf/gff file", + "pattern": "*.{gff,gff3,gtf}" + } + } + ], + [ + { + "config": { + "type": "file", + "description": "Optional input agat config file", + "pattern": "*.{yaml,yml}" + } + } + ] + ], + "output": [ + { + "gff": [ + { + "meta": { + "type": "file", + "description": "Output gff3 file with introns", + "pattern": "*.gff" + } + }, + { + "${output}": { + "type": "file", + "description": "Output gff3 file with introns", + "pattern": "*.gff" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1045,59 +1399,74 @@ "doi": "10.5281/zenodo.3552717", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "gff": { - "type": "file", - "description": "Input GFF3 file that will be read", - "pattern": "*.{gff,gff3}" - } - }, - { - "kill_list": { - "type": "file", - "description": "Kill list. One value per line.", - "pattern": "*.txt" - } - }, - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.yaml" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gff": { - "type": "file", - "description": "Output GFF file.", - "pattern": "*.gff" - } + ], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gff": { + "type": "file", + "description": "Input GFF3 file that will be read", + "pattern": "*.{gff,gff3}" + } + } + ], + [ + { + "kill_list": { + "type": "file", + "description": "Kill list. One value per line.", + "pattern": "*.txt" + } + } + ], + [ + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.yaml" + } + } + ] + ], + "output": [ + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Output GFF file.", + "pattern": "*.gff" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1131,52 +1500,65 @@ "doi": "10.5281/zenodo.3552717", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gffs": { - "type": "list", - "description": "A list of GFFs to merge", - "pattern": "[ *.{gff,gff3} ]" - } - }, - { - "config": { - "type": "file", - "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml\nlocally type: \"agat config --expose\". The --config option gives you the possibility to use your\nown AGAT config file (located elsewhere or named differently).\n", - "pattern": "*.yaml" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gff": { - "type": "file", - "description": "Output GFF file.", - "pattern": "*.gff" - } + ], + "identifier": "biotools:AGAT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gffs": { + "type": "list", + "description": "A list of GFFs to merge", + "pattern": "[ *.{gff,gff3} ]" + } + } + ], + [ + { + "config": { + "type": "file", + "description": "Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,\notherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml\nlocally type: \"agat config --expose\". The --config option gives you the possibility to use your\nown AGAT config file (located elsewhere or named differently).\n", + "pattern": "*.yaml" + } + } + ] + ], + "output": [ + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Output GFF file.", + "pattern": "*.gff" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1210,39 +1592,57 @@ "doi": "10.5281/zenodo.3552717", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:AGAT" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}" + } } - } + ] ], "output": [ { - "stats_txt": { - "type": "file", - "description": "Output of Statistics execution", - "pattern": "*.{txt}" - } + "stats_txt": [ + { + "meta": { + "type": "file", + "description": "Output of Statistics execution", + "pattern": "*.{txt}" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output of Statistics execution", + "pattern": "*.{txt}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1277,39 +1677,57 @@ "doi": "10.5281/zenodo.3552717", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:AGAT" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation file in GFF3/GTF format", - "pattern": "*.{gff, gtf}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "Annotation file in GFF3/GTF format", + "pattern": "*.{gff, gtf}" + } } - } + ] ], "output": [ { - "stats_txt": { - "type": "file", - "description": "Output of Statistics execution", - "pattern": "*.{txt}" - } + "stats_txt": [ + { + "meta": { + "type": "file", + "description": "Output of Statistics execution", + "pattern": "*.{txt}" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output of Statistics execution", + "pattern": "*.{txt}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1342,52 +1760,67 @@ "tool_dev_url": "https://github.com/VishnuRaghuram94/AgrVATE", "licence": [ "MIT" - ] + ], + "identifier": "biotools:agrvate" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A Staphylococcus aureus fasta file.", - "pattern": "*.fasta" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A Staphylococcus aureus fasta file.", + "pattern": "*.fasta" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "summary": { - "type": "file", - "description": "A summary of the agrvate assessement", - "pattern": "*-summary.tab" - } + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${fasta.baseName}-results/${fasta.baseName}-summary.tab": { + "type": "file", + "description": "A summary of the agrvate assessement", + "pattern": "*-summary.tab" + } + } + ] }, { - "results_dir": { - "type": "directory", - "description": "Results of the agrvate assessement", - "pattern": "*-results" - } + "results_dir": [ + { + "${fasta.baseName}-results": { + "type": "directory", + "description": "Results of the agrvate assessement", + "pattern": "*-results" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1419,52 +1852,63 @@ "doi": "10.1093/bioinformatics/bts723", "licence": [ "NCSA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "asm": { - "type": "file", - "description": "Assembly in FASTA format", - "pattern": "*.{fasta,fa}" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing sorted read mappings", - "pattern": "*.{bam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "ale": { - "type": "file", - "description": "Output TXT file containing ALE results", - "pattern": "*_ALEoutput.{txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "asm": { + "type": "file", + "description": "Assembly in FASTA format", + "pattern": "*.{fasta,fa}" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing sorted read mappings", + "pattern": "*.{bam}" + } + } + ] + ], + "output": [ + { + "ale": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_ALEoutput.txt": { + "type": "file", + "description": "Output TXT file containing ALE results", + "pattern": "*_ALEoutput.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1496,65 +1940,80 @@ "tool_dev_url": "https://github.com/cancerit/alleleCount", "licence": [ "GPL 3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "loci": { - "type": "file", - "description": "loci file ", - "pattern": "*.{tsv}" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file. Required when passing CRAM files." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "allelecount": { - "type": "file", - "description": "Allele count file", - "pattern": "*.{alleleCount}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + } + ], + [ + { + "loci": { + "type": "file", + "description": "loci file ", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Input genome fasta file. Required when passing CRAM files." + } + } + ] + ], + "output": [ + { + "allelecount": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.alleleCount": { + "type": "file", + "description": "Allele count file", + "pattern": "*.{alleleCount}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1596,129 +2055,244 @@ "tool_dev_url": "https://github.com/Darcy220606/AMPcombi/tree/dev", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "amp_input": { - "type": "list", - "description": "The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools.", - "pattern": "[*amptool.tsv, *amptool.tsv]" - } - }, - { - "faa_input": { - "type": "file", - "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", - "pattern": "*.faa" - } - }, - { - "opt_amp_db": { - "type": "directory", - "description": "The path to the folder containing the fasta and tsv database files.", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sample_dir": { - "type": "directory", - "description": "The output directory that contains the summary output and related alignment files for one sample.", - "pattern": "/*" - } - }, - { - "txt": { - "type": "file", - "description": "An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.", - "pattern": "/*/*_diamond_matches.txt" - } - }, - { - "csv": { - "type": "file", - "description": "A file containing the summary report of all predicted AMP hits from all AMP tools given as input and the corresponding taxonomic and functional classification from the alignment step.", - "pattern": "/*/*_ampcombi.csv" - } - }, - { - "faa": { - "type": "file", - "description": "A fasta file containing the amino acid sequences of all predicted AMP hits.", - "pattern": "/*/*_amp.faa" - } - }, - { - "summary_csv": { - "type": "file", - "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", - "pattern": "AMPcombi_summary.csv" - } - }, - { - "summary_html": { - "type": "file", - "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", - "pattern": "AMPcombi_summary.html" - } - }, - { - "log": { - "type": "file", - "description": "A log file that captures the standard output ina log file. Can be activated by `--log`.", - "pattern": "*.log" - } - }, - { - "results_db": { - "type": "directory", - "description": "If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", - "pattern": "/amp_ref_database" - } - }, - { - "results_db_dmnd": { - "type": "file", - "description": "AMP reference database converted to DIAMOND database format.", - "pattern": "/amp_ref_database/*.dmnd" - } - }, - { - "results_db_fasta": { - "type": "file", - "description": "AMP reference database fasta file, cleaned of diamond-uncompatible characters.", - "pattern": "/amp_ref_database/*.clean.fasta" - } - }, - { - "results_db_tsv": { - "type": "file", - "description": "AMP reference database in tsv-format with two columns containing header and sequence.", - "pattern": "/amp_ref_database/*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_input": { + "type": "list", + "description": "The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools.", + "pattern": "[*amptool.tsv, *amptool.tsv]" + } + } + ], + [ + { + "faa_input": { + "type": "file", + "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", + "pattern": "*.faa" + } + } + ], + [ + { + "opt_amp_db": { + "type": "directory", + "description": "The path to the folder containing the fasta and tsv database files.", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "sample_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/": { + "type": "directory", + "description": "The output directory that contains the summary output and related alignment files for one sample.", + "pattern": "/*" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/*diamond_matches.txt": { + "type": "file", + "description": "An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.", + "pattern": "/*/*_diamond_matches.txt" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/*ampcombi.csv": { + "type": "file", + "description": "A file containing the summary report of all predicted AMP hits from all AMP tools given as input and the corresponding taxonomic and functional classification from the alignment step.", + "pattern": "/*/*_ampcombi.csv" + } + } + ] + }, + { + "faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/*amp.faa": { + "type": "file", + "description": "A fasta file containing the amino acid sequences of all predicted AMP hits.", + "pattern": "/*/*_amp.faa" + } + } + ] + }, + { + "summary_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "AMPcombi_summary.csv": { + "type": "file", + "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", + "pattern": "AMPcombi_summary.csv" + } + } + ] + }, + { + "summary_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "AMPcombi_summary.html": { + "type": "file", + "description": "A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`.", + "pattern": "AMPcombi_summary.html" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "A log file that captures the standard output ina log file. Can be activated by `--log`.", + "pattern": "*.log" + } + } + ] + }, + { + "results_db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/": { + "type": "directory", + "description": "If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", + "pattern": "/amp_ref_database" + } + } + ] + }, + { + "results_db_dmnd": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/*.dmnd": { + "type": "file", + "description": "AMP reference database converted to DIAMOND database format.", + "pattern": "/amp_ref_database/*.dmnd" + } + } + ] + }, + { + "results_db_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/*.clean.fasta": { + "type": "file", + "description": "AMP reference database fasta file, cleaned of diamond-uncompatible characters.", + "pattern": "/amp_ref_database/*.clean.fasta" + } + } + ] + }, + { + "results_db_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "amp_ref_database/*.tsv": { + "type": "file", + "description": "AMP reference database in tsv-format with two columns containing header and sequence.", + "pattern": "/amp_ref_database/*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1756,47 +2330,66 @@ "tool_dev_url": "https://github.com/Darcy220606/AMPcombi/tree/dev", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "summary_file": { - "type": "file", - "description": "A file corresponding to the Ampcombi_summary.tsv that is generated by running 'ampcombi complete'. It is a file containing all the merged AMP results from all samples and all tools.", - "pattern": "*.tsv" + [ + { + "summary_file": { + "type": "file", + "description": "A file corresponding to the Ampcombi_summary.tsv that is generated by running 'ampcombi complete'. It is a file containing all the merged AMP results from all samples and all tools.", + "pattern": "*.tsv" + } } - } + ] ], "output": [ { - "cluster_tsv": { - "type": "file", - "description": "A file containing all the results from the merged input table 'Ampcombi_summary.tsv', but also including the cluster id number. The clustering is done using MMseqs2 cluster.", - "pattern": "*.tsv" - } + "cluster_tsv": [ + { + "Ampcombi_summary_cluster.tsv": { + "type": "file", + "description": "A file containing all the results from the merged input table 'Ampcombi_summary.tsv', but also including the cluster id number. The clustering is done using MMseqs2 cluster.", + "pattern": "*.tsv" + } + } + ] }, { - "rep_cluster_tsv": { - "type": "file", - "description": "A file containing the representative sequences of the clusters estimated by the tool. The clustering is done using MMseqs2 cluster.", - "pattern": "*.tsv" - } + "rep_cluster_tsv": [ + { + "Ampcombi_summary_cluster_representative_seq.tsv": { + "type": "file", + "description": "A file containing the representative sequences of the clusters estimated by the tool. The clustering is done using MMseqs2 cluster.", + "pattern": "*.tsv" + } + } + ] }, { - "log": { - "type": "file", - "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", - "pattern": "*.log" - } + "log": [ + { + "Ampcombi_cluster.log": { + "type": "file", + "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", + "pattern": "*.log" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1844,40 +2437,55 @@ "tool_dev_url": "https://github.com/Darcy220606/AMPcombi/tree/dev", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "summaries": { - "type": "list", - "description": "The path to the list of files corresponding to each sample as generated by ampcombi2/parsetables.", - "pattern": "[*_ampcombi.tsv, *_ampcombi.tsv]" + [ + { + "summaries": { + "type": "list", + "description": "The path to the list of files corresponding to each sample as generated by ampcombi2/parsetables.", + "pattern": "[*_ampcombi.tsv, *_ampcombi.tsv]" + } } - } + ] ], "output": [ { - "tsv": { - "type": "file", - "description": "A file containing the complete AMPcombi summaries from all processed samples.", - "pattern": "*.tsv" - } + "tsv": [ + { + "Ampcombi_summary.tsv": { + "type": "file", + "description": "A file containing the complete AMPcombi summaries from all processed samples.", + "pattern": "*.tsv" + } + } + ] }, { - "log": { - "type": "file", - "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", - "pattern": "*.log" - } + "log": [ + { + "Ampcombi_complete.log": { + "type": "file", + "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", + "pattern": "*.log" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -1925,136 +2533,253 @@ "tool_dev_url": "https://github.com/Darcy220606/AMPcombi/tree/dev", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "amp_input": { - "type": "list", - "description": "The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools.", - "pattern": "[*amptool.tsv, *amptool.tsv]" - } - }, - { - "faa_input": { - "type": "file", - "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", - "pattern": "*.faa" - } - }, - { - "gbk_input": { - "type": "file", - "description": "The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where \"sample_1\" is the sample name.", - "pattern": "*.gbk" - } - }, - { - "opt_amp_db": { - "type": "directory", - "description": "The path to the folder containing the fasta and tsv database files.", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "sample_dir": { - "type": "directory", - "description": "The output directory that contains the summary output and related alignment files for one sample.", - "pattern": "/*" - } - }, - { - "contig_gbks": { - "type": "directory", - "description": "The output subdirectory that contains the gbk files containing the AMP hits for each sample.", - "pattern": "/*/contig_gbks" - } - }, - { - "txt": { - "type": "file", - "description": "An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.", - "pattern": "/*/*_diamond_matches.txt" - } - }, - { - "tsv": { - "type": "file", - "description": "A file containing the summary report of all predicted AMP hits from all AMP tools given as input, the corresponding taxonomic and functional classification from the alignment step and the estimated physiochemical properties.", - "pattern": "/*/*_ampcombi.tsv" - } - }, - { - "faa": { - "type": "file", - "description": "A fasta file containing the amino acid sequences of all predicted AMP hits.", - "pattern": "/*/*_amp.faa" - } - }, - { - "sample_log": { - "type": "file", - "description": "A log file that captures the standard output per sample in a log file. Can be activated by `--log`.", - "pattern": "/*/*.log" - } - }, - { - "full_log": { - "type": "file", - "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", - "pattern": "Ampcombi_parse_tables.log" - } - }, - { - "results_db": { - "type": "directory", - "description": "If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", - "pattern": "/amp_ref_database" - } - }, - { - "results_db_dmnd": { - "type": "file", - "description": "AMP reference database converted to DIAMOND database format.", - "pattern": "/amp_ref_database/*.dmnd" - } - }, - { - "results_db_fasta": { - "type": "file", - "description": "AMP reference database fasta file, cleaned of diamond-uncompatible characters.", - "pattern": "/amp_ref_database/*.clean.fasta" - } - }, - { - "results_db_tsv": { - "type": "file", - "description": "AMP reference database in tsv-format with two columns containing header and sequence.", - "pattern": "/amp_ref_database/*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "amp_input": { + "type": "list", + "description": "The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools.", + "pattern": "[*amptool.tsv, *amptool.tsv]" + } + } + ], + [ + { + "faa_input": { + "type": "file", + "description": "The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa", + "pattern": "*.faa" + } + } + ], + [ + { + "gbk_input": { + "type": "file", + "description": "The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where \"sample_1\" is the sample name.", + "pattern": "*.gbk" + } + } + ], + [ + { + "opt_amp_db": { + "type": "directory", + "description": "The path to the folder containing the fasta and tsv database files.", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "sample_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${meta.id}/": { + "type": "directory", + "description": "The output directory that contains the summary output and related alignment files for one sample.", + "pattern": "/*" + } + } + ] + }, + { + "contig_gbks": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${meta.id}/contig_gbks/": { + "type": "directory", + "description": "The output subdirectory that contains the gbk files containing the AMP hits for each sample.", + "pattern": "/*/contig_gbks" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${meta.id}/${meta.id}_diamond_matches.txt": { + "type": "file", + "description": "An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.", + "pattern": "/*/*_diamond_matches.txt" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${meta.id}/${meta.id}_ampcombi.tsv": { + "type": "file", + "description": "A file containing the summary report of all predicted AMP hits from all AMP tools given as input, the corresponding taxonomic and functional classification from the alignment step and the estimated physiochemical properties.", + "pattern": "/*/*_ampcombi.tsv" + } + } + ] + }, + { + "faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${meta.id}/${meta.id}_amp.faa": { + "type": "file", + "description": "A fasta file containing the amino acid sequences of all predicted AMP hits.", + "pattern": "/*/*_amp.faa" + } + } + ] + }, + { + "sample_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${meta.id}/${meta.id}_ampcombi.log": { + "type": "file", + "description": "A log file that captures the standard output per sample in a log file. Can be activated by `--log`.", + "pattern": "/*/*.log" + } + } + ] + }, + { + "full_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "Ampcombi_parse_tables.log": { + "type": "file", + "description": "A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`.", + "pattern": "Ampcombi_parse_tables.log" + } + } + ] + }, + { + "results_db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "amp_ref_database/": { + "type": "directory", + "description": "If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder.", + "pattern": "/amp_ref_database" + } + } + ] + }, + { + "results_db_dmnd": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "amp_ref_database/*.dmnd": { + "type": "file", + "description": "AMP reference database converted to DIAMOND database format.", + "pattern": "/amp_ref_database/*.dmnd" + } + } + ] + }, + { + "results_db_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "amp_ref_database/*.clean.fasta": { + "type": "file", + "description": "AMP reference database fasta file, cleaned of diamond-uncompatible characters.", + "pattern": "/amp_ref_database/*.clean.fasta" + } + } + ] + }, + { + "results_db_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "amp_ref_database/*.tsv": { + "type": "file", + "description": "AMP reference database in tsv-format with two columns containing header and sequence.", + "pattern": "/amp_ref_database/*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2093,73 +2818,100 @@ "doi": "10.1093/bioinformatics/btaa653", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "faa": { - "type": "file", - "description": "FASTA file containing amino acid sequences", - "pattern": "*.{faa,fasta}" - } - }, - { - "model": { - "type": "string", - "description": "Built-in model for AMP prediction", - "pattern": "{precursor,mature}" - } - }, - { - "min_length": { - "type": "integer", - "description": "Minimum protein length for which predictions will be generated", - "pattern": "[0-9]+" - } - }, - { - "min_probability": { - "type": "float", - "description": "Cut-off for AMP prediction", - "pattern": "[0-9].[0-9]+" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "amps_faa": { - "type": "file", - "description": "File containing AMP predictions in amino acid FASTA format", - "pattern": "*.{faa}" - } - }, - { - "amps_tsv": { - "type": "file", - "description": "File containing AMP predictions in TSV format", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:ampir" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "faa": { + "type": "file", + "description": "FASTA file containing amino acid sequences", + "pattern": "*.{faa,fasta}" + } + } + ], + [ + { + "model": { + "type": "string", + "description": "Built-in model for AMP prediction", + "pattern": "{precursor,mature}" + } + } + ], + [ + { + "min_length": { + "type": "integer", + "description": "Minimum protein length for which predictions will be generated", + "pattern": "[0-9]+" + } + } + ], + [ + { + "min_probability": { + "type": "float", + "description": "Cut-off for AMP prediction", + "pattern": "[0-9].[0-9]+" + } + } + ] + ], + "output": [ + { + "amps_faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.faa": { + "type": "file", + "description": "File containing AMP predictions in amino acid FASTA format", + "pattern": "*.{faa}" + } + } + ] + }, + { + "amps_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "File containing AMP predictions in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2199,51 +2951,64 @@ "doi": "10.1186/s12864-022-08310-4", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "faa": { - "type": "file", - "description": "amino acid sequences fasta", - "pattern": "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}" - } - }, - { - "model_dir": { - "type": "directory", - "description": "Directory of where models are stored (optional)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "amino acid sequences with prediction (AMP, non-AMP) and probability scores", - "pattern": "*.{tsv}" - } + ], + "identifier": "biotools:amplify" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "faa": { + "type": "file", + "description": "amino acid sequences fasta", + "pattern": "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}" + } + } + ], + [ + { + "model_dir": { + "type": "directory", + "description": "Directory of where models are stored (optional)" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "amino acid sequences with prediction (AMP, non-AMP) and probability scores", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2295,68 +3060,95 @@ "doi": "10.1186/s13059-019-1903-0", "licence": [ "GPL >=3" - ] - } - } - ], - "input": [ - { - "maltextract_results": { - "type": "directory", - "description": "MaltExtract output directory", - "pattern": "results/" - } - }, - { - "taxon_list": { - "type": "file", - "description": "List of target taxa to evaluate used in MaltExtract", - "pattern": "*.txt" - } - }, - { - "filter": { - "type": "string", - "description": "The filter mode used in MaltExtract", - "pattern": "def_anc|default|scan|ancient|crawl" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "Candidate summary heatmap in MultiQC compatible JSON format", - "pattern": "heatmap_overview_Wevid.json" - } - }, - { - "summary_pdf": { - "type": "file", - "description": "Candidate summary heatmap in PDF format", - "pattern": "heatmap_overview_Wevid.pdf" - } - }, - { - "tsv": { - "type": "file", - "description": "Candidate summary heatmap in TSV format", - "pattern": "heatmap_overview_Wevid.tsv" - } - }, - { - "candidate_pdfs": { - "type": "directory", - "description": "Directory of per sample output PDFs organised by reference", - "pattern": "pdf_candidate_profiles/" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "maltextract_results": { + "type": "directory", + "description": "MaltExtract output directory", + "pattern": "results/" + } + } + ], + [ + { + "taxon_list": { + "type": "file", + "description": "List of target taxa to evaluate used in MaltExtract", + "pattern": "*.txt" + } + } + ], + [ + { + "filter": { + "type": "string", + "description": "The filter mode used in MaltExtract", + "pattern": "def_anc|default|scan|ancient|crawl" + } + } + ] + ], + "output": [ + { + "json": [ + { + "results/heatmap_overview_Wevid.json": { + "type": "file", + "description": "Candidate summary heatmap in MultiQC compatible JSON format", + "pattern": "heatmap_overview_Wevid.json" + } + } + ] + }, + { + "summary_pdf": [ + { + "results/heatmap_overview_Wevid.pdf": { + "type": "file", + "description": "Candidate summary heatmap in PDF format", + "pattern": "heatmap_overview_Wevid.pdf" + } + } + ] + }, + { + "tsv": [ + { + "results/heatmap_overview_Wevid.tsv": { + "type": "file", + "description": "Candidate summary heatmap in TSV format", + "pattern": "heatmap_overview_Wevid.tsv" + } + } + ] + }, + { + "candidate_pdfs": [ + { + "results/pdf_candidate_profiles/": { + "type": "directory", + "description": "Directory of per sample output PDFs organised by reference", + "pattern": "pdf_candidate_profiles/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2389,71 +3181,102 @@ "doi": "10.1038/s41598-021-91456-0", "licence": [ "Public Domain" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Nucleotide or protein sequences in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - } - }, - { - "db": { - "type": "file", - "description": "A compressed tarball of the AMRFinderPlus database to query", - "pattern": "*.tar.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "report": { - "type": "file", - "description": "AMRFinder+ final report", - "pattern": "*.tsv" - } - }, - { - "mutation_report": { - "type": "file", - "description": "Report of organism-specific point-mutations", - "pattern": "*-mutations.tsv" - } - }, - { - "tool_version": { - "type": "string", - "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" - } - }, - { - "db_version": { - "type": "string", - "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" - } + ], + "identifier": "biotools:amrfinderplus" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide or protein sequences in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "A compressed tarball of the AMRFinderPlus database to query", + "pattern": "*.tar.gz" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "AMRFinder+ final report", + "pattern": "*.tsv" + } + } + ] + }, + { + "mutation_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-mutations.tsv": { + "type": "file", + "description": "Report of organism-specific point-mutations", + "pattern": "*-mutations.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "tool_version": [ + { + "VER": { + "type": "string", + "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" + } + } + ] + }, + { + "db_version": [ + { + "DBVER": { + "type": "string", + "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" + } + } + ] } ], "authors": [ @@ -2496,30 +3319,33 @@ "doi": "10.1038/s41598-021-91456-0", "licence": [ "Public Domain" - ] + ], + "identifier": "biotools:amrfinderplus" } } ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "amrfinderdb.tar.gz": { + "type": "file", + "description": "The latest AMRFinder+ database in a compressed tarball", + "pattern": "*.tar.gz" + } + } + ] }, { - "db": { - "type": "file", - "description": "The latest AMRFinder+ database in a compressed tarball", - "pattern": "*.tar.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2559,57 +3385,70 @@ "licence": [ "GPL v3", "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "icounts": { - "type": "file", - "description": "Internal format for dumping binary single chrs. Useful for ANGSD contamination", - "pattern": "*.icnts.gz" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information related to the hapmap_file.\ne.g. [ id:'test' ]\n" - } - }, - { - "hapmap_file": { - "type": "file", - "description": "A list of variable sites to look for heterozygosity." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Contamination estimation output.", - "pattern": "*.txt" - } + ], + "identifier": "biotools:angsd" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "icounts": { + "type": "file", + "description": "Internal format for dumping binary single chrs. Useful for ANGSD contamination", + "pattern": "*.icnts.gz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information related to the hapmap_file.\ne.g. [ id:'test' ]\n" + } + }, + { + "hapmap_file": { + "type": "file", + "description": "A list of variable sites to look for heterozygosity." + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Contamination estimation output.", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2643,94 +3482,155 @@ "doi": "10.1186/s12859-014-0356-4", "licence": [ "GPL v3, MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A list of BAM or CRAM files", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "List of BAM/CRAM index files", - "pattern": "*.{bai,csi}" - } - }, - { - "minqfile": { - "type": "file", - "description": "File with individual quality score thresholds", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "depth_sample": { - "type": "file", - "description": "Distribution of sequencing depths", - "pattern": "*.depthSample" - } - }, - { - "depth_global": { - "type": "file", - "description": "Distribution of sequencing depths", - "pattern": "*.depthGlobal" - } - }, - { - "qs": { - "type": "file", - "description": "Distribution of scores", - "pattern": "*.qs" - } - }, - { - "pos": { - "type": "file", - "description": "Various types of depth statistics (depending on value for -dumpCounts)", - "pattern": "*.pos.gz" - } - }, - { - "counts": { - "type": "file", - "description": "Various types of statistics (related to pos.gz)", - "pattern": "*.counts.gz" - } - }, - { - "icounts": { - "type": "file", - "description": "Internal format for dumping binary single chrs. Useful for ANGSD contamination", - "pattern": "*.icnts.gz" - } + ], + "identifier": "biotools:angsd" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A list of BAM or CRAM files", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "List of BAM/CRAM index files", + "pattern": "*.{bai,csi}" + } + }, + { + "minqfile": { + "type": "file", + "description": "File with individual quality score thresholds", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "depth_sample": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthSample": { + "type": "file", + "description": "Distribution of sequencing depths", + "pattern": "*.depthSample" + } + } + ] + }, + { + "depth_global": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthGlobal": { + "type": "file", + "description": "Distribution of sequencing depths", + "pattern": "*.depthGlobal" + } + } + ] + }, + { + "qs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.qs": { + "type": "file", + "description": "Distribution of scores", + "pattern": "*.qs" + } + } + ] + }, + { + "pos": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pos.gz": { + "type": "file", + "description": "Various types of depth statistics (depending on value for -dumpCounts)", + "pattern": "*.pos.gz" + } + } + ] + }, + { + "counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.counts.gz": { + "type": "file", + "description": "Various types of statistics (related to pos.gz)", + "pattern": "*.counts.gz" + } + } + ] + }, + { + "icounts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.icnts.gz": { + "type": "file", + "description": "Internal format for dumping binary single chrs. Useful for ANGSD contamination", + "pattern": "*.icnts.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2764,71 +3664,86 @@ "licence": [ "GPL v3", "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A list of BAM or CRAM files", - "pattern": "*.{bam,cram}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference genome in FASTA format", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "error_file": { - "type": "file", - "description": "A file containing information about type specific errors.", - "pattern": "*.error.chunkunordered" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "genotype_likelihood": { - "type": "file", - "description": "File containing genotype likelihoods per sample", - "pattern": "*.{glf,beagle}.gz" - } + ], + "identifier": "biotools:angsd" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A list of BAM or CRAM files", + "pattern": "*.{bam,cram}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A reference genome in FASTA format", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "error_file": { + "type": "file", + "description": "A file containing information about type specific errors.", + "pattern": "*.error.chunkunordered" + } + } + ] + ], + "output": [ + { + "genotype_likelihood": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{glf,beagle}.gz": { + "type": "file", + "description": "File containing genotype likelihoods per sample", + "pattern": "*.{glf,beagle}.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -2865,124 +3780,163 @@ "doi": "10.1093/bioinformatics/bty304", "licence": [ "GPL-3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sv_vcf": { - "type": "file", - "description": "A VCF or BED file containing the structural variants to be annotated", - "pattern": "*.{bed,vcf,vcf.gz}" - } - }, - { - "sv_vcf_index": { - "type": "file", - "description": "OPTIONAL - The index for gzipped VCF files", - "pattern": "*.tbi" - } - }, - { - "candidate_small_variants": { - "type": "file", - "description": "OPTIONAL - A file containing candidate small variants", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing annotations information\n" - } - }, - { - "annotations": { - "type": "directory", - "description": "The directory containing the annotations (URL to download this will be made available soon)\nFor now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing candidate genes information\n" - } - }, - { - "candidate_genes": { - "type": "file", - "description": "OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated)", - "pattern": "*.txt" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing candidate false positive SNV information\n" - } - }, - { - "false_positive_snv": { - "type": "file", - "description": "OPTIONAL - A VCF file containing small variant candidates", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing candidate gene transcripts information\n" - } - }, - { - "gene_transcripts": { - "type": "file", - "description": "OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated)", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "A TSV file containing the annotated variants", - "pattern": "*.tsv" - } - }, - { - "unannotated_tsv": { - "type": "file", - "description": "OPTIONAL - TSV file containing the unannotated variants", - "pattern": "*.unannotated.tsv" - } - }, - { - "vcf": { - "type": "file", - "description": "OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args)\n", - "pattern": "*.vcf" - } + ], + "identifier": "biotools:AnnotSV" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sv_vcf": { + "type": "file", + "description": "A VCF or BED file containing the structural variants to be annotated", + "pattern": "*.{bed,vcf,vcf.gz}" + } + }, + { + "sv_vcf_index": { + "type": "file", + "description": "OPTIONAL - The index for gzipped VCF files", + "pattern": "*.tbi" + } + }, + { + "candidate_small_variants": { + "type": "file", + "description": "OPTIONAL - A file containing candidate small variants", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing annotations information\n" + } + }, + { + "annotations": { + "type": "directory", + "description": "The directory containing the annotations (URL to download this will be made available soon)\nFor now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing candidate genes information\n" + } + }, + { + "candidate_genes": { + "type": "file", + "description": "OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated)", + "pattern": "*.txt" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing candidate false positive SNV information\n" + } + }, + { + "false_positive_snv": { + "type": "file", + "description": "OPTIONAL - A VCF file containing small variant candidates", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing candidate gene transcripts information\n" + } + }, + { + "gene_transcripts": { + "type": "file", + "description": "OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated)", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV file containing the annotated variants", + "pattern": "*.tsv" + } + } + ] + }, + { + "unannotated_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unannotated.tsv": { + "type": "file", + "description": "OPTIONAL - TSV file containing the unannotated variants", + "pattern": "*.unannotated.tsv" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args)\n", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3015,24 +3969,33 @@ "tool_dev_url": "https://github.com/lgmgeo/AnnotSV", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:AnnotSV" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "annotations": [ + { + "AnnotSV_annotations": { + "type": "file", + "description": "A folder containing the annotations", + "pattern": "AnnotSV_annotations" + } + } + ] }, { - "annotations": { - "type": "file", - "description": "A folder containing the annotations", - "pattern": "AnnotSV_annotations" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3065,172 +4028,325 @@ "doi": "10.18129/B9.bioc.anota2seq", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "sample_treatment_col": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata\n" - } - }, - { - "counts": { - "type": "file", - "description": "Raw TSV or CSV format expression matrix\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" - } - }, - { - "translated_mrna": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".translated_mRNA.anota2seq.results.tsv" - } - }, - { - "total_mrna": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".total_mRNA.anota2seq.results.tsv" - } - }, - { - "translation": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in translation across conditions, being differences in translated RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".translation.anota2seq.results.tsv" - } - }, - { - "buffering": { - "type": "file", - "description": "anota2seq results for the 'translated mRNA' analysis, describing buffering across conditions, being stable levels of translated RNA (from riboseq samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".buffering.anota2seq.results.tsv" - } - }, - { - "mrna_abundance": { - "type": "file", - "description": "anota2seq results for the 'mRNA abunance' analysis, describing changes across conditions consistent between total mRNA and translated RNA (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", - "pattern": ".mRNA_abundance.anota2seq.results.tsv" - } - }, - { - "rdata": { - "type": "file", - "description": "Serialised Anota2seqDataSet object", - "pattern": ".Anota2seqDataSet.rds" - } - }, - { - "fold_change_plot": { - "type": "file", - "description": "A fold change plot in PNG format, from anota2seq's anota2seqPlotFC()\nmethod.\n", - "pattern": ".fold_change.png" - } - }, - { - "interaction_p_distribution_plot": { - "type": "file", - "description": "The distribution of p-values and adjusted p-values for the omnibus\ninteraction (both using densities and histograms). The second page of\nthe pdf displays the same plots but for the RVM statistics if RVM is\nused.\n", - "pattern": ".interaction_p_distribution.pdf" - } - }, - { - "residual_distribution_summary_plot": { - "type": "file", - "description": "Summary plot for assessing normal distribution of regression residuals.\n", - "pattern": ".residual_distribution_summary.jpeg" - } - }, - { - "residual_vs_fitted_plot": { - "type": "file", - "description": "QC plot showing residuals against fitted values.\n", - "pattern": ".residual_vs_fitted.jpeg" - } - }, - { - "rvm_fit_for_all_contrasts_group_plot": { - "type": "file", - "description": "QC plot showing the CDF of variance (theoretical vs empirical), all\ncontrasts.\n", - "pattern": ".rvm_fit_for_all_contrasts_group.jpg" - } - }, - { - "rvm_fit_for_interactions_plot": { - "type": "file", - "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\ninteractions.\n", - "pattern": ".rvm_fit_for_interactions.jpg" - } - }, - { - "rvm_fit_for_omnibus_group_plot": { - "type": "file", - "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\nomnibus group.\n", - "pattern": ".rvm_fit_for_omnibus_group.jpg" - } - }, - { - "simulated_vs_obt_dfbetas_without_interaction_plot": { - "type": "file", - "description": "Bar graphs of the frequencies of outlier dfbetas using different\ndfbetas thresholds.\n", - "pattern": ".simulated_vs_obt_dfbetas_without_interaction.pdf" - } - }, - { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:anota2seq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "sample_treatment_col": { + "type": "string", + "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" + } + }, + { + "reference": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" + } + }, + { + "target": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata\n" + } + }, + { + "counts": { + "type": "file", + "description": "Raw TSV or CSV format expression matrix\n" + } + } + ] + ], + "output": [ + { + "translated_mrna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.translated_mRNA.anota2seq.results.tsv": { + "type": "file", + "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", + "pattern": ".translated_mRNA.anota2seq.results.tsv" + } + } + ] + }, + { + "total_mrna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.total_mRNA.anota2seq.results.tsv": { + "type": "file", + "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", + "pattern": ".total_mRNA.anota2seq.results.tsv" + } + } + ] + }, + { + "translation": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.translation.anota2seq.results.tsv": { + "type": "file", + "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in translation across conditions, being differences in translated RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", + "pattern": ".translation.anota2seq.results.tsv" + } + } + ] + }, + { + "buffering": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.buffering.anota2seq.results.tsv": { + "type": "file", + "description": "anota2seq results for the 'translated mRNA' analysis, describing buffering across conditions, being stable levels of translated RNA (from riboseq samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", + "pattern": ".buffering.anota2seq.results.tsv" + } + } + ] + }, + { + "mrna_abundance": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.mRNA_abundance.anota2seq.results.tsv": { + "type": "file", + "description": "anota2seq results for the 'mRNA abunance' analysis, describing changes across conditions consistent between total mRNA and translated RNA (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.", + "pattern": ".mRNA_abundance.anota2seq.results.tsv" + } + } + ] + }, + { + "rdata": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.Anota2seqDataSet.rds": { + "type": "file", + "description": "Serialised Anota2seqDataSet object", + "pattern": ".Anota2seqDataSet.rds" + } + } + ] + }, + { + "fold_change_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.fold_change.png": { + "type": "file", + "description": "A fold change plot in PNG format, from anota2seq's anota2seqPlotFC()\nmethod.\n", + "pattern": ".fold_change.png" + } + } + ] + }, + { + "interaction_p_distribution_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.interaction_p_distribution.pdf": { + "type": "file", + "description": "The distribution of p-values and adjusted p-values for the omnibus\ninteraction (both using densities and histograms). The second page of\nthe pdf displays the same plots but for the RVM statistics if RVM is\nused.\n", + "pattern": ".interaction_p_distribution.pdf" + } + } + ] + }, + { + "residual_distribution_summary_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.residual_distribution_summary.jpeg": { + "type": "file", + "description": "Summary plot for assessing normal distribution of regression residuals.\n", + "pattern": ".residual_distribution_summary.jpeg" + } + } + ] + }, + { + "residual_vs_fitted_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.residual_vs_fitted.jpeg": { + "type": "file", + "description": "QC plot showing residuals against fitted values.\n", + "pattern": ".residual_vs_fitted.jpeg" + } + } + ] + }, + { + "rvm_fit_for_all_contrasts_group_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.rvm_fit_for_all_contrasts_group.jpg": { + "type": "file", + "description": "QC plot showing the CDF of variance (theoretical vs empirical), all\ncontrasts.\n", + "pattern": ".rvm_fit_for_all_contrasts_group.jpg" + } + } + ] + }, + { + "rvm_fit_for_interactions_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.rvm_fit_for_interactions.jpg": { + "type": "file", + "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\ninteractions.\n", + "pattern": ".rvm_fit_for_interactions.jpg" + } + } + ] + }, + { + "rvm_fit_for_omnibus_group_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.rvm_fit_for_omnibus_group.jpg": { + "type": "file", + "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\nomnibus group.\n", + "pattern": ".rvm_fit_for_omnibus_group.jpg" + } + } + ] + }, + { + "simulated_vs_obt_dfbetas_without_interaction_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.simulated_vs_obt_dfbetas_without_interaction.pdf": { + "type": "file", + "description": "Bar graphs of the frequencies of outlier dfbetas using different\ndfbetas thresholds.\n", + "pattern": ".simulated_vs_obt_dfbetas_without_interaction.pdf" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. e.g. [ id:'contrast1',\nblocking:'patient' ]\n" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3278,171 +4394,329 @@ "doi": "10.1093/nar/gkab335", "licence": [ "AGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequence_input": { - "type": "file", - "description": "nucleotide sequence file (annotated)", - "pattern": "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" - } - }, - { - "databases": { - "type": "directory", - "description": "Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory\n\"data/databases\")\n", - "pattern": "*/" - } - }, - { - "antismash_dir": { - "type": "directory", - "description": "A local copy of an AntiSMASH installation folder. This is required when running with\ndocker and singularity (not required for conda), due to attempted 'modifications' of\nfiles during database checks in the installation directory, something that cannot\nbe done in immutable docker/singularity containers. Therefore, a local installation\ndirectory needs to be mounted (including all modified files from the downloading step)\nto the container as a workaround.\n", - "pattern": "*/" - } - }, - { - "gff": { - "type": "file", - "description": "Annotations in GFF3 format (only if sequence_input is in FASTA format)", - "pattern": "*.gff" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "clusterblast_file": { - "type": "file", - "description": "Output of ClusterBlast algorithm", - "pattern": "clusterblast/*_c*.txt" - } - }, - { - "html_accessory_files": { - "type": "directory", - "description": "Accessory files for the HTML output", - "pattern": "{css/,images/,js/}" - } - }, - { - "knownclusterblast_html": { - "type": "file", - "description": "Tables with MIBiG hits in HTML format", - "pattern": "knownclusterblast/region*/ctg*.html" - } - }, - { - "knownclusterblast_dir": { - "type": "directory", - "description": "Directory with MIBiG hits", - "pattern": "knownclusterblast/" - } - }, - { - "knownclusterblast_txt": { - "type": "file", - "description": "Tables with MIBiG hits", - "pattern": "knownclusterblast/*_c*.txt" - } - }, - { - "svg_files_clusterblast": { - "type": "file", - "description": "SVG images showing the % identity of the aligned hits against their queries", - "pattern": "svg/clusterblast*.svg" - } - }, - { - "svg_files_knownclusterblast": { - "type": "file", - "description": "SVG images showing the % identity of the aligned hits against their queries", - "pattern": "svg/knownclusterblast*.svg" - } - }, - { - "gbk_input": { - "type": "file", - "description": "Nucleotide sequence and annotations in GenBank format; converted from input file", - "pattern": "*.gbk" - } - }, - { - "json_results": { - "type": "file", - "description": "Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)", - "pattern": "*.json" - } - }, - { - "log": { - "type": "file", - "description": "Contains all the logging output that antiSMASH produced during its run", - "pattern": "*.log" - } - }, - { - "zip": { - "type": "file", - "description": "Contains a compressed version of the output folder in zip format", - "pattern": "*.zip" - } - }, - { - "gbk_results": { - "type": "file", - "description": "Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit", - "pattern": "*region*.gbk" - } - }, - { - "clusterblastoutput": { - "type": "file", - "description": "Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm", - "pattern": "clusterblastoutput.txt" - } - }, - { - "html": { - "type": "file", - "description": "Graphical web view of results in HTML format", - "patterN": "index.html" - } - }, - { - "knownclusterblastoutput": { - "type": "file", - "description": "Raw BLAST output of known clusters of the MIBiG database", - "pattern": "knownclusterblastoutput.txt" - } - }, - { - "json_sideloading": { - "type": "file", - "description": "Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation \"Annotation sideloading\")", - "pattern": "regions.js" - } + ], + "identifier": "biotools:antismash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequence_input": { + "type": "file", + "description": "nucleotide sequence file (annotated)", + "pattern": "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" + } + } + ], + [ + { + "databases": { + "type": "directory", + "description": "Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory\n\"data/databases\")\n", + "pattern": "*/" + } + } + ], + [ + { + "antismash_dir": { + "type": "directory", + "description": "A local copy of an AntiSMASH installation folder. This is required when running with\ndocker and singularity (not required for conda), due to attempted 'modifications' of\nfiles during database checks in the installation directory, something that cannot\nbe done in immutable docker/singularity containers. Therefore, a local installation\ndirectory needs to be mounted (including all modified files from the downloading step)\nto the container as a workaround.\n", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "clusterblast_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/clusterblast/*_c*.txt": { + "type": "file", + "description": "Output of ClusterBlast algorithm", + "pattern": "clusterblast/*_c*.txt" + } + } + ] + }, + { + "html_accessory_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/{css,images,js}": { + "type": "directory", + "description": "Accessory files for the HTML output", + "pattern": "{css/,images/,js/}" + } + } + ] + }, + { + "knownclusterblast_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblast/region*/ctg*.html": { + "type": "file", + "description": "Tables with MIBiG hits in HTML format", + "pattern": "knownclusterblast/region*/ctg*.html" + } + } + ] + }, + { + "knownclusterblast_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblast/": { + "type": "directory", + "description": "Directory with MIBiG hits", + "pattern": "knownclusterblast/" + } + } + ] + }, + { + "knownclusterblast_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblast/*_c*.txt": { + "type": "file", + "description": "Tables with MIBiG hits", + "pattern": "knownclusterblast/*_c*.txt" + } + } + ] + }, + { + "svg_files_clusterblast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/svg/clusterblast*.svg": { + "type": "file", + "description": "SVG images showing the % identity of the aligned hits against their queries", + "pattern": "svg/clusterblast*.svg" + } + } + ] + }, + { + "svg_files_knownclusterblast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/svg/knownclusterblast*.svg": { + "type": "file", + "description": "SVG images showing the % identity of the aligned hits against their queries", + "pattern": "svg/knownclusterblast*.svg" + } + } + ] + }, + { + "gbk_input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.gbk": { + "type": "file", + "description": "Nucleotide sequence and annotations in GenBank format; converted from input file", + "pattern": "*.gbk" + } + } + ] + }, + { + "json_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.json": { + "type": "file", + "description": "Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)", + "pattern": "*.json" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.log": { + "type": "file", + "description": "Contains all the logging output that antiSMASH produced during its run", + "pattern": "*.log" + } + } + ] + }, + { + "zip": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.zip": { + "type": "file", + "description": "Contains a compressed version of the output folder in zip format", + "pattern": "*.zip" + } + } + ] + }, + { + "gbk_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*region*.gbk": { + "type": "file", + "description": "Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit", + "pattern": "*region*.gbk" + } + } + ] + }, + { + "clusterblastoutput": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/clusterblastoutput.txt": { + "type": "file", + "description": "Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm", + "pattern": "clusterblastoutput.txt" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/index.html": { + "type": "file", + "description": "Graphical web view of results in HTML format", + "patterN": "index.html" + } + } + ] + }, + { + "knownclusterblastoutput": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/knownclusterblastoutput.txt": { + "type": "file", + "description": "Raw BLAST output of known clusters of the MIBiG database", + "pattern": "knownclusterblastoutput.txt" + } + } + ] + }, + { + "json_sideloading": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/regions.js": { + "type": "file", + "description": "Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation \"Annotation sideloading\")", + "pattern": "regions.js" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3491,54 +4765,73 @@ "doi": "10.1093/nar/gkab335", "licence": [ "AGPL v3" - ] + ], + "identifier": "biotools:antismash" } } ], "input": [ - { - "database_css": { - "type": "directory", - "description": "antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", - "pattern": "css" + [ + { + "database_css": { + "type": "directory", + "description": "antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", + "pattern": "css" + } } - }, - { - "database_detection": { - "type": "directory", - "description": "antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", - "pattern": "detection" + ], + [ + { + "database_detection": { + "type": "directory", + "description": "antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", + "pattern": "detection" + } } - }, - { - "database_modules": { - "type": "directory", - "description": "antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", - "pattern": "modules" + ], + [ + { + "database_modules": { + "type": "directory", + "description": "antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.\n", + "pattern": "modules" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "database": [ + { + "antismash_db": { + "type": "directory", + "description": "Download directory for antiSMASH databases", + "pattern": "antismash_db" + } + } + ] }, { - "database": { - "type": "directory", - "description": "Download directory for antiSMASH databases", - "pattern": "antismash_db" - } + "antismash_dir": [ + { + "antismash_dir": { + "type": "directory", + "description": "antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.\n", + "pattern": "antismash_dir" + } + } + ] }, { - "antismash_dir": { - "type": "directory", - "description": "antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.\n", - "pattern": "antismash_dir" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3577,73 +4870,118 @@ "doi": "10.1093/bioinformatics/btz474", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads.", - "pattern": "*.bam" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "extracted_reads_fastq": { - "type": "file", - "description": "FASTQ file(s) containing chromosome 6 reads and related HLA sequences", - "pattern": "*.fq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log file for run summary", - "pattern": "*.log" - } - }, - { - "intermediate_sam": { - "type": "file", - "description": "Optional intermediate SAM file", - "pattern": "*.sam" - } - }, - { - "intermediate_bam": { - "type": "file", - "description": "Optional intermediate BAM file", - "pattern": "*.bam" - } - }, - { - "intermediate_sorted_bam": { - "type": "file", - "description": "Optional intermediate sorted BAM file", - "pattern": "*.sorted.bam" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads.", + "pattern": "*.bam" + } + } + ] + ], + "output": [ + { + "extracted_reads_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fq.gz": { + "type": "file", + "description": "FASTQ file(s) containing chromosome 6 reads and related HLA sequences", + "pattern": "*.fq.gz" + } + } + ] + }, + { + "log": [ + { + "*.log": { + "type": "file", + "description": "Log file for run summary", + "pattern": "*.log" + } + } + ] + }, + { + "intermediate_sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp_files/**.sam": { + "type": "file", + "description": "Optional intermediate SAM file", + "pattern": "*.sam" + } + } + ] + }, + { + "intermediate_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp_files/**.bam": { + "type": "file", + "description": "Optional intermediate BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "intermediate_sorted_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp_files/**.sorted.bam": { + "type": "file", + "description": "Optional intermediate sorted BAM file", + "pattern": "*.sorted.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3680,59 +5018,74 @@ "tool_dev_url": "https://github.com/BigDataBiology/argNorm", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input_tsv": { - "type": "file", - "description": "ARG annotation output", - "pattern": "*.tsv" - } - }, - { - "tool": { - "type": "string", - "description": "ARG annotation tool used", - "pattern": "argsoap|abricate|deeparg|resfinder|amrfinderplus" - } - }, - { - "db": { - "type": "string", - "description": "Database used for ARG annotation", - "pattern": "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Normalized argNorm output", - "pattern": "*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:argnorm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input_tsv": { + "type": "file", + "description": "ARG annotation output", + "pattern": "*.tsv" + } + } + ], + [ + { + "tool": { + "type": "string", + "description": "ARG annotation tool used", + "pattern": "argsoap|abricate|deeparg|resfinder|amrfinderplus" + } + } + ], + [ + { + "db": { + "type": "string", + "description": "Database used for ARG annotation", + "pattern": "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Normalized argNorm output", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3770,45 +5123,56 @@ "tool_dev_url": "https://github.com/aria2/aria2/", "licence": [ "GPL v2" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "source_url": { + "type": "string", + "description": "Source URL to be downloaded", + "pattern": "{http,https}*" + } } - }, - { - "source_url": { - "type": "string", - "description": "Source URL to be downloaded", - "pattern": "{http,https}*" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "downloaded_file": { - "type": "file", - "description": "Downloaded file from source", - "pattern": "*.*" - } + "downloaded_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$downloaded_file": { + "type": "file", + "description": "Downloaded file from source", + "pattern": "*.*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3858,38 +5222,56 @@ "doi": "10.1099/mgen.0.000131", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "db_name": { + "type": "string", + "description": "A database to setup up for Ariba" + } } - }, - { - "db_name": { - "type": "string", - "description": "A database to setup up for Ariba" - } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "meta": { + "type": "file", + "description": "An Ariba prepared database", + "pattern": "*.tar.gz" + } + }, + { + "${db_name}.tar.gz": { + "type": "file", + "description": "An Ariba prepared database", + "pattern": "*.tar.gz" + } + } + ] }, { - "db": { - "type": "file", - "description": "An Ariba prepared database", - "pattern": "*.tar.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -3923,46 +5305,72 @@ "doi": "10.1099/mgen.0.000131", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Paired-end reads in FASTQ format", - "pattern": "*_R[1|2].{fastq.gz,fq.gz}" - } - }, - { - "db": { - "type": "file", - "description": "An Ariba prepared database", - "pattern": "*.tar.gz" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "file", - "description": "A directory of Ariba analysis outputs", - "pattern": "*" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Paired-end reads in FASTQ format", + "pattern": "*_R[1|2].{fastq.gz,fq.gz}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "db": { + "type": "file", + "description": "An Ariba prepared database", + "pattern": "*.tar.gz" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "file", + "description": "A directory of Ariba analysis outputs", + "pattern": "*" + } + }, + { + "${prefix}/*": { + "type": "file", + "description": "A directory of Ariba analysis outputs", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -6136,6 +7544,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -6165,143 +7577,178 @@ "doi": "10.1101/gr.257246.119", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly FASTA file", - "pattern": "*.{fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Annotation GTF file", - "pattern": "*.{gtf}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "blacklist": { - "type": "file", - "description": "Blacklist file", - "pattern": "*.{tsv}" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "known_fusions": { - "type": "file", - "description": "Known fusions file", - "pattern": "*.{tsv}" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "structural_variants": { - "type": "file", - "description": "Structural variants file", - "pattern": "*.{tsv}" - } - }, - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "tags": { - "type": "file", - "description": "Tags file", - "pattern": "*.{tsv}" - } - }, - { - "meta8": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "protein_domains": { - "type": "file", - "description": "Protein domains file", - "pattern": "*.{gff3}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fusions": { - "type": "file", - "description": "File contains fusions which pass all of Arriba's filters.", - "pattern": "*.{fusions.tsv}" - } - }, - { - "fusions_fail": { - "type": "file", - "description": "File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.", - "pattern": "*.{fusions.discarded.tsv}" - } + ], + "identifier": "biotools:Arriba" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembly FASTA file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation GTF file", + "pattern": "*.{gtf}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "blacklist": { + "type": "file", + "description": "Blacklist file", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "known_fusions": { + "type": "file", + "description": "Known fusions file", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "structural_variants": { + "type": "file", + "description": "Structural variants file", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "tags": { + "type": "file", + "description": "Tags file", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "protein_domains": { + "type": "file", + "description": "Protein domains file", + "pattern": "*.{gff3}" + } + } + ] + ], + "output": [ + { + "fusions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fusions.tsv": { + "type": "file", + "description": "File contains fusions which pass all of Arriba's filters.", + "pattern": "*.{fusions.tsv}" + } + } + ] + }, + { + "fusions_fail": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fusions.discarded.tsv": { + "type": "file", + "description": "File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.", + "pattern": "*.{fusions.discarded.tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -6336,24 +7783,33 @@ "doi": "10.1101/gr.257246.119", "licence": [ "MIT" - ] + ], + "identifier": "biotools:Arriba" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "reference": [ + { + "*": { + "type": "directory", + "description": "Folder with arriba references", + "pattern": "*" + } + } + ] }, { - "reference": { - "type": "directory", - "description": "Folder with arriba references", - "pattern": "*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -6382,77 +7838,114 @@ "doi": "10.1093/bioinformatics/btr708", "licence": [ "GPL version 3 license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of input DNA/RNA reference", - "pattern": "*.{fasta,fa}" - } - }, - { - "sequencing_system": { - "type": "string", - "description": "The name of Illumina sequencing system of the built-in profile used for simulation" - } - }, - { - "fold_coverage": { - "type": "integer", - "description": "The fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon" - } - }, - { - "read_length": { - "type": "integer", - "description": "The length of reads to be simulated" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Simulated reads", - "pattern": "*.fq.gz" - } - }, - { - "aln": { - "type": "file", - "description": "OPTIONAL Alignment file of the simulated reads. Enabled by default, to disable, use -na/--noALN.", - "pattern": "*.aln" - } - }, - { - "sam": { - "type": "file", - "description": "OPTIONAL Alignment file in SAM format of the simulated reads. Enabled with -sam/--samout.", - "pattern": "*.sam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of input DNA/RNA reference", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "sequencing_system": { + "type": "string", + "description": "The name of Illumina sequencing system of the built-in profile used for simulation" + } + } + ], + [ + { + "fold_coverage": { + "type": "integer", + "description": "The fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon" + } + } + ], + [ + { + "read_length": { + "type": "integer", + "description": "The length of reads to be simulated" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fq.gz": { + "type": "file", + "description": "Simulated reads", + "pattern": "*.fq.gz" + } + } + ] + }, + { + "aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.aln": { + "type": "file", + "description": "OPTIONAL Alignment file of the simulated reads. Enabled by default, to disable, use -na/--noALN.", + "pattern": "*.aln" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "OPTIONAL Alignment file in SAM format of the simulated reads. Enabled with -sam/--samout.", + "pattern": "*.sam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -6491,45 +7984,56 @@ "tool_dev_url": "https://github.com/artic-network/fieldbioinformatics", "licence": [ "MIT" - ] + ], + "identifier": "biotools:artic" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq_dir": { + "type": "directory", + "description": "Directory containing the fastq files with demultiplexed reads", + "pattern": "*" + } } - }, - { - "fastq_dir": { - "type": "directory", - "description": "Directory containing the fastq files with demultiplexed reads", - "pattern": "*" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Aggregated FastQ files", - "pattern": "*.{fastq.gz}" - } + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Aggregated FastQ files", + "pattern": "*.{fastq.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -6569,169 +8073,294 @@ "tool_dev_url": "https://github.com/artic-network/fieldbioinformatics", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FastQ file containing reads", - "pattern": "*.{fastq.gz}" - } - }, - { - "fast5_dir": { - "type": "directory", - "description": "Directory containing MinION FAST5 files", - "pattern": "*" - } - }, - { - "sequencing_summary": { - "type": "file", - "description": "Path to Guppy sequencing summary", - "pattern": "*.{txt}" - } - }, - { - "primer_scheme_fasta": { - "type": "file", - "description": "Sequence of the reference genome used in the scheme in FASTA format\n", - "pattern": "*.{reference.fasta}" - } - }, - { - "primer_scheme_bed": { - "type": "file", - "description": "bed files containing coordinates of each primer in the scheme,\nrelative to the reference genome\n", - "pattern": "*.{scheme.bed}" - } - }, - { - "medaka_model_file": { - "type": "file", - "description": "Medaka model file to use (if option --medaka is set)\n", - "pattern": "*.hdf5" - } - }, - { - "medaka_model_string": { - "type": "string", - "description": "Medaka model string to use (if option --medaka is set)\n", - "pattern": "*" - } - }, - { - "scheme": { - "type": "string", - "description": "Name of the primer scheme" - } - }, - { - "scheme_version": { - "type": "string", - "description": "Version of the primer scheme" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "file", - "description": "Aggregated FastQ files", - "pattern": "*.fastq.gz" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{sorted.bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{sorted.bai}" - } - }, - { - "bam_trimmed": { - "type": "file", - "description": "BAM file with the primers left on", - "pattern": "*.{trimmed.rg.sorted.bam}" - } - }, - { - "bai_trimmed": { - "type": "file", - "description": "BAM index file of bam_trimmed", - "pattern": "*.{sorted.bai}" - } - }, - { - "bam_primertrimmed": { - "type": "file", - "description": "BAM containing reads after primer-binding site trimming", - "pattern": "*.{trimmed.rg.sorted.bam}" - } - }, - { - "bai_primertrimmed": { - "type": "file", - "description": "BAM index file of bam_primertrimmed", - "pattern": "*.{primertrimmed.rg.sorted.bam.bai}" - } - }, - { - "fasta": { - "type": "file", - "description": "FAST file with consensus sequence", - "pattern": "*.{consensus.fasta}" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file containing detected variants passing quality filter", - "pattern": "*.{pass.vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index", - "pattern": "*.{pass.vcf.gz.tbi}" - } - }, - { - "json": { - "type": "file", - "description": "JSON file for MultiQC", - "pattern": "*.json" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:artic" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FastQ file containing reads", + "pattern": "*.{fastq.gz}" + } + } + ], + [ + { + "fast5_dir": { + "type": "directory", + "description": "Directory containing MinION FAST5 files", + "pattern": "*" + } + } + ], + [ + { + "sequencing_summary": { + "type": "file", + "description": "Path to Guppy sequencing summary", + "pattern": "*.{txt}" + } + } + ], + [ + { + "\"primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta\"": { + "type": "file", + "description": "Scheme reference file" + } + } + ], + [ + { + "\"primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed\"": { + "type": "file", + "description": "Scheme BED file" + } + } + ], + [ + { + "medaka_model_file": { + "type": "file", + "description": "Medaka model file to use (if option --medaka is set)\n", + "pattern": "*.hdf5" + } + } + ], + [ + { + "medaka_model_string": { + "type": "string", + "description": "Medaka model string to use (if option --medaka is set)\n", + "pattern": "*" + } + } + ], + [ + { + "scheme": { + "type": "string", + "description": "Name of the primer scheme" + } + } + ], + [ + { + "scheme_version": { + "type": "string", + "description": "Version of the primer scheme" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Aggregated FastQ files", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sorted.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{sorted.bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sorted.bam.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{sorted.bai}" + } + } + ] + }, + { + "bam_trimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.trimmed.rg.sorted.bam": { + "type": "file", + "description": "BAM file with the primers left on", + "pattern": "*.{trimmed.rg.sorted.bam}" + } + } + ] + }, + { + "bai_trimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.trimmed.rg.sorted.bam.bai": { + "type": "file", + "description": "BAM index file of bam_trimmed", + "pattern": "*.{sorted.bai}" + } + } + ] + }, + { + "bam_primertrimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.primertrimmed.rg.sorted.bam": { + "type": "file", + "description": "BAM containing reads after primer-binding site trimming", + "pattern": "*.{trimmed.rg.sorted.bam}" + } + } + ] + }, + { + "bai_primertrimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.primertrimmed.rg.sorted.bam.bai": { + "type": "file", + "description": "BAM index file of bam_primertrimmed", + "pattern": "*.{primertrimmed.rg.sorted.bam.bai}" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.consensus.fasta": { + "type": "file", + "description": "FAST file with consensus sequence", + "pattern": "*.{consensus.fasta}" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.pass.vcf.gz": { + "type": "file", + "description": "VCF file containing detected variants passing quality filter", + "pattern": "*.{pass.vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.pass.vcf.gz.tbi": { + "type": "file", + "description": "VCF index", + "pattern": "*.{pass.vcf.gz.tbi}" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file for MultiQC", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -6771,136 +8400,241 @@ "doi": "10.1093/bioinformatics/btaa538", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "args": { - "type": "map", - "description": "Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.\n\n```\n{\n [\n \"gender\": \"XX\",\n \"genomeVersion\": \"hg19\"\n \"purity\": (optional),\n \"ploidy\": (optional),\n \"gc_files\": (optional),\n \"minCounts\": (optional),\n \"BED_file\": (optional) but recommended for WES,\n \"chrom_names\": (optional),\n \"min_base_qual\": (optional),\n \"min_map_qual\": (optional),\n \"ref_fasta\": (optional),\n \"skip_allele_counting_tumour\": (optional),\n \"skip_allele_counting_normal\": (optional)\n ]\n}\n```\n" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_normal": { - "type": "file", - "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/.", - "pattern": "*.{bam,cram}" - } - }, - { - "index_normal": { - "type": "file", - "description": "index for normal_bam/cram", - "pattern": "*.{bai,crai}" - } - }, - { - "input_tumor": { - "type": "file", - "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation", - "pattern": "*.{bam,cram}" - } - }, - { - "index_tumor": { - "type": "file", - "description": "index for tumor_bam/cram", - "pattern": "*.{bai,crai}" - } - }, - { - "allele_files": { - "type": "file", - "description": "allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS" - } - }, - { - "loci_files": { - "type": "file", - "description": "loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command `if [[ $(samtools view | head -n1 | cut -f3)\\\" == *\\\"chr\\\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi`" - } - }, - { - "bed_file": { - "type": "file", - "description": "Bed file for ASCAT WES (optional, but recommended for WES)" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file (optional)" - } - }, - { - "gc_file": { - "type": "file", - "description": "GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content" - } - }, - { - "rt_file": { - "type": "file", - "description": "replication timing correction file (optional, provide only in combination with gc_file)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "allelefreqs": { - "type": "file", - "description": "Files containing allee frequencies per chromosome", - "pattern": "*{alleleFrequencies_chr*.txt}" - } - }, - { - "metrics": { - "type": "file", - "description": "File containing quality metrics", - "pattern": "*.{metrics.txt}" - } - }, - { - "png": { - "type": "file", - "description": "ASCAT plots", - "pattern": "*.{png}" - } - }, - { - "purityploidy": { - "type": "file", - "description": "File with purity and ploidy data", - "pattern": "*.{purityploidy.txt}" - } - }, - { - "segments": { - "type": "file", - "description": "File with segments data", - "pattern": "*.{segments.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ascat" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_normal": { + "type": "file", + "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/.", + "pattern": "*.{bam,cram}" + } + }, + { + "index_normal": { + "type": "file", + "description": "index for normal_bam/cram", + "pattern": "*.{bai,crai}" + } + }, + { + "input_tumor": { + "type": "file", + "description": "BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation", + "pattern": "*.{bam,cram}" + } + }, + { + "index_tumor": { + "type": "file", + "description": "index for tumor_bam/cram", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "allele_files": { + "type": "file", + "description": "allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS" + } + } + ], + [ + { + "loci_files": { + "type": "file", + "description": "loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command `if [[ $(samtools view | head -n1 | cut -f3)\\\" == *\\\"chr\\\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi`" + } + } + ], + [ + { + "bed_file": { + "type": "file", + "description": "Bed file for ASCAT WES (optional, but recommended for WES)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference fasta file (optional)" + } + } + ], + [ + { + "gc_file": { + "type": "file", + "description": "GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content" + } + } + ], + [ + { + "rt_file": { + "type": "file", + "description": "replication timing correction file (optional, provide only in combination with gc_file)" + } + } + ] + ], + "output": [ + { + "allelefreqs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*alleleFrequencies_chr*.txt": { + "type": "file", + "description": "Files containing allee frequencies per chromosome", + "pattern": "*{alleleFrequencies_chr*.txt}" + } + } + ] + }, + { + "bafs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*BAF.txt": { + "type": "file", + "description": "BAF file" + } + } + ] + }, + { + "cnvs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cnvs.txt": { + "type": "file", + "description": "CNV file" + } + } + ] + }, + { + "logrs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*LogR.txt": { + "type": "file", + "description": "LogR file" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*metrics.txt": { + "type": "file", + "description": "File containing quality metrics", + "pattern": "*.{metrics.txt}" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*png": { + "type": "file", + "description": "ASCAT plots", + "pattern": "*.{png}" + } + } + ] + }, + { + "purityploidy": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*purityploidy.txt": { + "type": "file", + "description": "File with purity and ploidy data", + "pattern": "*.{purityploidy.txt}" + } + } + ] + }, + { + "segments": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*segments.txt": { + "type": "file", + "description": "File with segments data", + "pattern": "*.{segments.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -6946,45 +8680,72 @@ "doi": "10.1093/bioinformatics/btac544", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "images": { - "type": "file", - "description": "Overlapping tile image data in formats from most commercial microscopes", - "pattern": "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "tif": { - "type": "file", - "description": "A pyramidal, tiled OME-TIFF file created from input images.", - "pattern": "*.ome.tif" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ASHLAR" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "images": { + "type": "file", + "description": "Overlapping tile image data in formats from most commercial microscopes", + "pattern": "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}" + } + } + ], + [ + { + "opt_dfp": { + "type": "file", + "description": "Optional dark field image data" + } + } + ], + [ + { + "opt_ffp": { + "type": "file", + "description": "Optional flat field image data" + } + } + ] + ], + "output": [ + { + "tif": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ome.tif": { + "type": "file", + "description": "A pyramidal, tiled OME-TIFF file created from input images.", + "pattern": "*.ome.tif" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7025,45 +8786,56 @@ "tool_dev_url": "https://github.com/rpetit3/assembly-scan", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "FASTA file for a given assembly", - "pattern": "*.fasta" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "FASTA file for a given assembly", + "pattern": "*.fasta" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Assembly statistics in JSON format", + "pattern": "*.json" + } + } + ] }, { - "json": { - "type": "file", - "description": "Assembly statistics in JSON format", - "pattern": "*.json" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7104,97 +8876,128 @@ "doi": "10.1016/j.cels.2020.02.009", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file with the same prefix as bam file. Required if tss_file input is provided.", - "pattern": "*.bam.bai" - } - }, - { - "peak_file": { - "type": "file", - "description": "A BED file of peaks called for alignments in the BAM file", - "pattern": "*.bed" - } - }, - { - "organism": { - "type": "string", - "description": "The subject of the experiment, which determines the list of autosomes (see \"Reference Genome Configuration\" section at https://github.com/ParkerLab/ataqv)." - } - }, - { - "mito_name": { - "type": "string", - "description": "Name of the mitochondrial sequence." - } - }, - { - "tss_file": { - "type": "file", - "description": "A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed.", - "pattern": "*.bed" - } - }, - { - "excl_regs_file": { - "type": "file", - "description": "A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.", - "pattern": "*.bed" - } - }, - { - "autosom_ref_file": { - "type": "file", - "description": "A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "json": { - "type": "file", - "description": "The JSON file to which metrics will be written." - } - }, - { - "problems": { - "type": "file", - "description": "If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with \".problems\" appended. If no read groups are found, the reads will be written to one file named after the BAM file.", - "pattern": "*.problems" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ataqv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file with the same prefix as bam file. Required if tss_file input is provided.", + "pattern": "*.bam.bai" + } + }, + { + "peak_file": { + "type": "file", + "description": "A BED file of peaks called for alignments in the BAM file", + "pattern": "*.bed" + } + } + ], + [ + { + "organism": { + "type": "string", + "description": "The subject of the experiment, which determines the list of autosomes (see \"Reference Genome Configuration\" section at https://github.com/ParkerLab/ataqv)." + } + } + ], + [ + { + "mito_name": { + "type": "string", + "description": "Name of the mitochondrial sequence." + } + } + ], + [ + { + "tss_file": { + "type": "file", + "description": "A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed.", + "pattern": "*.bed" + } + } + ], + [ + { + "excl_regs_file": { + "type": "file", + "description": "A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.", + "pattern": "*.bed" + } + } + ], + [ + { + "autosom_ref_file": { + "type": "file", + "description": "A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong." + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ataqv.json": { + "type": "file", + "description": "The JSON file to which metrics will be written." + } + } + ] + }, + { + "problems": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.problems": { + "type": "file", + "description": "If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with \".problems\" appended. If no read groups are found, the reads will be written to one file named after the BAM file.", + "pattern": "*.problems" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7234,33 +9037,44 @@ "tool_dev_url": "https://github.com/ParkerLab/ataqv", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:ataqv" } } ], "input": [ - { - "json": { - "type": "file", - "description": "The JSON file with ataqv metrics", - "pattern": "*.json" + [ + { + "\"jsons/*\"": { + "type": "file", + "description": "JSON files", + "pattern": "*.json" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "html": [ + { + "html": { + "type": "directory", + "description": "Web application to visualize results in HTML format", + "pattern": "*.html" + } + } + ] }, { - "html": { - "type": "directory", - "description": "Web application to visualize results in HTML format", - "pattern": "*.html" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7300,94 +9114,113 @@ "doi": "10.1101/105346", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A BAM/ file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "The BAI file for the input BAM file", - "pattern": "*.bai" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file used to generate the BAM file", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the FASTA file used for to generate the BAM file", - "pattern": "*.fai" - } - }, - { - "recal": { - "type": "file", - "description": "Optional recalibration file from atlas recal function in text format", - "pattern": "*.txt" - } - }, - { - "pmd": { - "type": "file", - "description": "Optional PMD file from atlas pmd function in text format", - "pattern": "*.txt" - } - }, - { - "known_alleles": { - "type": "file", - "description": "Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.", - "pattern": "*.{txt.tsv}" - } - }, - { - "method": { - "type": "string", - "description": "Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.", - "pattern": "MLE|Bayesian|allelePresence|randomBase|majorityBase" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with variant calls", - "pattern": "*.vcf.gz" - } + ], + "identifier": "biotools:atlas_db" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A BAM/ file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "The BAI file for the input BAM file", + "pattern": "*.bai" + } + }, + { + "pmd": { + "type": "file", + "description": "Optional PMD file from atlas pmd function in text format", + "pattern": "*.txt" + } + }, + { + "recal": { + "type": "file", + "description": "Optional recalibration file from atlas recal function in text format", + "pattern": "*.txt" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference FASTA file used to generate the BAM file", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "The index of the FASTA file used for to generate the BAM file", + "pattern": "*.fai" + } + } + ], + [ + { + "known_alleles": { + "type": "file", + "description": "Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.", + "pattern": "*.{txt.tsv}" + } + } + ], + [ + { + "method": { + "type": "string", + "description": "Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.", + "pattern": "MLE|Bayesian|allelePresence|randomBase|majorityBase" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with variant calls", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7420,94 +9253,139 @@ "doi": "10.1101/105346", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Single input BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "The BAI file for the input BAM file", - "pattern": "*.bai" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference genome provided as FASTA file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "The FAI file for the reference genome FASTA file", - "pattern": "*.fai" - } - }, - { - "pool_rg_txt": { - "type": "file", - "description": "Optional. Provide the names of read groups that should be merged for PMD estimation.\nAll read groups that should be pooled listed on one line, separated by any white space.\nOther read groups will be recalibrated separately.\n", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "empiric": { - "type": "file", - "description": "A list of pmd patterns estimated with the empirical method for each readgroup", - "pattern": "*_PMD_input_Empiric.txt" - } - }, - { - "exponential": { - "type": "file", - "description": "A list of pmd patterns estimated with the exponential method for each readgroup", - "pattern": "*_PMD_input_Exponential.txt" - } - }, - { - "counts": { - "type": "file", - "description": "The counts of all possible transitions for each read position\n(or up to a certain position, see specific command length)\n", - "pattern": "*_PMD_Table_counts.txt" - } - }, - { - "table": { - "type": "file", - "description": "For all possible transitions the ratio of the transition counts,\nwhich are taken from the _counts.txt table, over the total amount\nof the base that was mutated, for each position and readgroup\n", - "pattern": "*_PMD_Table.txt" - } + ], + "identifier": "biotools:atlas_db" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Single input BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "The BAI file for the input BAM file", + "pattern": "*.bai" + } + }, + { + "pool_rg_txt": { + "type": "file", + "description": "Optional. Provide the names of read groups that should be merged for PMD estimation.\nAll read groups that should be pooled listed on one line, separated by any white space.\nOther read groups will be recalibrated separately.\n", + "pattern": "*.txt" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference genome provided as FASTA file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "The FAI file for the reference genome FASTA file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "empiric": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_input_Empiric.txt": { + "type": "file", + "description": "A list of pmd patterns estimated with the empirical method for each readgroup", + "pattern": "*_PMD_input_Empiric.txt" + } + } + ] + }, + { + "exponential": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_input_Exponential.txt": { + "type": "file", + "description": "A list of pmd patterns estimated with the exponential method for each readgroup", + "pattern": "*_PMD_input_Exponential.txt" + } + } + ] + }, + { + "counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_Table_counts.txt": { + "type": "file", + "description": "The counts of all possible transitions for each read position\n(or up to a certain position, see specific command length)\n", + "pattern": "*_PMD_Table_counts.txt" + } + } + ] + }, + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PMD_Table.txt": { + "type": "file", + "description": "For all possible transitions the ratio of the transition counts,\nwhich are taken from the _counts.txt table, over the total amount\nof the base that was mutated, for each position and readgroup\n", + "pattern": "*_PMD_Table.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7541,73 +9419,94 @@ "doi": "10.1101/105346", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai" - } - }, - { - "empiric": { - "type": "file", - "description": "Optional txt file from PMD estimations (atlas/pmd)", - "pattern": "*.txt" - } - }, - { - "alleles": { - "type": "file", - "description": "Optional bed file with known alleles", - "pattern": "*.bed" - } - }, - { - "invariant_sites": { - "type": "file", - "description": "Optional bed file with invariant site coordinates", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "recal_patterns": { - "type": "file", - "description": "file containing the sequencing bias for each of the Read Group pools", - "pattern": "*.txt" - } + ], + "identifier": "biotools:atlas_db" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai" + } + }, + { + "empiric": { + "type": "file", + "description": "Optional txt file from PMD estimations (atlas/pmd)", + "pattern": "*.txt" + } + }, + { + "readgroups": { + "type": "file", + "description": "read groups" + } + } + ], + [ + { + "alleles": { + "type": "file", + "description": "Optional bed file with known alleles", + "pattern": "*.bed" + } + } + ], + [ + { + "invariant_sites": { + "type": "file", + "description": "Optional bed file with invariant site coordinates", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "recal_patterns": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "file containing the sequencing bias for each of the Read Group pools", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7641,73 +9540,94 @@ "doi": "10.1101/105346", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Single input BAM file.", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "The BAI file for the input BAM file", - "pattern": "*.bai" - } - }, - { - "read_group_settings": { - "type": "file", - "description": "TXT file containing the split and merge settings for\neach readgroup. Each line consist of one readgroup,\nsingle/double identifier and the maximum cycle number\nof the sequencer. e.g. \"RG1 single 100\"\n", - "pattern": "*.txt" - } - }, - { - "blacklist": { - "type": "file", - "description": "blacklist.txt (optional), A txt file with blacklisted read names\nthat should be ignored and just written to file, each on a new line\n", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "A BAM file with suffix_mergedReads.bam", - "pattern": "*_mergedReads.bam" - } - }, - { - "txt": { - "type": "file", - "description": "A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz", - "pattern": "*.txt.gz" - } + ], + "identifier": "biotools:atlas_db" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Single input BAM file.", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "The BAI file for the input BAM file", + "pattern": "*.bai" + } + }, + { + "read_group_settings": { + "type": "file", + "description": "TXT file containing the split and merge settings for\neach readgroup. Each line consist of one readgroup,\nsingle/double identifier and the maximum cycle number\nof the sequencer. e.g. \"RG1 single 100\"\n", + "pattern": "*.txt" + } + }, + { + "blacklist": { + "type": "file", + "description": "blacklist.txt (optional), A txt file with blacklisted read names\nthat should be ignored and just written to file, each on a new line\n", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_mergedReads.bam": { + "type": "file", + "description": "A BAM file with suffix_mergedReads.bam", + "pattern": "*_mergedReads.bam" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7739,59 +9659,90 @@ "tool_dev_url": "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on input GTF file\ne.g. [ id:'test' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information in input FASTA file\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "gtf annotation file", - "pattern": "*.{gtf}" - } - }, - { - "fasta": { - "type": "file", - "description": "An optional cDNA file for extracting meta info and/or filtering.\n", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "feature_annotation": { - "type": "file", - "description": "TSV file with feature annotation", - "pattern": "*.{tsv}" - } - }, - { - "filtered_cdna": { - "type": "file", - "description": "Where --parse-cdnas is specified in ext.args and an input fasta file is\nprovided, filtered sequences are output to the specified file. No file\nwill be output if this is not specified (for example for use of\n--dummy-from-cdnas only). See documentation at\nhttps://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.\n", - "pattern": "*.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on input GTF file\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "gtf annotation file", + "pattern": "*.{gtf}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information in input FASTA file\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "An optional cDNA file for extracting meta info and/or filtering.\n", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "feature_annotation": [ + { + "meta": { + "type": "file", + "description": "TSV file with feature annotation", + "pattern": "*.{tsv}" + } + }, + { + "*.anno.tsv": { + "type": "file", + "description": "TSV file with feature annotation", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "filtered_cdna": [ + { + "meta": { + "type": "file", + "description": "Where --parse-cdnas is specified in ext.args and an input fasta file is\nprovided, filtered sequences are output to the specified file. No file\nwill be output if this is not specified (for example for use of\n--dummy-from-cdnas only). See documentation at\nhttps://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.\n", + "pattern": "*.{tsv}" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "Where --parse-cdnas is specified in ext.args and an input fasta file is\nprovided, filtered sequences are output to the specified file. No file\nwill be output if this is not specified (for example for use of\n--dummy-from-cdnas only). See documentation at\nhttps://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.\n", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7837,59 +9788,86 @@ "doi": "10.1186/s13059-020-02123-y", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file (Mandatory)", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "config": { - "type": "file", - "description": "Optional AuthentiCT configuration text file", - "pattern": "*" - } - }, - { - "positions": { - "type": "file", - "description": "Optional text file with positions that sequences should overlap", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Maximum likelihood estimates with associated standard errors", - "pattern": "*.txt" - } + ], + "identifier": "biotools:authentict" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file (Mandatory)", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "config": { + "type": "file", + "description": "Optional AuthentiCT configuration text file", + "pattern": "*" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "positions": { + "type": "file", + "description": "Optional text file with positions that sequences should overlap", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Maximum likelihood estimates with associated standard errors", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -7926,71 +9904,88 @@ "tool_dev_url": "https://github.com/SchapiroLabor/Background_subtraction", "licence": [ "MIT licence" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "image": { - "type": "file", - "description": "Multi-channel image file", - "pattern": "*.{tif,tiff}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "markerfile": { - "type": "file", - "description": "Marker file with channel names, exposure times, and specified background to subtract (and remove to exclude channels from output)", - "pattern": "*.csv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "backsub_tif": { - "type": "file", - "description": "Background corrected pyramidal ome.tif", - "pattern": "*.{tif}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "markerout": { - "type": "file", - "description": "Marker file adjusted to match the background corrected image", - "pattern": "*.{csv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "image": { + "type": "file", + "description": "Multi-channel image file", + "pattern": "*.{tif,tiff}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "markerfile": { + "type": "file", + "description": "Marker file with channel names, exposure times, and specified background to subtract (and remove to exclude channels from output)", + "pattern": "*.csv" + } + } + ] + ], + "output": [ + { + "backsub_tif": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ome.tif": { + "type": "file", + "description": "Background corrected pyramidal ome.tif", + "pattern": "*.{tif}" + } + } + ] + }, + { + "markerout": [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Marker file adjusted to match the background corrected image", + "pattern": "*.{csv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8032,52 +10027,73 @@ "doi": "10.7717/peerj.11396", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing phage contigs/scaffolds/chromosomes (if it is a multi-FASTA file be sure to add the `--multi_fasta` argument)", - "pattern": "*.{fasta,fna,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bacphlip_results": { - "type": "file", - "description": "TSV file containing Temperate and Virulent scores for each phage sequence", - "pattern": "*.bacphlip" - } - }, - { - "hmmsearch_results": { - "type": "file", - "description": "TSV file containing binary output indicating gene presence/absence based on hmmsearch results", - "pattern": "*.hmmsearch.tsv" - } + ], + "identifier": "biotools:bacphlip" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing phage contigs/scaffolds/chromosomes (if it is a multi-FASTA file be sure to add the `--multi_fasta` argument)", + "pattern": "*.{fasta,fna,fa}" + } + } + ] + ], + "output": [ + { + "bacphlip_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bacphlip": { + "type": "file", + "description": "TSV file containing Temperate and Virulent scores for each phage sequence", + "pattern": "*.bacphlip" + } + } + ] + }, + { + "hmmsearch_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hmmsearch.tsv": { + "type": "file", + "description": "TSV file containing binary output indicating gene presence/absence based on hmmsearch results", + "pattern": "*.hmmsearch.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8116,125 +10132,232 @@ "doi": "10.1099/mgen.0.000685", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file to be annotated. Has to contain at least a non-empty string dummy value.\n" - } - }, - { - "db": { - "type": "file", - "description": "Path to the Bakta database. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/').\n" - } - }, - { - "proteins": { - "type": "file", - "description": "FASTA/GenBank file of trusted proteins to first annotate from (optional)" - } - }, - { - "prodigal_tf": { - "type": "file", - "description": "Training file to use for Prodigal (optional)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "genome statistics and annotation summary", - "pattern": "*.txt" - } - }, - { - "tsv": { - "type": "file", - "description": "annotations as simple human readble tab separated values", - "pattern": "*.tsv" - } - }, - { - "gff": { - "type": "file", - "description": "annotations & sequences in GFF3 format", - "pattern": "*.gff3" - } - }, - { - "gbff": { - "type": "file", - "description": "annotations & sequences in (multi) GenBank format", - "pattern": "*.gbff" - } - }, - { - "embl": { - "type": "file", - "description": "annotations & sequences in (multi) EMBL format", - "pattern": "*.embl" - } - }, - { - "fna": { - "type": "file", - "description": "replicon/contig DNA sequences as FASTA", - "pattern": "*.fna" - } - }, - { - "faa": { - "type": "file", - "description": "CDS/sORF amino acid sequences as FASTA", - "pattern": "*.faa" - } - }, - { - "ffn": { - "type": "file", - "description": "feature nucleotide sequences as FASTA", - "pattern": "*.ffn" - } - }, - { - "hypotheticals_tsv": { - "type": "file", - "description": "additional information on hypothetical protein CDS as simple human readble tab separated values", - "pattern": "*.hypotheticals.tsv" - } - }, - { - "hypotheticals_faa": { - "type": "file", - "description": "hypothetical protein CDS amino acid sequences as FASTA", - "pattern": "*.hypotheticals.faa" - } + ], + "identifier": "biotools:bakta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file to be annotated. Has to contain at least a non-empty string dummy value.\n" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Path to the Bakta database. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/').\n" + } + } + ], + [ + { + "proteins": { + "type": "file", + "description": "FASTA/GenBank file of trusted proteins to first annotate from (optional)" + } + } + ], + [ + { + "prodigal_tf": { + "type": "file", + "description": "Training file to use for Prodigal (optional)" + } + } + ] + ], + "output": [ + { + "embl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.embl": { + "type": "file", + "description": "annotations & sequences in (multi) EMBL format", + "pattern": "*.embl" + } + } + ] + }, + { + "faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.faa": { + "type": "file", + "description": "CDS/sORF amino acid sequences as FASTA", + "pattern": "*.faa" + } + } + ] + }, + { + "ffn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.ffn": { + "type": "file", + "description": "feature nucleotide sequences as FASTA", + "pattern": "*.ffn" + } + } + ] + }, + { + "fna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fna": { + "type": "file", + "description": "replicon/contig DNA sequences as FASTA", + "pattern": "*.fna" + } + } + ] + }, + { + "gbff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.gbff": { + "type": "file", + "description": "annotations & sequences in (multi) GenBank format", + "pattern": "*.gbff" + } + } + ] + }, + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.gff3": { + "type": "file", + "description": "annotations & sequences in GFF3 format", + "pattern": "*.gff3" + } + } + ] + }, + { + "hypotheticals_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.hypotheticals.tsv": { + "type": "file", + "description": "additional information on hypothetical protein CDS as simple human readble tab separated values", + "pattern": "*.hypotheticals.tsv" + } + } + ] + }, + { + "hypotheticals_faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.hypotheticals.faa": { + "type": "file", + "description": "hypothetical protein CDS amino acid sequences as FASTA", + "pattern": "*.hypotheticals.faa" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "annotations as simple human readble tab separated values", + "pattern": "*.tsv" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "genome statistics and annotation summary", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8288,24 +10411,33 @@ "doi": "10.1099/mgen.0.000685", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:bakta" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "db*": { + "type": "directory", + "description": "BAKTA database directory", + "pattern": "db*/" + } + } + ] }, { - "db": { - "type": "directory", - "description": "BAKTA database directory", - "pattern": "db*/" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8353,52 +10485,63 @@ "tool_dev_url": "https://github.com/PacificBiosciences/bam2fastx", "licence": [ "BSD-3-clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "PacBio BAM file", - "pattern": "*.bam" - } - }, - { - "index": { - "type": "file", - "description": "PacBio BAM file index (.pbi)", - "pattern": "*.pbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Gzipped FASTQ file", - "pattern": "*.fastq.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "PacBio BAM file", + "pattern": "*.bam" + } + }, + { + "index": { + "type": "file", + "description": "PacBio BAM file index (.pbi)", + "pattern": "*.pbi" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Gzipped FASTQ file", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8431,45 +10574,56 @@ "tool_dev_url": "https://github.com/maxibor/bamAlignCleaner", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8503,66 +10657,87 @@ "doi": "10.1038/s41598-017-01703-6", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information `[ id:'sample1']`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAI index of the input BAM file", - "pattern": "*.bam.bai" - } - }, - { - "bedpe": { - "type": "file", - "description": "BEDPE file of primer pair locations", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information `[ id:'sample1']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file containing clipped query sequences according to the given primer pair locations", - "pattern": "*.primerclipped.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAI index of the output BAM file", - "pattern": "*.primerclipped.bam.bai" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information `[ id:'sample1']`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAI index of the input BAM file", + "pattern": "*.bam.bai" + } + }, + { + "bedpe": { + "type": "file", + "description": "BEDPE file of primer pair locations", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information `[ id:'sample1']`\n" + } + }, + { + "*.primerclipped.bam": { + "type": "file", + "description": "Sorted BAM file containing clipped query sequences according to the given primer pair locations", + "pattern": "*.primerclipped.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information `[ id:'sample1']`\n" + } + }, + { + "*.primerclipped.bam.bai": { + "type": "file", + "description": "BAI index of the output BAM file", + "pattern": "*.primerclipped.bam.bai" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8598,53 +10773,82 @@ "doi": "10.1158/1541-7786.MCR-16-0431", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "primary_aligned_bam": { - "type": "file", - "description": "BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "contaminant_aligned_bam": { - "type": "file", - "description": "BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "primary_filtered_bam": { - "type": "file", - "description": "Bam file containing the reads which align better to the primary genome.", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "contamination_bam": { - "type": "file", - "description": "Bam file containing the reads which align better to the contaminant genome.", - "pattern": "*.{bam,cram,sam}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "primary_aligned_bam": { + "type": "file", + "description": "BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "contaminant_aligned_bam": { + "type": "file", + "description": "BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "primary_filtered_bam": [ + { + "meta": { + "type": "file", + "description": "Bam file containing the reads which align better to the primary genome.", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Bam file containing the reads which align better to the primary genome.", + "pattern": "*.{bam,cram,sam}" + } + } + ] + }, + { + "contamination_bam": [ + { + "meta": { + "type": "file", + "description": "Bam file containing the reads which align better to the contaminant genome.", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "${prefix2}.bam": { + "type": "file", + "description": "Bam file containing the reads which align better to the contaminant genome.", + "pattern": "*.{bam,cram,sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8677,45 +10881,56 @@ "tool_dev_url": "https://github.com/guigolab", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "biotools:bamstats-ip" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "json containing bam statistics", + "pattern": "*.json" + } + } + ] }, { - "json": { - "type": "file", - "description": "json containing bam statistics", - "pattern": "*.json" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8745,45 +10960,56 @@ "tool_dev_url": "https://github.com/10XGenomics/bamtofastq", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "fastq compressed file", + "pattern": "*.fastq.gz" + } + } + ] }, { - "fastq": { - "type": "file", - "description": "fastq compressed file", - "pattern": "*.fastq.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8823,45 +11049,56 @@ "tool_dev_url": "http://github.com/pezmaster31/bamtools", "licence": [ "MIT" - ] + ], + "identifier": "biotools:bamtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "data": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bed,fasta,fastq,json,pileup,sam,yaml}": { + "type": "file", + "description": "Output file", + "pattern": "*.{bed,fasta,fastq,json,pileup,sam,yaml}" + } + } + ] }, { - "out": { - "type": "file", - "description": "The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)", - "pattern": "*.{bed,fasta,fastq,json,pileup,sam,yaml}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8901,45 +11138,56 @@ "tool_dev_url": "http://github.com/pezmaster31/bamtools", "licence": [ "MIT" - ] + ], + "identifier": "biotools:bamtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A list of one or more BAM files to merge and then split", - "pattern": "*.bam" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A list of one or more BAM files to merge and then split", + "pattern": "*.bam" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Several Bam files", + "pattern": "*.bam" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Several Bam files", - "pattern": "*.bam" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -8979,45 +11227,56 @@ "tool_dev_url": "http://github.com/pezmaster31/bamtools", "licence": [ "MIT" - ] + ], + "identifier": "biotools:bamtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "File containing alignment statistics", + "pattern": "*.stats" + } + } + ] }, { - "stats": { - "type": "file", - "description": "File containing alignment statistics", - "pattern": "*.stats" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9058,57 +11317,68 @@ "doi": "10.1101/gr.176552.114", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "trim_left": { - "type": "integer", - "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." - } - }, - { - "trim_right": { - "type": "integer", - "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Trimmed but unsorted BAM file", - "pattern": "*.bam" - } + ], + "identifier": "biotools:bamutil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "trim_left": { + "type": "integer", + "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." + } + }, + { + "trim_right": { + "type": "integer", + "description": "Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming." + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Trimmed but unsorted BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9140,56 +11410,77 @@ "documentation": "https://github.com/rrwick/Bandage", "licence": [ "GPL-3.0-or-later" - ] - } + ], + "identifier": "biotools:bandage" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Assembly graph in GFA 1.0 format", + "pattern": "*.gfa" + } + } + ] + ], + "output": [ + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Bandage image in PNG format", + "pattern": "*.png" + } + } + ] + }, + { + "svg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Bandage image in SVG format", + "pattern": "*.svg" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Assembly graph in GFA 1.0 format", - "pattern": "*.gfa" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "png": { - "type": "file", - "description": "Bandage image in PNG format", - "pattern": "*.png" - } - }, - { - "svg": { - "type": "file", - "description": "Bandage image in SVG format", - "pattern": "*.svg" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@heuermh" + "authors": [ + "@heuermh" ], "maintainers": [ "@heuermh" @@ -9223,51 +11514,62 @@ "tool_dev_url": "https://github.com/tseemann/barrnap", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq or fasta file nucleotides (it can be amino acids as well)", - "pattern": "*.{fna,fasta,faa,fastq}" - } - }, - { - "dbname": { - "type": "string", - "description": "database to use(bacteria, archaea, eukaryota, metazoan mitochondria)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gff": { - "type": "file", - "description": "gff file containing coordinates of genes", - "pattern": "*.gff" - } + ], + "identifier": "biotools:barrnap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.fasta" + } + }, + { + "dbname": { + "type": "string", + "description": "database to use(bacteria, archaea, eukaryota, metazoan mitochondria)" + } + } + ] + ], + "output": [ + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "gff file containing coordinates of genes", + "pattern": "*.gff" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9298,93 +11600,164 @@ "documentation": "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq", "licence": [ "http://go.elembio.link/eula" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "run_manifest": { - "type": "file", - "description": "RunManifest file", - "pattern": "*.{csv}" - } - }, - { - "run_dir": { - "type": "directory", - "description": "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sample_fastq": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "output/Samples/*/*_R*.fastq.gz" - } - }, - { - "sample_json": { - "type": "file", - "description": "Demultiplexed sample stats", - "pattern": "output/Samples/*/*.json" - } - }, - { - "qc_report": { - "type": "file", - "description": "QC HTML report", - "pattern": "output/*.html" - } - }, - { - "run_stats": { - "type": "file", - "description": "QC HTML report", - "pattern": "output/*.html" - } - }, - { - "generated_run_manifest": { - "type": "file", - "description": "Updated Run Manifest JSON from the run_manifest csv", - "pattern": "output/RunManifest.json" - } - }, - { - "metrics": { - "type": "file", - "description": "Sample metrics", - "pattern": "output/Metrics.csv" - } - }, - { - "unassigned": { - "type": "file", - "description": "Unassigned Sequences", - "pattern": "output/UnassignedSequences.csv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "run_manifest": { + "type": "file", + "description": "RunManifest file", + "pattern": "*.{csv}" + } + }, + { + "run_dir": { + "type": "directory", + "description": "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied" + } + } + ] + ], + "output": [ + { + "sample_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/Samples/**/*_R*.fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "output/Samples/*/*_R*.fastq.gz" + } + } + ] + }, + { + "sample_json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/Samples/**/*_stats.json": { + "type": "file", + "description": "Demultiplexed sample stats", + "pattern": "output/Samples/*/*.json" + } + } + ] + }, + { + "qc_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/*.html": { + "type": "file", + "description": "QC HTML report", + "pattern": "output/*.html" + } + } + ] + }, + { + "run_stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/RunStats.json": { + "type": "file", + "description": "QC HTML report", + "pattern": "output/*.html" + } + } + ] + }, + { + "generated_run_manifest": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/RunManifest.json": { + "type": "file", + "description": "Updated Run Manifest JSON from the run_manifest csv", + "pattern": "output/RunManifest.json" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/Metrics.csv": { + "type": "file", + "description": "Sample metrics", + "pattern": "output/Metrics.csv" + } + } + ] + }, + { + "unassigned": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/UnassignedSequences.csv": { + "type": "file", + "description": "Unassigned Sequences", + "pattern": "output/UnassignedSequences.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9424,45 +11797,56 @@ "doi": "10.1038/ncomms14836", "license": [ "MIT License" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "image": { - "type": "file", - "description": "Tiff file to be used for dark and flat field illumination correction", - "pattern": "*.{tiff,tif}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "image": { + "type": "file", + "description": "Tiff file to be used for dark and flat field illumination correction", + "pattern": "*.{tiff,tif}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fields": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tiff": { + "type": "file", + "description": "Tiff fields for dark and flat field illumination correction", + "pattern": "*.{tiff,tif}" + } + } + ] }, { - "fields": { - "type": "file", - "description": "Tiff fields for dark and flat field illumination correction", - "pattern": "*.{tiff,tif}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9502,50 +11886,80 @@ "documentation": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/", "licence": [ "UC-LBL license (see package)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "ref": { - "type": "file", - "description": "Either \"ref\" a directory containing an index, the name of another directory\nwith a \"ref\" subdirectory containing an index or the name of a fasta formatted\nnucleotide file containg the reference to map to.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "ref": { + "type": "file", + "description": "Either \"ref\" a directory containing an index, the name of another directory\nwith a \"ref\" subdirectory containing an index or the name of a fasta formatted\nnucleotide file containg the reference to map to.\n" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9587,57 +12001,80 @@ "documentation": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/", "licence": [ "UC-LBL license (see package)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "contaminants": { - "type": "file", - "description": "Reference files containing adapter and/or contaminant sequences for sequence kmer matching\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*fastq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "Bbduk log file", - "pattern": "*bbduk.log" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "contaminants": { + "type": "file", + "description": "Reference files containing adapter and/or contaminant sequences for sequence kmer matching\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Bbduk log file", + "pattern": "*bbduk.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9682,72 +12119,109 @@ "documentation": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/", "licence": [ "UC-LBL license (see package)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input paired end fastq files\n", - "pattern": "*.{fastq,fq}.gz" - } - }, - { - "interleave": { - "type": "boolean", - "description": "Indicates whether the input paired reads are interleaved or not\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "merged": { - "type": "file", - "description": "merged reads", - "pattern": "*_merged.fastq" - } - }, - { - "unmerged": { - "type": "file", - "description": "unmerged reads", - "pattern": "*_unmerged.fastq" - } - }, - { - "ihist": { - "type": "file", - "description": "insert size histogram", - "pattern": "*_ihist.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "log file containing stdout and stderr from bbmerge.sh", - "pattern": "*.log" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired end fastq files\n", + "pattern": "*.{fastq,fq}.gz" + } + } + ], + [ + { + "interleave": { + "type": "boolean", + "description": "Indicates whether the input paired reads are interleaved or not\n" + } + } + ] + ], + "output": [ + { + "merged": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_merged.fastq.gz": { + "type": "file", + "description": "merged reads", + "pattern": "*_merged.fastq" + } + } + ] + }, + { + "unmerged": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_unmerged.fastq.gz": { + "type": "file", + "description": "unmerged reads", + "pattern": "*_unmerged.fastq" + } + } + ] + }, + { + "ihist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_ihist.txt": { + "type": "file", + "description": "insert size histogram", + "pattern": "*_ihist.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "log": [ + { + "*.log": { + "type": "file", + "description": "log file containing stdout and stderr from bbmerge.sh", + "pattern": "*.log" + } + } + ] } ], "authors": [ @@ -9779,45 +12253,73 @@ "tool_dev_url": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/", "licence": [ "BBMap - Bushnell B. - sourceforge.net/projects/bbmap/" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fastq,fq}(.gz)?" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fastq, fq}.gz" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fastq,fq}(.gz)?" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fastq, fq}.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9860,97 +12362,157 @@ "documentation": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/", "licence": [ "UC-LBL license (see package)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory to place generated index", - "pattern": "*" - } - }, - { - "primary_ref": { - "type": "file", - "description": "Path to the primary reference", - "pattern": "*" - } - }, - { - "other_ref_names": { - "type": "list", - "description": "List of other reference ids apart from the primary" - } - }, - { - "other_ref_paths": { - "type": "list", - "description": "Path to other references paths corresponding to \"other_ref_names\"" - } - }, - { - "only_build_index": { - "type": "string", - "description": "true = only build index; false = mapping" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "index": { - "type": "directory", - "description": "Directory with index files", - "pattern": "bbsplit" - } - }, - { - "primary_fastq": { - "type": "file", - "description": "Output reads that map to the primary reference", - "pattern": "*primary*fastq.gz" - } - }, - { - "all_fastq": { - "type": "file", - "description": "All reads mapping to any of the references", - "pattern": "*fastq.gz" - } - }, - { - "stats": { - "type": "file", - "description": "Tab-delimited text file containing mapping statistics", - "pattern": "*.txt" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Directory to place generated index", + "pattern": "*" + } + } + ], + [ + { + "primary_ref": { + "type": "file", + "description": "Path to the primary reference", + "pattern": "*" + } + } + ], + [ + { + "other_ref_names": { + "type": "list", + "description": "List of other reference ids apart from the primary" + } + }, + { + "other_ref_paths": { + "type": "list", + "description": "Path to other references paths corresponding to \"other_ref_names\"" + } + } + ], + [ + { + "only_build_index": { + "type": "string", + "description": "true = only build index; false = mapping" + } + } + ] + ], + "output": [ + { + "index": [ + { + "bbsplit": { + "type": "directory", + "description": "Directory with index files", + "pattern": "bbsplit" + } + } + ] + }, + { + "primary_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*primary*fastq.gz": { + "type": "file", + "description": "Output reads that map to the primary reference", + "pattern": "*primary*fastq.gz" + } + } + ] + }, + { + "all_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "All reads mapping to any of the references", + "pattern": "*fastq.gz" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*txt": { + "type": "file", + "description": "Tab-delimited text file containing mapping statistics", + "pattern": "*.txt" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -9994,51 +12556,72 @@ "documentation": "https://www.biostars.org/p/225338/", "licence": [ "UC-LBL license (see package)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "The reordered/clumped (and if necessary deduped) fastq reads", - "pattern": "*.clumped.fastq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "Clumpify log file", - "pattern": "*clumpify.log" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "The reordered/clumped (and if necessary deduped) fastq reads", + "pattern": "*.clumped.fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Clumpify log file", + "pattern": "*clumpify.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10069,69 +12652,96 @@ "documentation": "https://www.biostars.org/p/225338/", "licence": [ "UC-LBL license (see package)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively.\n" - } - }, - { - "names_to_filter": { - "type": "string", - "description": "String containing names of reads to filter out of the fastq files.\n" - } - }, - { - "output_format": { - "type": "string", - "description": "String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2\n" - } - }, - { - "interleaved_output": { - "type": "boolean", - "description": "Whether to produce an interleaved fastq output file\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*${output_format}" - } - }, - { - "log": { - "type": "file", - "description": "filterbyname.sh log file", - "pattern": "*.filterbyname.log" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and\npaired-end data, respectively.\n" + } + } + ], + [ + { + "names_to_filter": { + "type": "string", + "description": "String containing names of reads to filter out of the fastq files.\n" + } + } + ], + [ + { + "output_format": { + "type": "string", + "description": "String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2\n" + } + } + ], + [ + { + "interleaved_output": { + "type": "boolean", + "description": "Whether to produce an interleaved fastq output file\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${output_format}": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*${output_format}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "filterbyname.sh log file", + "pattern": "*.filterbyname.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10163,33 +12773,43 @@ "documentation": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/", "licence": [ "UC-LBL license (see package)" - ] + ], + "identifier": "biotools:bbmap" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "fasta formatted file with nucleotide sequences", - "pattern": "*.{fna,fa,fasta}" + [ + { + "fasta": { + "type": "file", + "description": "fasta formatted file with nucleotide sequences", + "pattern": "*.{fna,fa,fasta}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "ref": { + "type": "directory", + "description": "Directory containing the index files" + } + } + ] }, { - "db": { - "type": "directory", - "description": "Directory with index files", - "pattern": "ref" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10231,52 +12851,73 @@ "tool_dev_url": "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh", "licence": [ "UC-LBL license (see package)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "stats": { - "type": "file", - "description": "Per-scaffold coverage info", - "pattern": "*.stats.txt" - } - }, - { - "hist": { - "type": "file", - "description": "Histogram of # occurrences of each depth level", - "pattern": "*.hist.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "covstats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats.txt": { + "type": "file", + "description": "Coverage statistics", + "pattern": "*.stats.txt" + } + } + ] + }, + { + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist.txt": { + "type": "file", + "description": "Histogram of # occurrences of each depth level", + "pattern": "*.hist.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10316,45 +12957,56 @@ "documentation": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/", "licence": [ "UC-LBL license (see package)" - ] + ], + "identifier": "biotools:bbmap" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "file": { - "type": "file", - "description": "file with nucleotide sequences", - "pattern": "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, fq}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "file": { + "type": "file", + "description": "file with nucleotide sequences", + "pattern": "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, fq}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "hits": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": ".txt file containing hits from a query seuqnce to various reference sequences output", + "pattern": "*.{txt}" + } + } + ] }, { - "hits": { - "type": "file", - "description": ".txt file containing hits from a query seuqnce to various reference sequences output", - "pattern": "*.{txt}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10388,82 +13040,115 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Query VCF or BCF file, can be either uncompressed or compressed" - } - }, - { - "index": { - "type": "file", - "description": "Index of the query VCF or BCF file" - } - }, - { - "annotations": { - "type": "file", - "description": "Bgzip-compressed file with annotations" - } - }, - { - "annotations_index": { - "type": "file", - "description": "Index of the annotations file" - } - }, - { - "header_lines": { - "type": "file", - "description": "Contains lines to append to the output VCF header" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed annotated VCF file", - "pattern": "*{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Query VCF or BCF file, can be either uncompressed or compressed" + } + }, + { + "index": { + "type": "file", + "description": "Index of the query VCF or BCF file" + } + }, + { + "annotations": { + "type": "file", + "description": "Bgzip-compressed file with annotations" + } + }, + { + "annotations_index": { + "type": "file", + "description": "Index of the annotations file" + } + } + ], + [ + { + "header_lines": { + "type": "file", + "description": "Contains lines to append to the output VCF header" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "Compressed annotated VCF file", + "pattern": "*{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10520,82 +13205,119 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" + } + } + ], + [ + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" + } + } + ], + [ + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" + } + } + ], + [ + { + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "VCF normalized output file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10630,64 +13352,95 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n" - } - }, - { - "tbi": { - "type": "list", - "description": "List containing 2 or more index files (optional)\ne.g. [ 'file1.tbi', 'file2.tbi' ]\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF concatenated output file", - "pattern": "*.{vcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n" + } + }, + { + "tbi": { + "type": "list", + "description": "List containing 2 or more index files (optional)\ne.g. [ 'file1.tbi', 'file2.tbi' ]\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "VCF concatenated output file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10739,66 +13492,77 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}" - } - }, - { - "tbi": { - "type": "file", - "description": "tabix index file", - "pattern": "*.{tbi}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" - } - }, - { - "mask": { - "type": "file", - "description": "BED file used for masking", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference consensus file", - "pattern": "*.{fasta,fa}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf}" + } + }, + { + "tbi": { + "type": "file", + "description": "tabix index file", + "pattern": "*.{tbi}" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } + }, + { + "mask": { + "type": "file", + "description": "BED file used for masking", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "FASTA reference consensus file", + "pattern": "*.{fasta,fa}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10844,114 +13608,189 @@ "doi": "10.1093/gigascience/giab008", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "The input format. Each format needs a seperate parameter to be specified in the `args`:\n- GEN/SAMPLE file: `--gensample2vcf`\n- gVCF file: `--gvcf2vcf`\n- HAP/SAMPLE file: `--hapsample2vcf`\n- HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf`\n- TSV file: `--tsv2vcf`\n", - "pattern": "*.{gen,sample,g.vcf,hap,legend}{.gz,}" - } - }, - { - "input_index": { - "type": "file", - "description": "(Optional) The index for the input files, if needed", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Optional) The reference fasta, only needed for gVCF conversion", - "pattern": "*.{fa,fasta}" - } - }, - { - "bed": { - "type": "file", - "description": "(Optional) The BED file containing the regions for the VCF file", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf_gz": { - "type": "file", - "description": "VCF merged output file (bgzipped) => when `--output-type z` is used", - "pattern": "*.vcf.gz" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF merged output file => when `--output-type v` is used", - "pattern": "*.vcf" - } - }, - { - "bcf_gz": { - "type": "file", - "description": "BCF merged output file (bgzipped) => when `--output-type b` is used", - "pattern": "*.bcf.gz" - } - }, - { - "bcf": { - "type": "file", - "description": "BCF merged output file => when `--output-type u` is used", - "pattern": "*.bcf" - } - }, - { - "hap": { - "type": "file", - "description": "hap format used by IMPUTE2 and SHAPEIT", - "pattern": "*.hap.gz" - } - }, - { - "legend": { - "type": "file", - "description": "legend format used by IMPUTE2 and SHAPEIT", - "pattern": "*.legend.gz" - } - }, - { - "sample": { - "type": "file", - "description": "sample format used by IMPUTE2 and SHAPEIT", - "pattern": "*.samples" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "The input format. Each format needs a seperate parameter to be specified in the `args`:\n- GEN/SAMPLE file: `--gensample2vcf`\n- gVCF file: `--gvcf2vcf`\n- HAP/SAMPLE file: `--hapsample2vcf`\n- HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf`\n- TSV file: `--tsv2vcf`\n", + "pattern": "*.{gen,sample,g.vcf,hap,legend}{.gz,}" + } + }, + { + "input_index": { + "type": "file", + "description": "(Optional) The index for the input files, if needed", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Optional) The reference fasta, only needed for gVCF conversion", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "(Optional) The BED file containing the regions for the VCF file", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "vcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF merged output file (bgzipped) => when `--output-type z` is used", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF merged output file => when `--output-type v` is used", + "pattern": "*.vcf" + } + } + ] + }, + { + "bcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf.gz": { + "type": "file", + "description": "BCF merged output file (bgzipped) => when `--output-type b` is used", + "pattern": "*.bcf.gz" + } + } + ] + }, + { + "bcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "BCF merged output file => when `--output-type u` is used", + "pattern": "*.bcf" + } + } + ] + }, + { + "hap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap.gz": { + "type": "file", + "description": "hap format used by IMPUTE2 and SHAPEIT", + "pattern": "*.hap.gz" + } + } + ] + }, + { + "legend": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.legend.gz": { + "type": "file", + "description": "legend format used by IMPUTE2 and SHAPEIT", + "pattern": "*.legend.gz" + } + } + ] + }, + { + "samples": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.samples": { + "type": "file", + "description": "samples format used by IMPUTE2 and SHAPEIT", + "pattern": "*.samples" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -10998,98 +13837,135 @@ "doi": "10.1093/gigascience/giab008", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF/BCF file", - "pattern": "*.{vcf.gz,vcf,bcf}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta reference", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai information\n" - } - }, - { - "fai": { - "type": "file", - "description": "Fasta index", - "pattern": "*.{fai}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing gff3 information\n" - } - }, - { - "gff3": { - "type": "file", - "description": "GFF3 file", - "pattern": "*.{gff,gff.gz,gff3,gff3.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF with annotation, bgzipped per default", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF/BCF file", + "pattern": "*.{vcf.gz,vcf,bcf}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta reference", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai information\n" + } + }, + { + "fai": { + "type": "file", + "description": "Fasta index", + "pattern": "*.{fai}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing gff3 information\n" + } + }, + { + "gff3": { + "type": "file", + "description": "GFF3 file", + "pattern": "*.{gff,gff.gz,gff3,gff3.gz}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF with annotation, bgzipped per default", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11121,59 +13997,90 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF input file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF filtered output file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF input file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF filtered output file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11225,52 +14132,73 @@ "licence": [ "MIT", "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file (optionally GZIPPED)", - "pattern": "*.{vcf,vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index file", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index file for larger files (activated with -t parameter)", - "pattern": "*.tbi" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file (optionally GZIPPED)", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + ], + "output": [ + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index file", + "pattern": "*.csi" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index file for larger files (activated with -t parameter)", + "pattern": "*.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11315,50 +14243,61 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "List containing 2 or more vcf/bcf files. These must be compressed and have an associated index.\ne.g. [ 'file1.vcf.gz', 'file2.vcf' ]\n" - } - }, - { - "tbis": { - "type": "list", - "description": "List containing the tbi index files corresponding to the vcf/bcf input files\ne.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "directory", - "description": "Folder containing the set operations results perform on the vcf files", - "pattern": "${prefix}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "List containing 2 or more vcf/bcf files. These must be compressed and have an associated index.\ne.g. [ 'file1.vcf.gz', 'file2.vcf' ]\n" + } + }, + { + "tbis": { + "type": "list", + "description": "List containing the tbi index files corresponding to the vcf/bcf input files\ne.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]\n" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}\", type: \"dir": { + "type": "directory", + "description": "Folder containing the set operations results perform on the vcf files", + "pattern": "${prefix}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11392,96 +14331,123 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "file", - "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n" - } - }, - { - "tbis": { - "type": "file", - "description": "List containing the tbi index files corresponding to the vcfs input files\ne.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing bed information\ne.g. [ id:'genome' ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "(Optional) The bed regions to merge on", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "merged output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "index of merged output", - "pattern": "*.{csi,tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "List containing 2 or more vcf files\ne.g. [ 'file1.vcf', 'file2.vcf' ]\n" + } + }, + { + "tbis": { + "type": "file", + "description": "List containing the tbi index files corresponding to the vcfs input files\ne.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing bed information\ne.g. [ id:'genome' ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "(Optional) The bed regions to merge on", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bcf,vcf}{,.gz}": { + "type": "file", + "description": "merged output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{csi,tbi}": { + "type": "file", + "description": "index of merged output", + "pattern": "*.{csi,tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11533,91 +14499,136 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}" - } - }, - { - "intervals": { - "type": "file", - "description": "Input intervals file. A file (commonly '.bed') containing regions to subset" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the genome fasta, e.g. [ id: 'sarscov2' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" - } - }, - { - "save_mpileup": { - "type": "boolean", - "description": "Save mpileup file generated by bcftools mpileup" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF gzipped output file", - "pattern": "*.{vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "tabix index file", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "stats": { - "type": "file", - "description": "Text output file containing stats", - "pattern": "*{stats.txt}" - } - }, - { - "mpileup": { - "type": "file", - "description": "mpileup gzipped output for all positions", - "pattern": "{*.mpileup.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}" + } + }, + { + "intervals": { + "type": "file", + "description": "Input intervals file. A file (commonly '.bed') containing regions to subset" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "save_mpileup": { + "type": "boolean", + "description": "Save mpileup file generated by bcftools mpileup" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*vcf.gz": { + "type": "file", + "description": "VCF gzipped output file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*vcf.gz.tbi": { + "type": "file", + "description": "tabix index file", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*stats.txt": { + "type": "file", + "description": "Text output file containing stats", + "pattern": "*{stats.txt}" + } + } + ] + }, + { + "mpileup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup.gz": { + "type": "file", + "description": "mpileup gzipped output for all positions", + "pattern": "{*.mpileup.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11666,79 +14677,112 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be normalized\ne.g. 'file1.vcf'\n", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "An optional index of the VCF file (for when the VCF is compressed)\n", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be normalized\ne.g. 'file1.vcf'\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "An optional index of the VCF file (for when the VCF is compressed)\n", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11799,7 +14843,8 @@ "licence": [ "MIT" ], - "args_id": "$args" + "args_id": "$args", + "identifier": "biotools:bcftools" } }, { @@ -11812,76 +14857,111 @@ "licence": [ "MIT" ], - "args_id": "$args2" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF output file containing added INFO/INFO field", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "args_id": "$args2", + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" + } + } + ], + [ + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" + } + } + ], + [ + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF output file containing added INFO/INFO field", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -11914,98 +14994,139 @@ "doi": "10.1093/gigascience/giab008", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The input VCF to scatter", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "Optional index of the input VCF", - "pattern": "*.tbi" - } - }, - { - "sites_per_chunk": { - "type": "integer", - "description": "How many variants should be in each output file\nEither this or `scatter` or `scatter_file` have to be given\n" - } - }, - { - "scatter": { - "type": "string", - "description": "A comma delimited list of regions to scatter into\nEither this or `sites_per_chunk` or `scatter_file` have to be given\n" - } - }, - { - "scatter_file": { - "type": "file", - "description": "A file containing a region on each line with an optional second column containing the filename\nEither this or `sites_per_chunk` or `scatter` have to be given\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optional file containing the regions to work on", - "pattern": "*.bed" - } - }, - { - "targets": { - "type": "file", - "description": "Optional file containing the regions to work on (but streams instead of index-jumping)", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "scatter": { - "type": "file", - "description": "The resulting files of the scattering", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The input VCF to scatter", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "Optional index of the input VCF", + "pattern": "*.tbi" + } + } + ], + [ + { + "sites_per_chunk": { + "type": "integer", + "description": "How many variants should be in each output file\nEither this or `scatter` or `scatter_file` have to be given\n" + } + } + ], + [ + { + "scatter": { + "type": "string", + "description": "A comma delimited list of regions to scatter into\nEither this or `sites_per_chunk` or `scatter_file` have to be given\n" + } + } + ], + [ + { + "scatter_file": { + "type": "file", + "description": "A file containing a region on each line with an optional second column containing the filename\nEither this or `sites_per_chunk` or `scatter` have to be given\n" + } + } + ], + [ + { + "regions": { + "type": "file", + "description": "Optional file containing the regions to work on", + "pattern": "*.bed" + } + } + ], + [ + { + "targets": { + "type": "file", + "description": "Optional file containing the regions to work on (but streams instead of index-jumping)", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "scatter": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "The resulting files of the scattering", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12037,80 +15158,133 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file to split", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "OPTIONAL - The index of the input VCF/BCF", - "pattern": "*.tbi" - } - }, - { - "samples": { - "type": "file", - "description": "A tab-separated file determining which samples should be in which output file\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file\nEither this or a groups file should be given\n", - "pattern": "*" - } - }, - { - "groups": { - "type": "file", - "description": "A tab-separated file determining which samples should be in which output file(s)\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file(s)\nEither this or a samples file should be given\n", - "pattern": "*" - } - }, - { - "regions": { - "type": "file", - "description": "A BED file containing regions to use", - "pattern": "*.bed" - } - }, - { - "targets": { - "type": "file", - "description": "A BED file containing regions to use (but streams rather than index-jumps)", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The resulting VCF files from the split", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file to split", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "OPTIONAL - The index of the input VCF/BCF", + "pattern": "*.tbi" + } + } + ], + [ + { + "samples": { + "type": "file", + "description": "A tab-separated file determining which samples should be in which output file\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file\nEither this or a groups file should be given\n", + "pattern": "*" + } + } + ], + [ + { + "groups": { + "type": "file", + "description": "A tab-separated file determining which samples should be in which output file(s)\ncolumn 1: The sample name(s) in the input file\ncolumn 2: The sample name(s) to use in the output file (use `-` to keep the original name)\ncolumn 3: The name of the output file(s)\nEither this or a samples file should be given\n", + "pattern": "*" + } + } + ], + [ + { + "regions": { + "type": "file", + "description": "A BED file containing regions to use", + "pattern": "*.bed" + } + } + ], + [ + { + "targets": { + "type": "file", + "description": "A BED file containing regions to use (but streams rather than index-jumps)", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "The resulting VCF files from the split", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "TBI file", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "CSI file", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12148,76 +15322,111 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" + } + } + ], + [ + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" + } + } + ], + [ + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF normalized output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12250,69 +15459,86 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be qeuried.\n", - "pattern": "*.{vcf.gz, vcf}" - } - }, - { - "tbi": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\n", - "pattern": "*.tbi" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\n" - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\n" - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output": { - "type": "file", - "description": "BCFTools query output file" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be qeuried.\n", + "pattern": "*.{vcf.gz, vcf}" + } + }, + { + "tbi": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\n", + "pattern": "*.tbi" + } + } + ], + [ + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\n" + } + } + ], + [ + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\n" + } + } + ], + [ + { + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${suffix}": { + "type": "file", + "description": "BCFTools query output file" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12356,79 +15582,102 @@ "doi": "10.1093/gigascience/giab008", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF/BCF file", - "pattern": "*.{vcf.gz,vcf,bcf}" - } - }, - { - "header": { - "type": "file", - "description": "New header to add to the VCF", - "pattern": "*.{header.txt}" - } - }, - { - "samples": { - "type": "file", - "description": "File containing sample names to update (one sample per line)", - "pattern": "*.{samples.txt}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Fasta index to update header sequences with", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF with updated header, bgzipped per default", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Index of VCF with updated header", - "pattern": "*.{csi,tbi}" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF/BCF file", + "pattern": "*.{vcf.gz,vcf,bcf}" + } + }, + { + "header": { + "type": "file", + "description": "New header to add to the VCF", + "pattern": "*.{header.txt}" + } + }, + { + "samples": { + "type": "file", + "description": "File containing sample names to update (one sample per line)", + "pattern": "*.{samples.txt}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Fasta index to update header sequences with", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF with updated header, bgzipped per default", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{csi,tbi}": { + "type": "file", + "description": "Index of VCF with updated header", + "pattern": "*.{csi,tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12475,81 +15724,109 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,.vcf.gz}" - } - }, - { - "af_file": { - "type": "file", - "description": "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF." - } - }, - { - "af_file_tbi": { - "type": "file", - "description": "tbi index of af_file." - } - }, - { - "genetic_map": { - "type": "file", - "description": "Genetic map in the format required also by IMPUTE2." - } - }, - { - "regions_file": { - "type": "file", - "description": "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." - } - }, - { - "samples_file": { - "type": "file", - "description": "File of sample names to include or exclude if prefixed with '^'." - } - }, - { - "targets_file": { - "type": "file", - "description": "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "roh": { - "type": "file", - "description": "Contains site-specific and/or per-region runs of homo/autozygosity calls.", - "pattern": "*.{roh}" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,.vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "TBI file", + "patthern": "*.tbi" + } + } + ], + [ + { + "af_file": { + "type": "file", + "description": "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF." + } + }, + { + "af_file_tbi": { + "type": "file", + "description": "tbi index of af_file." + } + } + ], + [ + { + "genetic_map": { + "type": "file", + "description": "Genetic map in the format required also by IMPUTE2." + } + } + ], + [ + { + "regions_file": { + "type": "file", + "description": "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." + } + } + ], + [ + { + "samples_file": { + "type": "file", + "description": "File of sample names to include or exclude if prefixed with '^'." + } + } + ], + [ + { + "targets_file": { + "type": "file", + "description": "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." + } + } + ] + ], + "output": [ + { + "roh": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roh": { + "type": "file", + "description": "Contains site-specific and/or per-region runs of homo/autozygosity calls.", + "pattern": "*.{roh}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12588,59 +15865,90 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF/BCF file to be sorted", - "pattern": "*.{vcf.gz,vcf,bcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Sorted VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF/BCF file to be sorted", + "pattern": "*.{vcf.gz,vcf,bcf}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "Sorted VCF file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12703,52 +16011,63 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed vcf file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Compressed vcf file index", - "pattern": "*.{tbi,csi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "split_vcf": { - "type": "file", - "description": "Compressed vcf files per chromosome", - "pattern": "*.vcf.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed vcf file", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "Compressed vcf file index", + "pattern": "*.{tbi,csi}" + } + } + ] + ], + "output": [ + { + "split_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed vcf files per chromosome", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12782,82 +16101,133 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF input file", - "pattern": "*.{vcf}" - } - }, - { - "tbi": { - "type": "file", - "description": "The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.\n", - "pattern": "*.tbi" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)\n" - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)\n" - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" - } - }, - { - "exons": { - "type": "file", - "description": "Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).\ne.g. 'exons.tsv.gz'\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Faidx indexed reference sequence file to determine INDEL context.\ne.g. 'reference.fa'\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "stats": { - "type": "file", - "description": "Text output file containing stats", - "pattern": "*_{stats.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF input file", + "pattern": "*.{vcf}" + } + }, + { + "tbi": { + "type": "file", + "description": "The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.\n", + "pattern": "*.tbi" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)\n" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "exons": { + "type": "file", + "description": "Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).\ne.g. 'exons.tsv.gz'\n" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Faidx indexed reference sequence file to determine INDEL context.\ne.g. 'reference.fa'\n" + } + } + ] + ], + "output": [ + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*stats.txt": { + "type": "file", + "description": "Text output file containing stats", + "pattern": "*_{stats.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -12922,82 +16292,119 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" - } - }, - { - "index": { - "type": "file", - "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" - } - }, - { - "regions": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" - } - }, - { - "targets": { - "type": "file", - "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" - } - }, - { - "samples": { - "type": "file", - "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n" + } + }, + { + "index": { + "type": "file", + "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n" + } + } + ], + [ + { + "regions": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n" + } + } + ], + [ + { + "targets": { + "type": "file", + "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n" + } + } + ], + [ + { + "samples": { + "type": "file", + "description": "Optional, file of sample names to be included or excluded.\ne.g. 'file.tsv'\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bcf.gz}": { + "type": "file", + "description": "VCF normalized output file", + "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13046,87 +16453,171 @@ "documentation": "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf", "licence": [ "ILLUMINA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Input samplesheet", - "pattern": "*.{csv}" - } - }, - { - "run_dir": { - "type": "file", - "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "**_S*_L00?_R?_00?.fastq.gz" - } - }, - { - "fastq_idx": { - "type": "file", - "description": "Optional demultiplexed index FASTQ files", - "pattern": "**_S*_L00?_I?_00?.fastq.gz" - } - }, - { - "undetermined": { - "type": "file", - "description": "Optional undetermined sample FASTQ files", - "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz" - } - }, - { - "undetermined_idx": { - "type": "file", - "description": "Optional undetermined index FASTQ files", - "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz" - } - }, - { - "reports": { - "type": "file", - "description": "Demultiplexing Reports", - "pattern": "Reports/*" - } - }, - { - "stats": { - "type": "file", - "description": "Statistics files", - "pattern": "Stats/*" - } - }, - { - "interop": { - "type": "file", - "description": "Interop files", - "pattern": "*.{bin}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Input samplesheet", + "pattern": "*.{csv}" + } + }, + { + "run_dir": { + "type": "file", + "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "**_S*_L00?_R?_00?.fastq.gz" + } + }, + { + "output/**_S[1-9]*_R?_00?.fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "**_S*_L00?_R?_00?.fastq.gz" + } + } + ] + }, + { + "fastq_idx": [ + { + "meta": { + "type": "file", + "description": "Optional demultiplexed index FASTQ files", + "pattern": "**_S*_L00?_I?_00?.fastq.gz" + } + }, + { + "output/**_S[1-9]*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional demultiplexed index FASTQ files", + "pattern": "**_S*_L00?_I?_00?.fastq.gz" + } + } + ] + }, + { + "undetermined": [ + { + "meta": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz" + } + }, + { + "output/**Undetermined_S0*_R?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz" + } + } + ] + }, + { + "undetermined_idx": [ + { + "meta": { + "type": "file", + "description": "Optional undetermined index FASTQ files", + "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz" + } + }, + { + "output/**Undetermined_S0*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined index FASTQ files", + "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz" + } + } + ] + }, + { + "reports": [ + { + "meta": { + "type": "file", + "description": "Demultiplexing Reports", + "pattern": "Reports/*" + } + }, + { + "output/Reports": { + "type": "file", + "description": "Demultiplexing Reports", + "pattern": "Reports/*" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "file", + "description": "Statistics files", + "pattern": "Stats/*" + } + }, + { + "output/Stats": { + "type": "file", + "description": "Statistics files", + "pattern": "Stats/*" + } + } + ] + }, + { + "interop": [ + { + "meta": { + "type": "file", + "description": "Interop files", + "pattern": "*.{bin}" + } + }, + { + "InterOp/*.bin": { + "type": "file", + "description": "Interop files", + "pattern": "*.{bin}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13163,87 +16654,171 @@ "documentation": "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm", "licence": [ "ILLUMINA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Input samplesheet", - "pattern": "*.{csv}" - } - }, - { - "run_dir": { - "type": "file", - "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "**_S*_L00?_R?_00?.fastq.gz" - } - }, - { - "fastq_idx": { - "type": "file", - "description": "Optional demultiplexed index FASTQ files", - "pattern": "**_S*_L00?_I?_00?.fastq.gz" - } - }, - { - "undetermined": { - "type": "file", - "description": "Optional undetermined sample FASTQ files", - "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz" - } - }, - { - "undetermined_idx": { - "type": "file", - "description": "Optional undetermined index FASTQ files", - "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz" - } - }, - { - "reports": { - "type": "file", - "description": "Demultiplexing Reports", - "pattern": "Reports/*.{csv,xml}" - } - }, - { - "logs": { - "type": "file", - "description": "Log files", - "pattern": "Logs/*.{log,txt}" - } - }, - { - "interop": { - "type": "file", - "description": "Interop files", - "pattern": "*.{bin}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Input samplesheet", + "pattern": "*.{csv}" + } + }, + { + "run_dir": { + "type": "file", + "description": "Input run directory containing RunInfo.xml and BCL data\nCould be a directory or a tar of the directory\n" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "**_S*_L00?_R?_00?.fastq.gz" + } + }, + { + "output/**_S[1-9]*_R?_00?.fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "**_S*_L00?_R?_00?.fastq.gz" + } + } + ] + }, + { + "fastq_idx": [ + { + "meta": { + "type": "file", + "description": "Optional demultiplexed index FASTQ files", + "pattern": "**_S*_L00?_I?_00?.fastq.gz" + } + }, + { + "output/**_S[1-9]*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional demultiplexed index FASTQ files", + "pattern": "**_S*_L00?_I?_00?.fastq.gz" + } + } + ] + }, + { + "undetermined": [ + { + "meta": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz" + } + }, + { + "output/**Undetermined_S0*_R?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_S0_L00?_R?_00?.fastq.gz" + } + } + ] + }, + { + "undetermined_idx": [ + { + "meta": { + "type": "file", + "description": "Optional undetermined index FASTQ files", + "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz" + } + }, + { + "output/**Undetermined_S0*_I?_00?.fastq.gz": { + "type": "file", + "description": "Optional undetermined index FASTQ files", + "pattern": "Undetermined_S0_L00?_I?_00?.fastq.gz" + } + } + ] + }, + { + "reports": [ + { + "meta": { + "type": "file", + "description": "Demultiplexing Reports", + "pattern": "Reports/*.{csv,xml}" + } + }, + { + "output/Reports": { + "type": "file", + "description": "Demultiplexing Reports", + "pattern": "Reports/*.{csv,xml}" + } + } + ] + }, + { + "logs": [ + { + "meta": { + "type": "file", + "description": "Log files", + "pattern": "Logs/*.{log,txt}" + } + }, + { + "output/Logs": { + "type": "file", + "description": "Log files", + "pattern": "Logs/*.{log,txt}" + } + } + ] + }, + { + "interop": [ + { + "meta": { + "type": "file", + "description": "Interop files", + "pattern": "*.{bin}" + } + }, + { + "**/InterOp/*.bin\", includeInputs: true": { + "type": "file", + "description": "Interop files", + "pattern": "*.{bin}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13282,80 +16857,108 @@ "doi": "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "target VCF input file to be imputed and or phased", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "ref": { - "type": "file", - "description": "reference panel in bref3 or VCF format", - "pattern": "*.{vcf,vcf.gz,bref3}" - } - }, - { - "genmap": { - "type": "file", - "description": "a PLINK format genetic map with cM units", - "pattern": "*.{map,map.gz,map.zip}" - } - }, - { - "exclsamples": { - "type": "file", - "description": "text file containing samples one sample per line to be excluded from the analysis", - "pattern": "*.*" - } - }, - { - "exclmarkers": { - "type": "file", - "description": "text file containing markers one marker per line to be excluded from the analysis", - "pattern": "*.*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "bgzip compressed VCF file that contains phased non missing genotypes for all non reference samples", - "pattern": "*.vcf.gz" - } - }, - { - "log": { - "type": "file", - "description": "a summary of the analysis that includes the Beagle version, the command line arguments, and compute time.", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "target VCF input file to be imputed and or phased", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "refpanel": { + "type": "file", + "description": "target reference panel" + } + } + ], + [ + { + "genmap": { + "type": "file", + "description": "a PLINK format genetic map with cM units", + "pattern": "*.{map,map.gz,map.zip}" + } + } + ], + [ + { + "exclsamples": { + "type": "file", + "description": "text file containing samples one sample per line to be excluded from the analysis", + "pattern": "*.*" + } + } + ], + [ + { + "exclmarkers": { + "type": "file", + "description": "text file containing markers one marker per line to be excluded from the analysis", + "pattern": "*.*" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "bgzip compressed VCF file that contains phased non missing genotypes for all non reference samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "a summary of the analysis that includes the Beagle version, the command line arguments, and compute time.", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13388,65 +16991,78 @@ "tool_dev_url": "https://github.com/nvnieuwk/bedgovcf", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "The BED file to convert to VCF", - "pattern": "*.bed" - } - }, - { - "config": { - "type": "file", - "description": "The config file to use for the conversion", - "pattern": "*.{yml,yaml}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "The fasta index file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The converted VCF file", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "The BED file to convert to VCF", + "pattern": "*.bed" + } + }, + { + "config": { + "type": "file", + "description": "The config file to use for the conversion", + "pattern": "*.{yml,yaml}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The fasta index file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The converted VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13476,45 +17092,55 @@ "doi": "10.1093/bioinformatics/bts277", "licence": [ "GNU v2" - ] + ], + "identifier": "biotools:bedops" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sorted BAM/GFF/GTF/GVF/PSL file", - "pattern": "*.{bam,gff,gtf,gvf,psl}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "in_file": { + "type": "file", + "description": "Input file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Sorted BED file", + "pattern": "*.{bed}" + } + } + ] }, { - "bed": { - "type": "file", - "description": "Sorted BED file", - "pattern": "*.{bed}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13547,39 +17173,57 @@ "doi": "10.1093/bioinformatics/bts277", "licence": [ "GPL v2" - ] + ], + "identifier": "biotools:bedops" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "A reference file in GTF format", - "pattern": "*.{gtf,gtf.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "A reference file in GTF format", + "pattern": "*.{gtf,gtf.gz}" + } } - } + ] ], "output": [ { - "bed": { - "type": "file", - "description": "A reference file in BED format", - "pattern": "*.{bed}" - } + "bed": [ + { + "meta": { + "type": "file", + "description": "A reference file in BED format", + "pattern": "*.{bed}" + } + }, + { + "*.bed": { + "type": "file", + "description": "A reference file in BED format", + "pattern": "*.{bed}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13608,45 +17252,56 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/complement.html", "licence": [ "MIT" - ] + ], + "identifier": "biotools:bedtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Bed file containing genomic intervals.", - "pattern": "*.{bed}" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file containing genomic intervals.", + "pattern": "*.{bed}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13694,59 +17349,72 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/closest.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_1": { - "type": "file", - "description": "The file to find the closest features of", - "pattern": "*.{bed,vcf,gff}(.gz)?" - } - }, - { - "input_2": { - "type": "list", - "description": "The input file(s) to find the closest features from", - "pattern": "*.{bed,vcf,gff}(.gz)?" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA reference. Needed when the argument `--sorted` is used", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "The resulting BED file containing the closest features", - "pattern": "*.{bed,vcf,gff}" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_1": { + "type": "file", + "description": "The file to find the closest features of", + "pattern": "*.{bed,vcf,gff}(.gz)?" + } + }, + { + "input_2": { + "type": "list", + "description": "The input file(s) to find the closest features from", + "pattern": "*.{bed,vcf,gff}(.gz)?" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA reference. Needed when the argument `--sorted` is used", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "The resulting BED file containing the closest features", + "pattern": "*.{bed,vcf,gff}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13779,52 +17447,65 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/complement.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}" - } - }, - { - "sizes": { - "type": "file", - "description": "File which defines the chromosome lengths for a given genome", - "pattern": "*.{sizes}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Bed file with all genomic intervals that are not covered by at least one record from the input file.", - "pattern": "*.{bed}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "sizes": { + "type": "file", + "description": "File which defines the chromosome lengths for a given genome", + "pattern": "*.{sizes}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file with all genomic intervals that are not covered by at least one record from the input file.", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13876,59 +17557,72 @@ "licence": [ "GPL v2", "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_A": { - "type": "file", - "description": "BAM/BED/GFF/VCF file", - "pattern": "*.{bam,bed,gff,vcf}" - } - }, - { - "input_B": { - "type": "file", - "description": "One or more BAM/BED/GFF/VCF file", - "pattern": "*.{bam,bed,gff,vcf}" - } - }, - { - "genome_file": { - "type": "file", - "description": "Optional reference genome 2 column file that defines the expected chromosome order\nin the input files for use with the -sorted option.\nWhen `genome_file` is provided, `-sorted` option is added to the command.\n", - "pattern": "*.{fai,txt,chromsizes}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "File containing coverage of sequence alignments", - "pattern": "*.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_A": { + "type": "file", + "description": "BAM/BED/GFF/VCF file", + "pattern": "*.{bam,bed,gff,vcf}" + } + }, + { + "input_B": { + "type": "file", + "description": "One or more BAM/BED/GFF/VCF file", + "pattern": "*.{bam,bed,gff,vcf}" + } + } + ], + [ + { + "genome_file": { + "type": "file", + "description": "Optional reference genome 2 column file that defines the expected chromosome order\nin the input files for use with the -sorted option.\nWhen `genome_file` is provided, `-sorted` option is added to the command.\n", + "pattern": "*.{fai,txt,chromsizes}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing coverage of sequence alignments", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -13966,63 +17660,86 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bam|bed|gff|vcf}" - } - }, - { - "scale": { - "type": "integer", - "description": "Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch" - } - }, - { - "sizes": { - "type": "file", - "description": "Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column" - } - }, - { - "extension": { - "type": "string", - "description": "Extension of the output file (e. g., \".bg\", \".bedgraph\", \".txt\", \".tab\", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genomecov": { - "type": "file", - "description": "Computed genome coverage file", - "pattern": "*.${extension}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "BAM/BED/GFF/VCF", + "pattern": "*.{bam|bed|gff|vcf}" + } + }, + { + "scale": { + "type": "integer", + "description": "Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch" + } + } + ], + [ + { + "sizes": { + "type": "file", + "description": "Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column" + } + } + ], + [ + { + "extension": { + "type": "string", + "description": "Extension of the output file (e. g., \".bg\", \".bedgraph\", \".txt\", \".tab\", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments." + } + } + ], + [ + { + "sort": { + "type": "boolean", + "description": "Sort the output" + } + } + ] + ], + "output": [ + { + "genomecov": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "Computed genome coverage file", + "pattern": "*.${extension}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14082,52 +17799,65 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Bed feature file", - "pattern": "*.{bed}" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Output fasta file with extracted sequences", - "pattern": "*.{fa}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Bed feature file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Output fasta file with extracted sequences", + "pattern": "*.{fa}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14179,51 +17909,64 @@ "doi": "10.1093/bioinformatics/btq033", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}" - } - }, - { - "summary_column": { - "type": "integer", - "description": "Column to be summarized (1-based)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "Grouped by bed file with combined features", - "pattern": "*.{bed}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "summary_col": { + "type": "string", + "description": "Column to summarize" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Grouped by bed file with combined features", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14259,65 +18002,78 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals1": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bam|bed|gff|vcf}" - } - }, - { - "intervals2": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bam|bed|gff|vcf}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference chromosome sizes\ne.g. [ id:'test' ]\n" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intersect": { - "type": "file", - "description": "File containing the description of overlaps found between the two features", - "pattern": "*.${extension}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals1": { + "type": "file", + "description": "BAM/BED/GFF/VCF", + "pattern": "*.{bam|bed|gff|vcf}" + } + }, + { + "intervals2": { + "type": "file", + "description": "BAM/BED/GFF/VCF", + "pattern": "*.{bam|bed|gff|vcf}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference chromosome sizes\ne.g. [ id:'test' ]\n" + } + }, + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt}" + } + } + ] + ], + "output": [ + { + "intersect": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "File containing the description of overlaps found between the two features", + "pattern": "*.${extension}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14379,65 +18135,78 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_a": { - "type": "file", - "description": "VCF,GFF or BED file to use with the `-a` option", - "pattern": "*.{vcf,vcf.gz,bed,bed.gz,gff}" - } - }, - { - "input_b": { - "type": "file", - "description": "VCF,GFF or BED file to use with the `-b` option", - "pattern": "*.{vcf,vcf.gz,bed,bed.gz,gff}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome file information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genome_file": { - "type": "file", - "description": "A file containing all the contigs of the genome used to create the input files", - "pattern": "*.{txt,sizes,fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file containing the results", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_a": { + "type": "file", + "description": "VCF,GFF or BED file to use with the `-a` option", + "pattern": "*.{vcf,vcf.gz,bed,bed.gz,gff}" + } + }, + { + "input_b": { + "type": "file", + "description": "VCF,GFF or BED file to use with the `-b` option", + "pattern": "*.{vcf,vcf.gz,bed,bed.gz,gff}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome file information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genome_file": { + "type": "file", + "description": "A file containing all the contigs of the genome used to create the input files", + "pattern": "*.{txt,sizes,fai}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file containing the results", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14470,45 +18239,56 @@ "doi": "10.1093/bioinformatics/btq033", "licence": [ "MIT" - ] + ], + "identifier": "biotools:bedtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "regions": { - "type": "file", - "description": "BED file OR Genome details file ()", - "pattern": "*.{bed,tab,fai}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "BED file OR Genome details file ()", + "pattern": "*.{bed,tab,fai}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file containing the windows", + "pattern": "*.bed" + } + } + ] }, { - "bed": { - "type": "file", - "description": "BED file containing the windows", - "pattern": "*.bed" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14556,65 +18336,78 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/map.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals1": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bed|gff|vcf}" - } - }, - { - "intervals2": { - "type": "file", - "description": "BAM/BED/GFF/VCF", - "pattern": "*.{bed|gff|vcf}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference chromosome sizes\ne.g. [ id:'test' ]\n" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mapped": { - "type": "file", - "description": "File containing the description of overlaps found between the features in A and the features in B, with statistics", - "pattern": "*.${extension}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals1": { + "type": "file", + "description": "BAM/BED/GFF/VCF", + "pattern": "*.{bed|gff|vcf}" + } + }, + { + "intervals2": { + "type": "file", + "description": "BAM/BED/GFF/VCF", + "pattern": "*.{bed|gff|vcf}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference chromosome sizes\ne.g. [ id:'test' ]\n" + } + }, + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt}" + } + } + ] + ], + "output": [ + { + "mapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "File containing the description of overlaps found between the features in A and the features in B, with statistics", + "pattern": "*.${extension}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14644,52 +18437,65 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Bed feature file", - "pattern": "*.{bed}" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Output masked fasta file", - "pattern": "*.{fa}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Bed feature file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Output masked fasta file", + "pattern": "*.{fa}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14732,45 +18538,56 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/merge.html", "licence": [ "MIT" - ] + ], + "identifier": "biotools:bedtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Overlapped bed file with combined features", - "pattern": "*.{bed}" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Overlapped bed file with combined features", + "pattern": "*.{bed}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14832,52 +18649,65 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/multiinter.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "beds": { - "type": "list", - "description": "List of files to be merged", - "pattern": "*.{bed,vcf,gff}" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "Common interval bed", - "pattern": "*.{bed}" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "beds": { + "type": "list", + "description": "List of files to be merged", + "pattern": "*.{bed,vcf,gff}" + } + } + ], + [ + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Common interval bed", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14911,52 +18741,71 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt,.fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Shift BED file", - "pattern": "*.{bed}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt,.fai}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Shift BED file", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -14986,45 +18835,64 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input BED file", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Slopped BED file", - "pattern": "*.{bed}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input BED file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "sizes": { + "type": "file", + "description": "Chromosome sizes file" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Slopped BED file", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15065,52 +18933,65 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/sort.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "BED/BEDGRAPH", - "pattern": "*.{bed|bedGraph}" - } - }, - { - "genome_file": { - "type": "file", - "description": "Optional reference genome 2 column file that defines the expected chromosome order.\n", - "pattern": "*.{fai,txt,chromsizes}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sorted": { - "type": "file", - "description": "Sorted output file", - "pattern": "*.${extension}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "BED/BEDGRAPH", + "pattern": "*.{bed|bedGraph}" + } + } + ], + [ + { + "genome_file": { + "type": "file", + "description": "Optional reference genome 2 column file that defines the expected chromosome order.\n", + "pattern": "*.{fai,txt,chromsizes}" + } + } + ] + ], + "output": [ + { + "sorted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "Sorted output file", + "pattern": "*.${extension}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15175,45 +19056,62 @@ "licence": [ "MIT", "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "beds": { - "type": "list", - "description": "list of split BED files", - "pattern": "*.bed" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed" + } + }, + { + "count": { + "type": "integer", + "description": "Number of lines per split file" + } + } + ] + ], + "output": [ + { + "beds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "list", + "description": "list of split BED files", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15244,52 +19142,63 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals1": { - "type": "file", - "description": "BED/GFF/VCF", - "pattern": "*.{bed|gff|vcf}" - } - }, - { - "intervals2": { - "type": "file", - "description": "BED/GFF/VCF", - "pattern": "*.{bed|gff|vcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "File containing the difference between the two sets of features", - "patters": "*.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals1": { + "type": "file", + "description": "BED/GFF/VCF", + "pattern": "*.{bed|gff|vcf}" + } + }, + { + "intervals2": { + "type": "file", + "description": "BED/GFF/VCF", + "pattern": "*.{bed|gff|vcf}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing the difference between the two sets of features", + "patters": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15327,58 +19236,71 @@ "documentation": "https://bedtools.readthedocs.io/en/latest/content/tools/slop.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedgraph": { - "type": "file", - "description": "Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative\n", - "pattern": "*.{bedGraph,bedgraph}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing meta information for the reference chromosome sizes\ne.g. [ id:'test' ]\n" - } - }, - { - "chrom_sizes": { - "type": "file", - "description": "Chromosome sizes file", - "pattern": "*{.sizes,.txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Combined BED file with values from all bedGraph files", - "pattern": "*.{bed}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bedtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative\n", + "pattern": "*.{bedGraph,bedgraph}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing meta information for the reference chromosome sizes\ne.g. [ id:'test' ]\n" + } + }, + { + "chrom_sizes": { + "type": "file", + "description": "Chromosome sizes file", + "pattern": "*{.sizes,.txt}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Combined BED file with values from all bedGraph files", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15413,45 +19335,56 @@ "tool_dev_url": "https://github.com/lh3/bioawk", "licence": [ "Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in `$args`.", + "pattern": "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" + } } - }, - { - "input": { - "type": "file", - "description": "Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in `$args`.", - "pattern": "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "Manipulated and gzipped version of input sequence file following program specified in `args`.\nFile name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you!\n", + "pattern": "*.gz" + } + } + ] }, { - "output": { - "type": "file", - "description": "Manipulated and gzipped version of input sequence file following program specified in `args`.\nFile name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you!\n", - "pattern": "*.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15489,52 +19422,73 @@ "doi": "10.1186/1751-0473-9-13", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with duplicate reads marked/removed", - "pattern": "*.{bam}" - } - }, - { - "metrics": { - "type": "file", - "description": "Duplicate metrics file generated by biobambam", - "pattern": "*.{metrics.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with duplicate reads marked/removed", + "pattern": "*.{bam}" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Duplicate metrics file generated by biobambam", + "pattern": "*.{metrics.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15566,58 +19520,89 @@ "doi": "10.1186/1751-0473-9-13", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "List containing 1 or more bam files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Merged BAM file", - "pattern": "*.bam" - } - }, - { - "bam_index": { - "type": "file", - "description": "BAM index file", - "pattern": "*" - } - }, - { - "checksum": { - "type": "file", - "description": "Checksum file", - "pattern": "*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List containing 1 or more bam files" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Merged BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "bam_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*" + } + } + ] + }, + { + "checksum": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.md5": { + "type": "file", + "description": "Checksum file", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15650,78 +19635,121 @@ "doi": "10.1186/1751-0473-9-13", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "List containing 1 or more bam files" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format (optional)", - "pattern": "*.{fa,fasta,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with duplicate reads marked/removed", - "pattern": "*.bam" - } - }, - { - "bam_index": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "cram": { - "type": "file", - "description": "CRAM file with duplicate reads marked/removed", - "pattern": "*.cram" - } - }, - { - "metrics": { - "type": "file", - "description": "Duplicate metrics file generated by biobambam", - "pattern": "*.{metrics.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "List containing 1 or more bam files" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format (optional)", + "pattern": "*.{fa,fasta,fna}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with duplicate reads marked/removed", + "pattern": "*.bam" + } + } + ] + }, + { + "bam_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "CRAM file with duplicate reads marked/removed", + "pattern": "*.cram" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Duplicate metrics file generated by biobambam", + "pattern": "*.{metrics.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15754,66 +19782,99 @@ "doi": "10.1101/2020.01.10.902056", "licence": [ "Apache-2.0 license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "FASTA or FASTQ", - "pattern": "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}" - } - }, - { - "scheme_metadata": { - "type": "file", - "description": "Scheme subtype metadata table", - "pattern": "*.{tab,tsv,txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "summary": { - "type": "file", - "description": "Tab-delimited subtyping summary output", - "pattern": "*summary.txt" - } - }, - { - "kmer_results": { - "type": "file", - "description": "Tab-delimited subtyping kmer matching output", - "pattern": "*kmer-results.txt" - } - }, - { - "simple_summary": { - "type": "file", - "description": "A simple version of summary output", - "pattern": "*simple-summary.txt" - } + ], + "identifier": "biotools:biohansel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "FASTA or FASTQ", + "pattern": "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}" + } + } + ], + [ + { + "scheme_metadata": { + "type": "file", + "description": "Scheme subtype metadata table", + "pattern": "*.{tab,tsv,txt}" + } + } + ] + ], + "output": [ + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-summary.txt": { + "type": "file", + "description": "Tab-delimited subtyping summary output", + "pattern": "*summary.txt" + } + } + ] + }, + { + "kmer_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-kmer-results.txt": { + "type": "file", + "description": "Tab-delimited subtyping kmer matching output", + "pattern": "*kmer-results.txt" + } + } + ] + }, + { + "simple_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-simple-summary.txt": { + "type": "file", + "description": "A simple version of summary output", + "pattern": "*simple-summary.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15849,58 +19910,81 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input fastq files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "index": { - "type": "directory", - "description": "Biscuit genome index directory (generated with 'biscuit index')", - "pattern": "BiscuitIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Output BAM index", - "pattern": "*.{bai}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fastq files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Biscuit genome index directory (generated with 'biscuit index')", + "pattern": "BiscuitIndex" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "Output BAM index", + "pattern": "*.{bai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -15936,7 +20020,8 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] + ], + "identifier": "biotools:biscuit" } }, { @@ -15947,7 +20032,8 @@ "doi": "10.1093/bioinformatics/btu314", "licence": [ "MIT" - ] + ], + "identifier": "biotools:biscuit" } }, { @@ -15958,58 +20044,81 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input fastq files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "index": { - "type": "directory", - "description": "Biscuit genome index directory (generated with 'biscuit index')", - "pattern": "BiscuitIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Output BAM index", - "pattern": "*.{bai}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fastq files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Biscuit genome index directory (generated with 'biscuit index')", + "pattern": "BiscuitIndex" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "Output BAM index", + "pattern": "*.{bai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16046,57 +20155,70 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file contained mapped reads" - } - }, - { - "bai": { - "type": "file", - "description": "BAM file index" - } - }, - { - "index": { - "type": "directory", - "description": "Biscuit genome index directory (generated with 'biscuit index')", - "pattern": "BiscuitIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bsconv_bam": { - "type": "file", - "description": "Output BAM file containing filtered read alignments", - "pattern": "*.{bam}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file contained mapped reads" + } + }, + { + "bai": { + "type": "file", + "description": "BAM file index" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Biscuit genome index directory (generated with 'biscuit index')", + "pattern": "BiscuitIndex" + } + } + ] + ], + "output": [ + { + "bsconv_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing filtered read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16132,63 +20254,76 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Biscuit BAM file" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index" - } - }, - { - "snp_bed": { - "type": "file", - "description": "BED file containing SNP information (optional)" - } - }, - { - "index": { - "type": "directory", - "description": "Biscuit genome index directory (generated with 'biscuit index')", - "pattern": "BiscuitIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "epiread_bed": { - "type": "file", - "description": "Gzipped BED file with methylation (and optionally SNV) information", - "pattern": "*.{epiread.bed.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Biscuit BAM file" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index" + } + }, + { + "snp_bed": { + "type": "file", + "description": "BED file containing SNP information (optional)" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Biscuit genome index directory (generated with 'biscuit index')", + "pattern": "BiscuitIndex" + } + } + ] + ], + "output": [ + { + "epiread_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Gzipped BED file with methylation (and optionally SNV) information", + "pattern": "*.{epiread.bed.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16225,32 +20360,43 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] + ], + "identifier": "biotools:biscuit" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "index": { - "type": "directory", - "description": "Biscuit genome index directory", - "pattern": "BiscuitIndex" - } + "index": [ + { + "BiscuitIndex/*.fa*": { + "type": "directory", + "description": "Biscuit genome index directory", + "pattern": "BiscuitIndex" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16286,51 +20432,64 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Biscuit BED file (output of biscuit vcf2bed)\n" - } - }, - { - "index": { - "type": "directory", - "description": "Biscuit genome index directory (generated with 'biscuit index')", - "pattern": "BiscuitIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mergecg_bed": { - "type": "file", - "description": "Gzipped BED file with merged methylation information", - "pattern": "*.bed.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Biscuit BED file (output of biscuit vcf2bed)\n" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Biscuit genome index directory (generated with 'biscuit index')", + "pattern": "BiscuitIndex" + } + } + ] + ], + "output": [ + { + "mergecg_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Gzipped BED file with merged methylation information", + "pattern": "*.bed.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16367,77 +20526,90 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normal_bams": { + "type": "file", + "description": "BAM files to be analyzed. If no tumor_bam file is provided, any number of \"normal\" BAMs may be provided\n(\"normal\" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a\ntumor BAM file is provided, exactly one normal (germline) BAM must be provided.\n", + "pattern": "*.{bam}" + } + }, + { + "normal_bais": { + "type": "file", + "description": "BAM index file or files corresponding to the provided normal_bams", + "pattern": "*.{bai}" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "Optional. If a tumor BAM file is provided, pileup will run in \"somatic\" mode and will annotate variants with\ntheir somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a\ntumor BAM file is provided, exactly one normal BAM must be provided.\n", + "pattern": "*.{bam}" + } + }, + { + "tumor_bai": { + "type": "file", + "description": "Optional. BAM index file corresponding to provided tumor_bam", + "pattern": "*.{bai}" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Biscuit genome index directory (generated with 'biscuit index')", + "pattern": "BiscuitIndex" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "vcf file with methylation information", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal_bams": { - "type": "file", - "description": "BAM files to be analyzed. If no tumor_bam file is provided, any number of \"normal\" BAMs may be provided\n(\"normal\" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a\ntumor BAM file is provided, exactly one normal (germline) BAM must be provided.\n", - "pattern": "*.{bam}" - } - }, - { - "normal_bais": { - "type": "file", - "description": "BAM index file or files corresponding to the provided normal_bams", - "pattern": "*.{bai}" - } - }, - { - "tumor_bam": { - "type": "file", - "description": "Optional. If a tumor BAM file is provided, pileup will run in \"somatic\" mode and will annotate variants with\ntheir somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a\ntumor BAM file is provided, exactly one normal BAM must be provided.\n", - "pattern": "*.{bam}" - } - }, - { - "tumor_bai": { - "type": "file", - "description": "Optional. BAM index file corresponding to provided tumor_bam", - "pattern": "*.{bai}" - } - }, - { - "index": { - "type": "directory", - "description": "Biscuit genome index directory (generated with 'biscuit index')", - "pattern": "BiscuitIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file with methylation information", - "pattern": "*.{vcf.gz}" - } - } - ], - "authors": [ - "@njspix" + "authors": [ + "@njspix" ], "maintainers": [ "@njspix" @@ -16470,38 +20642,64 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file produced using Biscuit" - } - } - ], - "output": [ - { - "biscuit_qc_reports": { - "type": "file", - "description": "Summary files containing the following information:\n - CpG retention by position in read\n - CpH retention by position in read\n - Read duplication statistics\n - Insert size distribution\n - Distribution of mapping qualities\n - Proportion of reads mapping to each strand\n - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT\n", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:biscuit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file produced using Biscuit" + } + } + ], + [ + { + "index": { + "type": "file", + "description": "index file" + } + } + ] + ], + "output": [ + { + "biscuit_qc_reports": [ + { + "meta": { + "type": "file", + "description": "Summary files containing the following information:\n - CpG retention by position in read\n - CpH retention by position in read\n - Read duplication statistics\n - Insert size distribution\n - Distribution of mapping qualities\n - Proportion of reads mapping to each strand\n - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT\n", + "pattern": "*.txt" + } + }, + { + "*.txt": { + "type": "file", + "description": "Summary files containing the following information:\n - CpG retention by position in read\n - CpH retention by position in read\n - Read duplication statistics\n - Insert size distribution\n - Distribution of mapping qualities\n - Proportion of reads mapping to each strand\n - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT\n", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16537,44 +20735,55 @@ "tool_dev_url": "https://github.com/huishenlab/biscuit", "licence": [ "MIT" - ] + ], + "identifier": "biotools:biscuit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Biscuit vcf file (output of biscuit pileup)" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Biscuit vcf file (output of biscuit pileup)" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Gzipped BED file with methylation or SNV information", - "pattern": "*.{bed.gz}" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Gzipped BED file with methylation or SNV information", + "pattern": "*.{bed.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16612,65 +20821,98 @@ "doi": "10.1093/bioinformatics/btr167", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "index": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "unmapped": { - "type": "file", - "description": "Output FastQ file(s) containing unmapped reads", - "pattern": "*.{fq.gz}" - } - }, - { - "report": { - "type": "file", - "description": "Bismark alignment reports", - "pattern": "*{report.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bismark" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Bismark genome index directory", + "pattern": "BismarkIndex" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "Bismark alignment reports", + "pattern": "*{report.txt}" + } + } + ] + }, + { + "unmapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fq.gz": { + "type": "file", + "description": "Output FastQ file(s) containing unmapped reads", + "pattern": "*.{fq.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16715,65 +20957,98 @@ "doi": "10.1093/bioinformatics/btr167", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_file": { - "type": "file", - "description": "A file containing methylation calls per position, in the format produced by bismark_methylation_extractor.\n" - } - }, - { - "index": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage": { - "type": "file", - "description": "A file containing methylation calls per position.", - "pattern": "*.cov.gz" - } - }, - { - "report": { - "type": "file", - "description": "Genomic cytosine context results.", - "pattern": "*report.txt.gz" - } - }, - { - "summary": { - "type": "file", - "description": "Cyotosine context summary report.", - "pattern": "*cytosine_context_summary.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bismark" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage_file": { + "type": "file", + "description": "A file containing methylation calls per position, in the format produced by bismark_methylation_extractor.\n" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Bismark genome index directory", + "pattern": "BismarkIndex" + } + } + ] + ], + "output": [ + { + "coverage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cov.gz": { + "type": "file", + "description": "A file containing methylation calls per position.", + "pattern": "*.cov.gz" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt.gz": { + "type": "file", + "description": "Genomic cytosine context results.", + "pattern": "*report.txt.gz" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cytosine_context_summary.txt": { + "type": "file", + "description": "Cyotosine context summary report.", + "pattern": "*cytosine_context_summary.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16817,52 +21092,73 @@ "doi": "10.1093/bioinformatics/btr167", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing read alignments", - "pattern": "*.{bam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Deduplicated output BAM file containing read alignments", - "pattern": "*.{deduplicated.bam}" - } - }, - { - "report": { - "type": "file", - "description": "Bismark deduplication reports", - "pattern": "*.{deduplication_report.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bismark" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.deduplicated.bam": { + "type": "file", + "description": "Deduplicated output BAM file containing read alignments", + "pattern": "*.{deduplicated.bam}" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.deduplication_report.txt": { + "type": "file", + "description": "Bismark deduplication reports", + "pattern": "*.{deduplication_report.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16906,32 +21202,43 @@ "doi": "10.1093/bioinformatics/btr167", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:bismark" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "index": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } + "index": [ + { + "BismarkIndex": { + "type": "directory", + "description": "Bismark genome index directory", + "pattern": "BismarkIndex" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -16976,80 +21283,133 @@ "doi": "10.1093/bioinformatics/btr167", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "index": { - "type": "directory", - "description": "Bismark genome index directory", - "pattern": "BismarkIndex" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedgraph": { - "type": "file", - "description": "Bismark output file containing coverage and methylation metrics", - "pattern": "*.{bedGraph.gz}" - } - }, - { - "methylation_calls": { - "type": "file", - "description": "Bismark output file containing strand-specific methylation calls", - "pattern": "*.{txt.gz}" - } - }, - { - "coverage": { - "type": "file", - "description": "Bismark output file containing coverage metrics", - "pattern": "*.{cov.gz}" - } - }, - { - "report": { - "type": "file", - "description": "Bismark splitting reports", - "pattern": "*_{splitting_report.txt}" - } - }, - { - "mbias": { - "type": "file", - "description": "Text file containing methylation bias information", - "pattern": "*.{M-bias.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bismark" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Bismark genome index directory", + "pattern": "BismarkIndex" + } + } + ] + ], + "output": [ + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedGraph.gz": { + "type": "file", + "description": "Bismark output file containing coverage and methylation metrics", + "pattern": "*.{bedGraph.gz}" + } + } + ] + }, + { + "methylation_calls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Bismark output file containing strand-specific methylation calls", + "pattern": "*.{txt.gz}" + } + } + ] + }, + { + "coverage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cov.gz": { + "type": "file", + "description": "Bismark output file containing coverage metrics", + "pattern": "*.{cov.gz}" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_splitting_report.txt": { + "type": "file", + "description": "Bismark splitting reports", + "pattern": "*_{splitting_report.txt}" + } + } + ] + }, + { + "mbias": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.M-bias.txt": { + "type": "file", + "description": "Text file containing methylation bias information", + "pattern": "*.{M-bias.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17092,66 +21452,77 @@ "doi": "10.1093/bioinformatics/btr167", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "align_report": { - "type": "file", - "description": "Bismark alignment reports", - "pattern": "*{report.txt}" - } - }, - { - "splitting_report": { - "type": "file", - "description": "Bismark splitting reports", - "pattern": "*{splitting_report.txt}" - } - }, - { - "dedup_report": { - "type": "file", - "description": "Bismark deduplication reports", - "pattern": "*.{deduplication_report.txt}" - } - }, - { - "mbias": { - "type": "file", - "description": "Text file containing methylation bias information", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Bismark reports", - "pattern": "*.{html,txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bismark" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "align_report": { + "type": "file", + "description": "Bismark alignment reports", + "pattern": "*{report.txt}" + } + }, + { + "dedup_report": { + "type": "file", + "description": "Bismark deduplication reports", + "pattern": "*.{deduplication_report.txt}" + } + }, + { + "splitting_report": { + "type": "file", + "description": "Bismark splitting reports", + "pattern": "*{splitting_report.txt}" + } + }, + { + "mbias": { + "type": "file", + "description": "Text file containing methylation bias information", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.{html,txt}": { + "type": "file", + "description": "Bismark reports", + "pattern": "*.{html,txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17195,61 +21566,80 @@ "doi": "10.1093/bioinformatics/btr167", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "bam": { - "type": "list", - "description": "List of Bismark alignment BAM filenames", - "pattern": "*.bam" - } - }, - { - "align_report": { - "type": "file", - "description": "Bismark alignment reports", - "pattern": "*report.txt" - } - }, - { - "dedup_report": { - "type": "file", - "description": "Bismark deduplication reports", - "pattern": "*.deduplication_report.txt" - } - }, - { - "splitting_report": { - "type": "file", - "description": "Bismark splitting reports", - "pattern": "*splitting_report.txt" - } - }, - { - "mbias": { - "type": "file", - "description": "Text file containing methylation bias information", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "summary": { - "type": "file", - "description": "Bismark summary", - "pattern": "*.{html,txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bismark" + } + } + ], + "input": [ + [ + { + "bam": { + "type": "list", + "description": "List of Bismark alignment BAM filenames", + "pattern": "*.bam" + } + } + ], + [ + { + "align_report": { + "type": "file", + "description": "Bismark alignment reports", + "pattern": "*report.txt" + } + } + ], + [ + { + "dedup_report": { + "type": "file", + "description": "Bismark deduplication reports", + "pattern": "*.deduplication_report.txt" + } + } + ], + [ + { + "splitting_report": { + "type": "file", + "description": "Bismark splitting reports", + "pattern": "*splitting_report.txt" + } + } + ], + [ + { + "mbias": { + "type": "file", + "description": "Text file containing methylation bias information", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "summary": [ + { + "*report.{html": { + "type": "file", + "description": "Bismark summary", + "pattern": "*.{html,txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17289,70 +21679,93 @@ "doi": "10.1016/S0022-2836(05)80360-2", "licence": [ "US-Government-Work" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "entry": { - "type": "string", - "description": "Entry identifier of sequence in database. It cannot be used along with entry_batch" - } - }, - { - "entry_batch": { - "type": "file", - "description": "File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "file", - "description": "Input BLAST-indexed database", - "pattern": "*.{fa.*,fasta.*}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Output fasta file (default format)", - "pattern": "*.{fasta}" - } - }, - { - "text": { - "type": "file", - "description": "Output text file (generic format if fasta not used, i.e. `--outfmt` is supplied to `ext.args`)\n", - "pattern": "*.{txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "entry": { + "type": "string", + "description": "Entry identifier of sequence in database. It cannot be used along with entry_batch" + } + }, + { + "entry_batch": { + "type": "file", + "description": "File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "file", + "description": "Input BLAST-indexed database", + "pattern": "*.{fa.*,fasta.*}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Output fasta file (default format)", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "text": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output text file (generic format if fasta not used, i.e. `--outfmt` is supplied to `ext.args`)\n", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17385,58 +21798,71 @@ "doi": "10.1016/S0022-2836(05)80360-2", "licence": [ "US-Government-Work" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing queries sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the blast database", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "txt": { - "type": "file", - "description": "File containing blastn hits", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing queries sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the blast database", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing blastn hits", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17486,102 +21912,137 @@ "doi": "10.1016/S0022-2836(05)80360-2", "licence": [ "US-Government-Work" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing queries sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the blast database", + "pattern": "*" + } + } + ], + [ + { + "out_ext": { + "type": "string", + "description": "Specify the type of output file to be generated. `xml` corresponds to BLAST xml format.\n`tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format.\n", + "pattern": "xml|tsv|csv" + } + } + ] + ], + "output": [ + { + "xml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "File containing blastp hits in XML format", + "pattern": "*.{xml}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "File containing blastp hits in tabular format", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "File containing blastp hits in comma separated format", + "pattern": "*.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing queries sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the blast database", - "pattern": "*" - } - }, - { - "out_ext": { - "type": "string", - "description": "Specify the type of output file to be generated. `xml` corresponds to BLAST xml format.\n`tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format.\n", - "pattern": "xml|tsv|csv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "xml": { - "type": "file", - "description": "File containing blastp hits in XML format", - "pattern": "*.{xml}" - } - }, - { - "tsv": { - "type": "file", - "description": "File containing blastp hits in tabular format", - "pattern": "*.{tsv}" - } - }, - { - "csv": { - "type": "file", - "description": "File containing blastp hits in comma separated format", - "pattern": "*.csv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas" - ] - } - }, - { - "name": "blast_makeblastdb", - "path": "modules/nf-core/blast/makeblastdb/meta.yml", - "type": "module", - "meta": { - "name": "blast_makeblastdb", - "description": "Builds a BLAST database", - "keywords": [ - "fasta", - "blast", - "database" - ], - "tools": [ + "authors": [ + "@vagkaratzas" + ], + "maintainers": [ + "@vagkaratzas" + ] + } + }, + { + "name": "blast_makeblastdb", + "path": "modules/nf-core/blast/makeblastdb/meta.yml", + "type": "module", + "meta": { + "name": "blast_makeblastdb", + "description": "Builds a BLAST database", + "keywords": [ + "fasta", + "blast", + "database" + ], + "tools": [ { "blast": { "description": "BLAST finds regions of similarity between biological sequences.\n", @@ -17590,45 +22051,56 @@ "doi": "10.1016/S0022-2836(05)80360-2", "licence": [ "US-Government-Work" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Output directory containing blast database files", - "pattern": "*" - } + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}": { + "type": "directory", + "description": "Output directory containing blast database files", + "pattern": "*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17678,58 +22150,71 @@ "doi": "10.1016/S0022-2836(05)80360-2", "licence": [ "US-Government-Work" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing queries sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the blast database", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "txt": { - "type": "file", - "description": "File containing blastn hits", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing queries sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the blast database", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing blastn hits", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17765,44 +22250,55 @@ "doi": "10.1016/S0022-2836(05)80360-2", "licence": [ "US-Government-Work" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" - } - }, - { - "name": { - "type": "string", - "description": "Name of the NCBI BLAST database to be downloaded" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" + } + }, + { + "name": { + "type": "string", + "description": "Name of the NCBI BLAST database to be downloaded" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" - } - }, - { - "db": { - "type": "directory", - "description": "Output directory containing blast database files", - "pattern": "*" - } + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'mito', single_end:false ]\n" + } + }, + { + "prefix": { + "type": "directory", + "description": "Output directory containing blast database files", + "pattern": "*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17834,58 +22330,71 @@ "doi": "10.1101/gr.229202", "licence": [ "Free for academic, nonprofit and personal use" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "query": { - "type": "file", - "description": "Sequence file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing subject information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "subject": { - "type": "file", - "description": "Sequence file", - "pattern": "*.{fa,nib,2bit}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "psl": { - "type": "file", - "description": "Search results", - "pattern": "*.{psl}" - } + ], + "identifier": "biotools:blat" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "query": { + "type": "file", + "description": "Sequence file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing subject information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "subject": { + "type": "file", + "description": "Sequence file", + "pattern": "*.{fa,nib,2bit}" + } + } + ] + ], + "output": [ + { + "psl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.psl": { + "type": "file", + "description": "Search results", + "pattern": "*.{psl}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -17920,119 +22429,211 @@ "doi": "10.1038/nmeth.1923", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Bowtie2 genome index files", - "pattern": "*.ebwt" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Bowtie2 genome fasta file", - "pattern": "*.fasta" - } - }, - { - "save_unaligned": { - "type": "boolean", - "description": "Save reads that do not map to the reference (true) or discard them (false)\n(default: false)\n" - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - } - ], - "output": [ - { - "sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.sam" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.bam" - } - }, - { - "cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.cram" - } - }, - { - "csi": { - "type": "file", - "description": "Output SAM/BAM index for large inputs", - "pattern": "*.csi" - } - }, - { - "crai": { - "type": "file", - "description": "Output CRAM index", - "pattern": "*.crai" - } - }, - { - "log": { - "type": "file", - "description": "Aligment log", - "pattern": "*.log" - } - }, - { - "fastq": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Bowtie2 genome index files", + "pattern": "*.ebwt" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Bowtie2 genome fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "save_unaligned": { + "type": "boolean", + "description": "Save reads that do not map to the reference (true) or discard them (false)\n(default: false)\n" + } + } + ], + [ + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ] + ], + "output": [ + { + "sam": [ + { + "meta": { + "type": "file", + "description": "Output SAM file containing read alignments", + "pattern": "*.sam" + } + }, + { + "*.sam": { + "type": "file", + "description": "Output SAM file containing read alignments", + "pattern": "*.sam" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.bam" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.bam" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.cram" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.cram" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "file", + "description": "Output SAM/BAM index for large inputs", + "pattern": "*.csi" + } + }, + { + "*.csi": { + "type": "file", + "description": "Output SAM/BAM index for large inputs", + "pattern": "*.csi" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "file", + "description": "Output CRAM index", + "pattern": "*.crai" + } + }, + { + "*.crai": { + "type": "file", + "description": "Output CRAM index", + "pattern": "*.crai" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Aligment log", + "pattern": "*.log" + } + }, + { + "*.log": { + "type": "file", + "description": "Aligment log", + "pattern": "*.log" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -18122,44 +22723,55 @@ "doi": "10.1038/nmeth.1923", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Bowtie2 genome index files", - "pattern": "*.bt2" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bowtie2": { + "type": "file", + "description": "Bowtie2 genome index files", + "pattern": "*.bt2" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -18250,71 +22862,115 @@ "arxiv": "arXiv:1303.3997", "licence": [ "Artistic-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'sarscov2' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Bowtie genome index files", - "pattern": "*.ebwt" - } - }, - { - "save_unaligned": { - "type": "boolean", - "description": "Whether to save fastq files containing the reads which did not align." - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "fastq": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log file", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:bowtie" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'sarscov2' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Bowtie genome index files", + "pattern": "*.ebwt" + } + } + ], + [ + { + "save_unaligned": { + "type": "boolean", + "description": "Whether to save fastq files containing the reads which did not align." + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log file", + "pattern": "*.log" + } + }, + { + "*.out": { + "type": "file", + "description": "Log file", + "pattern": "*.log" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -18357,44 +23013,55 @@ "arxiv": "arXiv:1303.3997", "licence": [ "Artistic-2.0" - ] + ], + "identifier": "biotools:bowtie" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the genome fasta\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information about the genome fasta\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing nformation about the genome fasta\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Folder containing bowtie genome index files", - "pattern": "*.ebwt" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing nformation about the genome fasta\ne.g. [ id:'test' ]\n" + } + }, + { + "bowtie": { + "type": "file", + "description": "Folder containing bowtie genome index files", + "pattern": "*.ebwt" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -18440,59 +23107,84 @@ "doi": "10.7717/peerj-cs.104", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "kraken_report": { - "type": "file", - "description": "TSV file with six columns coming from kraken2 output", - "pattern": "*.{tsv}" - } - }, - { - "database": { - "type": "file", - "description": "Directory containing the kraken2/Bracken files for analysis", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reports": { - "type": "file", - "description": "TSV output report of the re-estimated abundances", - "pattern": "*.{tsv}" - } - }, - { - "txt": { - "type": "file", - "description": "TXT file of bracken corrected results of Kraken2 report output", - "pattern": "*.txt" - } + ], + "identifier": "biotools:bracken" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kraken_report": { + "type": "file", + "description": "TSV file with six columns coming from kraken2 output", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "database": { + "type": "file", + "description": "Directory containing the kraken2/Bracken files for analysis", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "reports": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{tsv}" + } + }, + { + "bracken_report": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.txt" + } + }, + { + "bracken_kraken_style_report": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -18532,49 +23224,76 @@ "doi": "10.7717/peerj-cs.104 ", "licence": [ "GPL v3" - ] - } + ], + "identifier": "biotools:bracken" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "kraken2db": { + "type": "directory", + "description": "A Kraken2 database directory", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "kraken2db , includeInputs: true": { + "type": "directory", + "description": "A Kraken2 database directory with required bracken files in side", + "pattern": "*/" + } + } + ] + }, + { + "bracken_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${kraken2db}/database*\", includeInputs: true": { + "type": "directory", + "description": "Bracken files required to extend the Kraken2 database" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "kraken2db": { - "type": "directory", - "description": "A Kraken2 database directory", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "db": { - "type": "directory", - "description": "A Kraken2 database directory with required bracken files in side", - "pattern": "*/" - } - } - ], - "authors": [ - "@jfy133" + "authors": [ + "@jfy133" ], "maintainers": [ "@jfy133" @@ -18610,45 +23329,56 @@ "doi": "10.7717/peerj-cs.104", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:bracken" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "List of output files from bracken", - "pattern": "*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "List of output files from bracken", + "pattern": "*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Combined output in table format", + "pattern": "*.txt" + } + } + ] }, { - "txt": { - "type": "file", - "description": "Combined output in table format", - "pattern": "*.txt" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -19802,6 +24532,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -19831,126 +24569,225 @@ "doi": "10.1007/978-1-4939-9173-0_14", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Nucleic or amino acid sequence file in FASTA format.", - "pattern": "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" - } - }, - { - "mode": { - "type": "string", - "description": "The mode to run Busco in. One of genome, proteins, or transcriptome", - "pattern": "{genome,proteins,transcriptome}" - } - }, - { - "lineage": { - "type": "string", - "description": "The BUSCO lineage to use, or \"auto\" to automatically select lineage" - } - }, - { - "busco_lineages_path": { - "type": "directory", - "description": "Path to local BUSCO lineages directory." - } - }, - { - "config_file": { - "type": "file", - "description": "Path to BUSCO config file." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "batch_summary": { - "type": "file", - "description": "Summary of all sequence files analyzed", - "pattern": "*-busco.batch_summary.txt" - } - }, - { - "short_summaries_txt": { - "type": "file", - "description": "Short Busco summary in plain text format", - "pattern": "short_summary.*.txt" - } - }, - { - "short_summaries_json": { - "type": "file", - "description": "Short Busco summary in JSON format", - "pattern": "short_summary.*.json" - } - }, - { - "busco_dir": { - "type": "directory", - "description": "BUSCO lineage specific output", - "pattern": "*-busco" - } - }, - { - "full_table": { - "type": "file", - "description": "Full BUSCO results table", - "pattern": "full_table.tsv" - } - }, - { - "missing_busco_list": { - "type": "file", - "description": "List of missing BUSCOs", - "pattern": "missing_busco_list.tsv" - } - }, - { - "single_copy_proteins": { - "type": "file", - "description": "Fasta file of single copy proteins (transcriptome mode)", - "pattern": "single_copy_proteins.faa" - } - }, - { - "seq_dir": { - "type": "directory", - "description": "BUSCO sequence directory", - "pattern": "busco_sequences" - } - }, - { - "translated_dir": { - "type": "directory", - "description": "Six frame translations of each transcript made by the transcriptome mode", - "pattern": "translated_dir" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:busco" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleic or amino acid sequence file in FASTA format.", + "pattern": "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" + } + } + ], + [ + { + "mode": { + "type": "string", + "description": "The mode to run Busco in. One of genome, proteins, or transcriptome", + "pattern": "{genome,proteins,transcriptome}" + } + } + ], + [ + { + "lineage": { + "type": "string", + "description": "The BUSCO lineage to use, or \"auto\" to automatically select lineage" + } + } + ], + [ + { + "busco_lineages_path": { + "type": "directory", + "description": "Path to local BUSCO lineages directory." + } + } + ], + [ + { + "config_file": { + "type": "file", + "description": "Path to BUSCO config file." + } + } + ] + ], + "output": [ + { + "batch_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-busco.batch_summary.txt": { + "type": "file", + "description": "Summary of all sequence files analyzed", + "pattern": "*-busco.batch_summary.txt" + } + } + ] + }, + { + "short_summaries_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "short_summary.*.txt": { + "type": "file", + "description": "Short Busco summary in plain text format", + "pattern": "short_summary.*.txt" + } + } + ] + }, + { + "short_summaries_json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "short_summary.*.json": { + "type": "file", + "description": "Short Busco summary in JSON format", + "pattern": "short_summary.*.json" + } + } + ] + }, + { + "full_table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-busco/*/run_*/full_table.tsv": { + "type": "file", + "description": "Full BUSCO results table", + "pattern": "full_table.tsv" + } + } + ] + }, + { + "missing_busco_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-busco/*/run_*/missing_busco_list.tsv": { + "type": "file", + "description": "List of missing BUSCOs", + "pattern": "missing_busco_list.tsv" + } + } + ] + }, + { + "single_copy_proteins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-busco/*/run_*/single_copy_proteins.faa": { + "type": "file", + "description": "Fasta file of single copy proteins (transcriptome mode)", + "pattern": "single_copy_proteins.faa" + } + } + ] + }, + { + "seq_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-busco/*/run_*/busco_sequences": { + "type": "directory", + "description": "BUSCO sequence directory", + "pattern": "busco_sequences" + } + } + ] + }, + { + "translated_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-busco/*/translated_proteins": { + "type": "directory", + "description": "Six frame translations of each transcript made by the transcriptome mode", + "pattern": "translated_dir" + } + } + ] + }, + { + "busco_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-busco": { + "type": "directory", + "description": "BUSCO lineage specific output", + "pattern": "*-busco" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20002,33 +24839,44 @@ "doi": "10.1007/978-1-4939-9173-0_14", "licence": [ "MIT" - ] + ], + "identifier": "biotools:busco" } } ], "input": [ - { - "short_summary_txt": { - "type": "file", - "description": "One or more short summary txt files from BUSCO", - "pattern": "short_summary.*.txt" + [ + { + "short_summary_txt": { + "type": "file", + "description": "One or more short summary txt files from BUSCO", + "pattern": "short_summary.*.txt" + } } - } + ] ], "output": [ { - "png": { - "type": "file", - "description": "A summary plot in png format", - "pattern": "*.png" - } + "png": [ + { + "*.png": { + "type": "file", + "description": "A summary plot in png format", + "pattern": "*.png" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20065,57 +24913,70 @@ "doi": "10.1093/bioinformatics/btp324", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sai": { - "type": "file", - "description": "Single or paired SA coordinate files", - "pattern": "*.sai" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + } + } + ] + ], + "output": [ + { + "sai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sai": { + "type": "file", + "description": "Single or paired SA coordinate files", + "pattern": "*.sai" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20159,44 +25020,55 @@ "arxiv": "arXiv:1303.3997", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "*.{amb,ann,bwt,pac,sa}" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bwa": { + "type": "file", + "description": "BWA genome index files", + "pattern": "*.{amb,ann,bwt,pac,sa}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20313,86 +25185,149 @@ "arxiv": "arXiv:1303.3997", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fasta,fa}" - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.{cram}" - } - }, - { - "csi": { - "type": "file", - "description": "Optional index file for BAM file", - "pattern": "*.{csi}" - } - }, - { - "crai": { - "type": "file", - "description": "Optional index file for CRAM file", - "pattern": "*.{crai}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "file", + "description": "Optional index file for BAM file", + "pattern": "*.{csi}" + } + }, + { + "*.csi": { + "type": "file", + "description": "Optional index file for BAM file", + "pattern": "*.{csi}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "file", + "description": "Optional index file for CRAM file", + "pattern": "*.{crai}" + } + }, + { + "*.crai": { + "type": "file", + "description": "Optional index file for CRAM file", + "pattern": "*.{crai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20488,65 +25423,78 @@ "doi": "10.1093/bioinformatics/btp324", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ files specified alongside meta in input channel.", - "pattern": "*.{fastq,fq}.gz" - } - }, - { - "sai": { - "type": "file", - "description": "SAI file specified alongside meta and reads in input channel.", - "pattern": "*.sai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", - "pattern": "bwa/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ files specified alongside meta in input channel.", + "pattern": "*.{fastq,fq}.gz" + } + }, + { + "sai": { + "type": "file", + "description": "SAI file specified alongside meta and reads in input channel.", + "pattern": "*.sai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", + "pattern": "bwa/" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20594,65 +25542,78 @@ "doi": "10.1093/bioinformatics/btp324", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ files specified alongside meta in input channel.", - "pattern": "*.{fastq,fq}.gz" - } - }, - { - "sai": { - "type": "file", - "description": "SAI file specified alongside meta and reads in input channel.", - "pattern": "*.sai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", - "pattern": "bwa/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ files specified alongside meta in input channel.", + "pattern": "*.{fastq,fq}.gz" + } + }, + { + "sai": { + "type": "file", + "description": "SAI file specified alongside meta and reads in input channel.", + "pattern": "*.sai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX", + "pattern": "bwa/" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20694,44 +25655,55 @@ "documentation": "https://github.com/bwa-mem2/bwa-mem2#usage", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "*.{0123,amb,ann,bwt.2bit.64,pac}" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bwamem2": { + "type": "file", + "description": "BWA genome index files", + "pattern": "*.{0123,amb,ann,bwt.2bit.64,pac}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20801,105 +25773,162 @@ "arxiv": "arXiv:1303.3997", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.{sam}" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.{cram}" - } - }, - { - "crai": { - "type": "file", - "description": "Index file for CRAM file", - "pattern": "*.{crai}" - } - }, - { - "csi": { - "type": "file", - "description": "Index file for BAM file", - "pattern": "*.{csi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ] + ], + "output": [ + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "Output SAM file containing read alignments", + "pattern": "*.{sam}" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "Index file for CRAM file", + "pattern": "*.{crai}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Index file for BAM file", + "pattern": "*.{csi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -20964,44 +25993,55 @@ "doi": "10.1093/bioinformatics/btac137", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bwameme": { + "type": "file", + "description": "BWA-MEME genome index files", + "pattern": "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" + } + } + ] }, { - "index": { - "type": "file", - "description": "BWA-MEME genome index files", - "pattern": "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -21046,117 +26086,178 @@ "doi": "10.1093/bioinformatics/btac137", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - }, - { - "mbuffer": { - "type": "integer", - "description": "memory for mbuffer in megabytes (default 3072)" - } - }, - { - "sort_threads": { - "type": "integer", - "description": "number of threads to used during samtools sort (default 2)." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sam": { - "type": "file", - "description": "Output SAM file containing read alignments", - "pattern": "*.{sam}" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Output CRAM file containing read alignments", - "pattern": "*.{cram}" - } - }, - { - "crai": { - "type": "file", - "description": "Index file for CRAM file", - "pattern": "*.{crai}" - } - }, - { - "csi": { - "type": "file", - "description": "Index file for BAM file", - "pattern": "*.{csi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ], + [ + { + "mbuffer": { + "type": "integer", + "description": "memory for mbuffer in megabytes (default 3072)" + } + } + ], + [ + { + "samtools_threads": { + "type": "integer", + "description": "number of threads for samtools (default 2)" + } + } + ] + ], + "output": [ + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "Output SAM file containing read alignments", + "pattern": "*.{sam}" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "Index file for CRAM file", + "pattern": "*.{crai}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Index file for BAM file", + "pattern": "*.{csi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -21202,50 +26303,63 @@ "arxiv": "arXiv:1401.1129", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } } - }, - { - "index": { - "type": "directory", - "description": "Directory containing bwameth genome index" + ], + [ + { + "index": { + "type": "directory", + "description": "Directory containing bwameth genome index" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -21287,32 +26401,43 @@ "arxiv": "arXiv:1401.1129", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "index": { - "type": "directory", - "description": "Directory containing bwameth genome index", - "pattern": "index" - } + "index": [ + { + "bwameth": { + "type": "directory", + "description": "Directory containing bwameth genome index", + "pattern": "index" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -21351,52 +26476,65 @@ "doi": "10.1093/nar/gky1016", "licence": [ "Restricted. Free for non-commercial users." - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input file for annotation in vcf or vcf.gz format", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "annotation_dir": { - "type": "file", - "description": "Path to folder containing the vcf files with precomputed CADD scores.\nThis folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.\n", - "pattern": "*.{vcf,vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "Annotated tsv file", - "pattern": "*.{tsv,tsv.gz}" - } + ], + "identifier": "biotools:cadd_phred" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input file for annotation in vcf or vcf.gz format", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "annotation_dir": { + "type": "file", + "description": "Path to folder containing the vcf files with precomputed CADD scores.\nThis folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.\n", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv.gz": { + "type": "file", + "description": "Annotated tsv file", + "pattern": "*.{tsv,tsv.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -21435,79 +26573,108 @@ "doi": "10.1093/bioinformatics/btaa1027", "licence": [ "IU OPEN SOURCE LICENSE (see https://github.com/hahnlab/CAFE5/blob/master/LICENSE)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "infile": { - "type": "file", - "description": "Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue or OrthoFinder)", - "pattern": "*.{txt,tsv,tab}" - } - }, - { - "tree": { - "type": "file", - "description": "Newick formatted tree", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cafe": { - "type": "directory", - "description": "A folder with all the cafe output" - } - }, - { - "cafe_base_count": { - "type": "file", - "description": "File containing counts of genes per orthogroup", - "pattern": "*_count.tab" - } - }, - { - "cafe_significant_trees": { - "type": "file", - "description": "File containing significant trees (newick format)", - "pattern": "*.tre" - } - }, - { - "cafe_report": { - "type": "file", - "description": "File containing the final report from cafe", - "pattern": "*_report.cafe" - } - }, - { - "cafe_results": { - "type": "file", - "description": "File containing the main result files from cafe", - "pattern": "*results.txt" - } + ], + "identifier": "biotools:CaFE_Calculation_of_Free_Energy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "infile": { + "type": "file", + "description": "Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue or OrthoFinder)", + "pattern": "*.{txt,tsv,tab}" + } + } + ], + [ + { + "tree": { + "type": "file", + "description": "Newick formatted tree", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "cafe": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "A folder with all the cafe output" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "cafe_base_count": [ + { + "$prefix/*_count.tab": { + "type": "file", + "description": "File containing counts of genes per orthogroup", + "pattern": "*_count.tab" + } + } + ] + }, + { + "cafe_significant_trees": [ + { + "$prefix/*.tre": { + "type": "file", + "description": "File containing significant trees (newick format)", + "pattern": "*.tre" + } + } + ] + }, + { + "cafe_report": [ + { + "$prefix/*_report.cafe": { + "type": "file", + "description": "File containing the final report from cafe", + "pattern": "*_report.cafe" + } + } + ] + }, + { + "cafe_results": [ + { + "$prefix/*results.txt": { + "type": "file", + "description": "File containing the main result files from cafe", + "pattern": "*results.txt" + } + } + ] } ], "authors": [ @@ -21543,60 +26710,83 @@ "doi": "10.1038/s41467-021-22666-3", "licence": [ "MIT" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool.mcool}" + } + } + ], + [ + { + "resolution": { + "type": "integer", + "description": "In case a .mcool file is provided, which resolution level to use for the analysis" + } + } + ] + ], + "output": [ + { + "output_folder": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "Output folder containing sub-compartment (.tsv/.bed) and domain boundaries calls (.bed)" + } + } + ] + }, + { + "intermediate_data_folder": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" + } + }, + { + "${prefix}/intermediate_data/": { + "type": "directory", + "description": "Output folder containing intermediate data produced during the computation" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" - } - }, - { - "cool": { - "type": "file", - "description": "Path to COOL file", - "pattern": "*.{cool.mcool}" - } - }, - { - "resolution": { - "type": "integer", - "description": "In case a .mcool file is provided, which resolution level to use for the analysis" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. E.g. [ id:'test', single_end:false ]" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output_folder": { - "type": "directory", - "description": "Output folder containing sub-compartment (.tsv/.bed) and domain boundaries calls (.bed)" - } - }, - { - "intermediate_data_folder": { - "type": "directory", - "description": "Output folder containing intermediate data produced during the computation" - } - } - ], - "authors": [ - "@lucananni93" + "authors": [ + "@lucananni93" ], "maintainers": [ "@lucananni93" @@ -21626,108 +26816,193 @@ "doi": "10.1101/gr.215087.116", "licence": [ "GPL v2 and others" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:true ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fasta/fastq file", - "pattern": "*.{fasta,fastq}" - } - }, - { - "mode": { - "type": "string", - "description": "Canu mode depending on the input data (source and error rate)", - "pattern": "-pacbio|-nanopore|-pacbio-hifi" - } - }, - { - "genomesize": { - "type": "string", - "description": "An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g", - "pattern": "[g|m|k]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "report": { - "type": "file", - "description": "Most of the analysis reported during assembly", - "pattern": "*.report" - } - }, - { - "assembly": { - "type": "file", - "description": "Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements.", - "pattern": "*.contigs.fasta" - } - }, - { - "contigs": { - "type": "file", - "description": "Reads and low-coverage contigs which could not be incorporated into the primary assembly.", - "pattern": "*.unassembled.fasta" - } - }, - { - "corrected_reads": { - "type": "file", - "description": "The reads after correction.", - "pattern": "*.correctedReads.fasta.gz" - } - }, - { - "corrected_trimmed_reads": { - "type": "file", - "description": "The corrected reads after overlap based trimming", - "pattern": "*.trimmedReads.fasta.gz" - } - }, - { - "metadata": { - "type": "file", - "description": "(undocumented)", - "pattern": "*.contigs.layout" - } - }, - { - "contig_position": { - "type": "file", - "description": "The position of each read in a contig", - "pattern": "*.contigs.layout.readToTig" - } - }, - { - "contig_info": { - "type": "file", - "description": "A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line.", - "pattern": "*.contigs.layout.tigInfo" - } + ], + "identifier": "biotools:canu" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:true ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fasta/fastq file", + "pattern": "*.{fasta,fastq}" + } + } + ], + [ + { + "mode": { + "type": "string", + "description": "Canu mode depending on the input data (source and error rate)", + "pattern": "-pacbio|-nanopore|-pacbio-hifi" + } + } + ], + [ + { + "genomesize": { + "type": "string", + "description": "An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g", + "pattern": "[g|m|k]" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.report": { + "type": "file", + "description": "Most of the analysis reported during assembly", + "pattern": "*.report" + } + } + ] + }, + { + "assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.fasta.gz": { + "type": "file", + "description": "Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements.", + "pattern": "*.contigs.fasta" + } + } + ] + }, + { + "contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unassembled.fasta.gz": { + "type": "file", + "description": "Reads and low-coverage contigs which could not be incorporated into the primary assembly.", + "pattern": "*.unassembled.fasta" + } + } + ] + }, + { + "corrected_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.correctedReads.fasta.gz": { + "type": "file", + "description": "The reads after correction.", + "pattern": "*.correctedReads.fasta.gz" + } + } + ] + }, + { + "corrected_trimmed_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trimmedReads.fasta.gz": { + "type": "file", + "description": "The corrected reads after overlap based trimming", + "pattern": "*.trimmedReads.fasta.gz" + } + } + ] + }, + { + "metadata": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.layout": { + "type": "file", + "description": "(undocumented)", + "pattern": "*.contigs.layout" + } + } + ] + }, + { + "contig_position": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.layout.readToTig": { + "type": "file", + "description": "The position of each read in a contig", + "pattern": "*.contigs.layout.readToTig" + } + } + ] + }, + { + "contig_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.layout.tigInfo": { + "type": "file", + "description": "A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line.", + "pattern": "*.contigs.layout.tigInfo" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -21763,39 +27038,57 @@ "documentation": "https://man7.org/linux/man-pages/man1/cat.1.html", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files_in": { - "type": "file", - "description": "List of compressed / uncompressed files", - "pattern": "*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "files_in": { + "type": "file", + "description": "List of compressed / uncompressed files", + "pattern": "*" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "file_out": [ + { + "meta": { + "type": "file", + "description": "Concatenated file. Will be gzipped if file_out ends with \".gz\"", + "pattern": "${file_out}" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Concatenated file. Will be gzipped if file_out ends with \".gz\"", + "pattern": "${file_out}" + } + } + ] }, { - "file_out": { - "type": "file", - "description": "Concatenated file. Will be gzipped if file_out ends with \".gz\"", - "pattern": "${file_out}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -21889,44 +27182,55 @@ "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files to be concatenated.\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files to be concatenated.\n" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Merged fastq file", - "pattern": "*.{merged.fastq.gz}" - } + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.merged.fastq.gz": { + "type": "file", + "description": "Merged fastq file", + "pattern": "*.{merged.fastq.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22068,52 +27372,73 @@ "doi": "10.1093/bioinformatics/btl158", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "fasta file of sequences to be clustered", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file of the representative sequences for each cluster", - "pattern": "*.{fasta}" - } - }, - { - "clusters": { - "type": "file", - "description": "List of clusters", - "pattern": "*.{clstr}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "fasta file of sequences to be clustered", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "fasta file of the representative sequences for each cluster", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clstr": { + "type": "file", + "description": "List of clusters", + "pattern": "*.{clstr}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22155,52 +27480,73 @@ "doi": "10.1093/bioinformatics/btl158", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "fasta or fastq file of sequences to be clustered", - "pattern": "*.{fasta,fastq}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta or fastq file of the representative sequences for each cluster", - "pattern": "*.{fasta,fastq}" - } - }, - { - "clusters": { - "type": "file", - "description": "List of clusters", - "pattern": "*.{clstr}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "fasta or fastq file of sequences to be clustered", + "pattern": "*.{fasta,fastq}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{fa,fq}": { + "type": "file", + "description": "fasta or fastq file of the representative sequences for each cluster", + "pattern": "*.{fasta,fastq}" + } + } + ] + }, + { + "clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clstr": { + "type": "file", + "description": "List of clusters", + "pattern": "*.{clstr}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22236,73 +27582,94 @@ "doi": "10.1038/s41592-022-01498-z", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "img_data": { - "type": "file", - "description": "Quantification table with single cells as rows, markers (e.g. CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as columns", - "pattern": "*.csv" - } - }, - { - "signature": { - "type": "file", - "description": "Signature Matrix containing the definition of cell types according to markers", - "pattern": "*.csv" - } - }, - { - "high_thresholds": { - "type": "file", - "description": "csv file with user-defined probability high thresholds for anchor cell (row 1) and index cell (row 2) definition", - "pattern": "*.csv" - } - }, - { - "low_thresholds": { - "type": "file", - "description": "optional csv file with user-defined probability low thresholds for anchor cell (row 1) and index cell (row 2) definition", - "pattern": "*.csv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "celltypes": { - "type": "file", - "description": "File with final celltype annotations concatenated to the original input quantification, due to the mechanism its non-deterministic", - "pattern": "*.csv" - } - }, - { - "quality": { - "type": "file", - "description": "File with final calculated marker probabilities for inspection, non-deterministic", - "pattern": "*.csv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "img_data": { + "type": "file", + "description": "Quantification table with single cells as rows, markers (e.g. CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as columns", + "pattern": "*.csv" + } + } + ], + [ + { + "signature": { + "type": "file", + "description": "Signature Matrix containing the definition of cell types according to markers", + "pattern": "*.csv" + } + } + ], + [ + { + "high_thresholds": { + "type": "file", + "description": "csv file with user-defined probability high thresholds for anchor cell (row 1) and index cell (row 2) definition", + "pattern": "*.csv" + } + } + ], + [ + { + "low_thresholds": { + "type": "file", + "description": "optional csv file with user-defined probability low thresholds for anchor cell (row 1) and index cell (row 2) definition", + "pattern": "*.csv" + } + } + ] + ], + "output": [ + { + "celltypes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*results.csv": { + "type": "file", + "description": "File with final celltype annotations concatenated to the original input quantification, due to the mechanism its non-deterministic", + "pattern": "*.csv" + } + } + ] + }, + { + "quality": [ + { + "*quality.csv": { + "type": "file", + "description": "File with final calculated marker probabilities for inspection, non-deterministic", + "pattern": "*.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22335,53 +27702,71 @@ "tool_dev_url": "https://github.com/broadinstitute/CellBender", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "filtered": { - "type": "file", - "description": "AnnData file containing filtered data (without empty droplets)", - "pattern": "*.h5ad" - } - }, - { - "unfiltered": { - "type": "file", - "description": "AnnData file containing unfiltered data (with empty droplets)", - "pattern": "*.h5ad" - } - }, - { - "cellbender_h5": { - "type": "file", - "description": "CellBender h5 file containing ambient RNA estimates", - "pattern": "*.h5" - } - } - ], - "output": [ - { - "h5ad": { - "type": "file", - "description": "AnnData file containing decontaminated counts as `adata.X`", - "pattern": "*.h5ad" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:CellBender" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "filtered": { + "type": "file", + "description": "AnnData file containing filtered data (without empty droplets)", + "pattern": "*.h5ad" + } + }, + { + "unfiltered": { + "type": "file", + "description": "AnnData file containing unfiltered data (with empty droplets)", + "pattern": "*.h5ad" + } + }, + { + "cellbender_h5": { + "type": "file", + "description": "CellBender h5 file containing ambient RNA estimates", + "pattern": "*.h5" + } + } + ] + ], + "output": [ + { + "h5ad": [ + { + "meta": { + "type": "file", + "description": "AnnData file containing decontaminated counts as `adata.X`", + "pattern": "*.h5ad" + } + }, + { + "${prefix}.h5ad": { + "type": "file", + "description": "AnnData file containing decontaminated counts as `adata.X`", + "pattern": "*.h5ad" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22418,95 +27803,201 @@ "tool_dev_url": "https://github.com/broadinstitute/CellBender", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "h5ad": { - "type": "file", - "description": "AnnData file containing unfiltered data (with empty droplets)", - "pattern": "*.h5ad" - } - } - ], - "output": [ - { - "h5": { - "type": "file", - "description": "Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes.", - "pattern": "*.h5" - } - }, - { - "filtered_h5": { - "type": "file", - "description": "Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells.\n", - "pattern": "*.h5" - } - }, - { - "posterior_h5": { - "type": "file", - "description": "The full posterior probability of noise counts. This is not normally used downstream.\n", - "pattern": "*.h5" - } - }, - { - "barcodes": { - "type": "file", - "description": "CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. |\nBarcodes are written in plain text. This information is also contained in each of the above outputs, |\nbut is included as a separate output for convenient use in certain downstream applications.\n", - "pattern": "*.csv" - } - }, - { - "metrics": { - "type": "file", - "description": "Metrics describing the run, potentially to be used to flag problematic runs |\nwhen using CellBender as part of a large-scale automated pipeline.\n", - "pattern": "*.csv" - } - }, - { - "report": { - "type": "file", - "description": "HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings.\n", - "pattern": "*.html" - } - }, - { - "pdf": { - "type": "file", - "description": "PDF file that provides a standard graphical summary of the inference procedure.", - "pattern": "*.pdf" - } - }, - { - "log": { - "type": "file", - "description": "Log file produced by the cellbender remove-background run.", - "pattern": "*.log" - } - }, - { - "checkpoint": { - "type": "file", - "description": "Checkpoint file which contains the trained model and the full posterior.", - "pattern": "*.ckpt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:CellBender" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "h5ad": { + "type": "file", + "description": "AnnData file containing unfiltered data (with empty droplets)", + "pattern": "*.h5ad" + } + } + ] + ], + "output": [ + { + "h5": [ + { + "meta": { + "type": "file", + "description": "Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes.", + "pattern": "*.h5" + } + }, + { + "${prefix}.h5": { + "type": "file", + "description": "Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes.", + "pattern": "*.h5" + } + } + ] + }, + { + "filtered_h5": [ + { + "meta": { + "type": "file", + "description": "Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells.\n", + "pattern": "*.h5" + } + }, + { + "${prefix}_filtered.h5": { + "type": "file", + "description": "Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells.\n", + "pattern": "*.h5" + } + } + ] + }, + { + "posterior_h5": [ + { + "meta": { + "type": "file", + "description": "The full posterior probability of noise counts. This is not normally used downstream.\n", + "pattern": "*.h5" + } + }, + { + "${prefix}_posterior.h5": { + "type": "file", + "description": "The full posterior probability of noise counts. This is not normally used downstream.\n", + "pattern": "*.h5" + } + } + ] + }, + { + "barcodes": [ + { + "meta": { + "type": "file", + "description": "CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. |\nBarcodes are written in plain text. This information is also contained in each of the above outputs, |\nbut is included as a separate output for convenient use in certain downstream applications.\n", + "pattern": "*.csv" + } + }, + { + "${prefix}_cell_barcodes.csv": { + "type": "file", + "description": "CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. |\nBarcodes are written in plain text. This information is also contained in each of the above outputs, |\nbut is included as a separate output for convenient use in certain downstream applications.\n", + "pattern": "*.csv" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "file", + "description": "Metrics describing the run, potentially to be used to flag problematic runs |\nwhen using CellBender as part of a large-scale automated pipeline.\n", + "pattern": "*.csv" + } + }, + { + "${prefix}_metrics.csv": { + "type": "file", + "description": "Metrics describing the run, potentially to be used to flag problematic runs |\nwhen using CellBender as part of a large-scale automated pipeline.\n", + "pattern": "*.csv" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "file", + "description": "HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings.\n", + "pattern": "*.html" + } + }, + { + "${prefix}_report.html": { + "type": "file", + "description": "HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings.\n", + "pattern": "*.html" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "PDF file that provides a standard graphical summary of the inference procedure.", + "pattern": "*.pdf" + } + }, + { + "${prefix}.pdf": { + "type": "file", + "description": "PDF file that provides a standard graphical summary of the inference procedure.", + "pattern": "*.pdf" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log file produced by the cellbender remove-background run.", + "pattern": "*.log" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "Log file produced by the cellbender remove-background run.", + "pattern": "*.log" + } + } + ] + }, + { + "checkpoint": [ + { + "meta": { + "type": "file", + "description": "Checkpoint file which contains the trained model and the full posterior.", + "pattern": "*.ckpt" + } + }, + { + "ckpt.tar.gz": { + "type": "file", + "description": "Checkpoint file which contains the trained model and the full posterior.", + "pattern": "*.ckpt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22545,58 +28036,81 @@ "doi": "10.1038/s41592-022-01663-4", "licence": [ "BSD 3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n(sample id)\n" - } - }, - { - "image": { - "type": "file", - "description": "tif file for ready for segmentation", - "pattern": "*.{tif,tiff}" - } - }, - { - "model": { - "type": "file", - "description": "Optional input file. Cellpose 2 model trained by user using human-in-the-loop approach." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n[sample id]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "mask": { - "type": "file", - "description": "labelled mask output from cellpose in tif format", - "pattern": "*.{tif, tiff}" - } - }, - { - "flows": { - "type": "file", - "description": "cell flow output from cellpose", - "pattern": "*.{tif}" - } + ], + "identifier": "biotools:cellpose" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n(sample id)\n" + } + }, + { + "image": { + "type": "file", + "description": "tif file for ready for segmentation", + "pattern": "*.{tif,tiff}" + } + } + ], + [ + { + "model": { + "type": "file", + "description": "Optional input file. Cellpose 2 model trained by user using human-in-the-loop approach." + } + } + ] + ], + "output": [ + { + "mask": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n[sample id]\n" + } + }, + { + "*masks.tif": { + "type": "file", + "description": "labelled mask output from cellpose in tif format", + "pattern": "*.{tif, tiff}" + } + } + ] + }, + { + "flows": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n[sample id]\n" + } + }, + { + "*flows.tif": { + "type": "file", + "description": "cell flow output from cellpose", + "pattern": "*.{tif}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22641,45 +28155,65 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", "licence": [ "10x Genomics EULA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files. The order of the input files MUST be [\"sample1 R1\", \"sample1 R2\", \"sample2, R1\",\n\"sample2, R2\", ...]. This can usually be achieved by sorting the input files by file name.\n\nBackground: 10x data is always paired-end with R1 containing cell barcode and UMI\nand R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name\nconvention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically\nrenames files to match this convention based on the order of input files to avoid various\nissues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module\nthrows an error if a pair of R1 and R2 fastq files does not have the same filename except for the \"_R1\"/\"_R2\" part.\nRenaming the files does not affect the results (see README.md for detailed tests).\n", - "pattern": "*{R1,R2}*.fastq.gz" - } - }, - { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Cell Ranger" - } - } - ], - "output": [ - { - "outs": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", - "pattern": "${meta.id}/outs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files. The order of the input files MUST be [\"sample1 R1\", \"sample1 R2\", \"sample2, R1\",\n\"sample2, R2\", ...]. This can usually be achieved by sorting the input files by file name.\n\nBackground: 10x data is always paired-end with R1 containing cell barcode and UMI\nand R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name\nconvention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically\nrenames files to match this convention based on the order of input files to avoid various\nissues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module\nthrows an error if a pair of R1 and R2 fastq files does not have the same filename except for the \"_R1\"/\"_R2\" part.\nRenaming the files does not affect the results (see README.md for detailed tests).\n", + "pattern": "*{R1,R2}*.fastq.gz" + } + } + ], + [ + { + "reference": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ] + ], + "output": [ + { + "outs": [ + { + "meta": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "${meta.id}/outs/*" + } + }, + { + "**/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "${meta.id}/outs/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22721,40 +28255,132 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", "licence": [ "10X Genomics EULA" - ] - } - } - ], - "input": [ - { - "bcl": { - "type": "file", - "description": "Base call files", - "pattern": "*.bcl.bgzf" - } - }, - { - "csv": { - "type": "file", - "description": "Sample sheet", - "pattern": "*.csv" - } - } - ], - "output": [ - { - "fastq": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "Sample sheet", + "pattern": "*.csv" + } + }, + { + "bcl": { + "type": "file", + "description": "Base call files", + "pattern": "*.bcl.bgzf" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + }, + { + "*_outs/outs/fastq_path/**/*.fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "undetermined_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_outs/outs/fastq_path/Undetermined*.fastq.gz": { + "type": "file", + "description": "Undetermined FastQ files", + "pattern": "Undetermined*.fastq.gz" + } + } + ] + }, + { + "reports": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_outs/outs/fastq_path/Reports": { + "type": "directory", + "description": "Reports", + "pattern": "Reports" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_outs/outs/fastq_path/Stats": { + "type": "directory", + "description": "Stats", + "pattern": "Stats" + } + } + ] + }, + { + "interop": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_outs/outs/interop_path/*.bin": { + "type": "file", + "description": "InterOp files", + "pattern": "*.bin" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22796,33 +28422,44 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", "licence": [ "10X Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "gtf": { - "type": "file", - "description": "The reference GTF transcriptome file", - "pattern": "*.gtf" + [ + { + "gtf": { + "type": "file", + "description": "The reference GTF transcriptome file", + "pattern": "*.gtf" + } } - } + ] ], "output": [ { - "gtf": { - "type": "directory", - "description": "The filtered GTF transcriptome file", - "pattern": "*.filtered.gtf" - } + "gtf": [ + { + "*.gtf": { + "type": "directory", + "description": "The filtered GTF transcriptome file", + "pattern": "*.filtered.gtf" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22862,46 +28499,61 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov", "licence": [ "10X Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}" + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}" + } } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf" + ], + [ + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf" + } } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder", - "pattern": "str" + ], + [ + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder", + "pattern": "str" + } } - } + ] ], "output": [ { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Cell Ranger" - } + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -22942,53 +28594,70 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references", "licence": [ "10x Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder, e.g. `my_vdj_ref`. This flag is required", - "pattern": "str" + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file (optional)", + "pattern": "*.{fasta,fa}" + } } - }, - { - "genes": { - "type": "file", - "description": "Reference transcriptome GTF file (optional)", - "pattern": "*.gtf" + ], + [ + { + "gtf": { + "type": "file", + "description": "Reference genome GTF file (optional)", + "pattern": "*.gtf" + } } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file (optional)", - "pattern": "*.{fasta,fa}" + ], + [ + { + "seqs": { + "type": "file", + "description": "Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional)", + "pattern": "*.{fasta,fa}" + } } - }, - { - "seqs": { - "type": "file", - "description": "Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional)", - "pattern": "*.{fasta,fa}" + ], + [ + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder, e.g. `my_vdj_ref`. This flag is required", + "pattern": "str" + } } - } + ] ], "output": [ { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Cell Ranger" - } + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -23038,158 +28707,274 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp", "licence": [ "10X Genomics EULA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gex_fastqs": { - "type": "file", - "description": "FASTQ files for gene expression analysis", - "pattern": "*.fastq.gz" - } - }, - { - "vdj_fastqs": { - "type": "file", - "description": "FASTQ files for V(D)J immunoprofiling analysis", - "pattern": "*.fastq.gz" - } - }, - { - "ab_fastqs": { - "type": "file", - "description": "FASTQ files for antibody analysis", - "pattern": "*.fastq.gz" - } - }, - { - "beam_fastqs": { - "type": "file", - "description": "FASTQ files for Barcode-Enabled Antigen Mapping (antigen analysis)", - "pattern": "*.fastq.gz" - } - }, - { - "cmo_fastqs": { - "type": "file", - "description": "FASTQ files for cell multiplexing data", - "pattern": "*.fastq.gz" - } - }, - { - "gex_reference": { - "type": "directory", - "description": "Folder containing Cellranger gene expression reference. Can also be a gzipped tarball", - "pattern": "*.tar.gz" - } - }, - { - "gex_frna_probeset": { - "type": "file", - "description": "Fixed RNA profiling information containing custom probes in CSV format", - "pattern": "*.csv" - } - }, - { - "gex_targetpanel": { - "type": "file", - "description": "Declaration of the target panel for Targeted Gene Expression analysis", - "pattern": "*.csv" - } - }, - { - "vdj_reference": { - "type": "directory", - "description": "Folder containing Cellranger V(D)J reference. Can also be a gzipped tarball", - "pattern": "*.tar.gz" - } - }, - { - "vdj_primer_index": { - "type": "file", - "description": "List of custom V(D)J inner enrichment primers", - "pattern": "*.csv" - } - }, - { - "fb_reference": { - "type": "file", - "description": "The Feature Barcodes used for reference in Feature Barcoding Analysis", - "pattern": "*.csv" - } - }, - { - "beam_antigen_panel": { - "type": "file", - "description": "The BEAM manifest in Feature Barcode CSV format", - "pattern": "*.csv" - } - }, - { - "beam_control_panel": { - "type": "file", - "description": "The BEAM antigens set to control status, with corresponding MHC alleles, in Feature Barcode CSV format", - "pattern": "*.csv" - } - }, - { - "cmo_reference": { - "type": "file", - "description": "Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` option in Cellranger", - "pattern": "*.csv" - } - }, - { - "cmo_barcodes": { - "type": "file", - "description": "A CSV file appended to the Cellranger multi config linking samples to CMO IDs", - "pattern": "*.csv" - } - }, - { - "cmo_barcode_assignment": { - "type": "file", - "description": "A CSV file that specifies the barcode-sample assignment in Cell Multiplexing analysis", - "pattern": "*.csv" - } - }, - { - "frna_sampleinfo": { - "type": "file", - "description": "Sample information for fixed RNA analysis", - "pattern": "*.csv" - } - } - ], - "output": [ - { - "config": { - "type": "file", - "description": "The resolved Cellranger multi config used for analysis", - "pattern": "cellranger_multi_config.csv" - } - }, - { - "outs": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger", - "pattern": "${meta.id}/outs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ], + [ + { + "meta_gex": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "gex_fastqs ": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta_vdj": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "vdj_fastqs ": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta_ab": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "ab_fastqs ": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta_beam": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "beam_fastqs ": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta_cmo": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "cmo_fastqs ": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta_crispr": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "crispr_fastqs": { + "type": "file", + "description": "FASTQ files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "gex_reference": { + "type": "directory", + "description": "Folder containing Cellranger gene expression reference. Can also be a gzipped tarball", + "pattern": "*.tar.gz" + } + } + ], + [ + { + "gex_frna_probeset": { + "type": "file", + "description": "Fixed RNA profiling information containing custom probes in CSV format", + "pattern": "*.csv" + } + } + ], + [ + { + "gex_targetpanel": { + "type": "file", + "description": "Declaration of the target panel for Targeted Gene Expression analysis", + "pattern": "*.csv" + } + } + ], + [ + { + "vdj_reference": { + "type": "directory", + "description": "Folder containing Cellranger V(D)J reference. Can also be a gzipped tarball", + "pattern": "*.tar.gz" + } + } + ], + [ + { + "vdj_primer_index": { + "type": "file", + "description": "List of custom V(D)J inner enrichment primers", + "pattern": "*.csv" + } + } + ], + [ + { + "fb_reference": { + "type": "file", + "description": "The Feature Barcodes used for reference in Feature Barcoding Analysis", + "pattern": "*.csv" + } + } + ], + [ + { + "beam_antigen_panel": { + "type": "file", + "description": "The BEAM manifest in Feature Barcode CSV format", + "pattern": "*.csv" + } + } + ], + [ + { + "beam_control_panel": { + "type": "file", + "description": "The BEAM antigens set to control status, with corresponding MHC alleles, in Feature Barcode CSV format", + "pattern": "*.csv" + } + } + ], + [ + { + "cmo_reference": { + "type": "file", + "description": "Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` option in Cellranger", + "pattern": "*.csv" + } + } + ], + [ + { + "cmo_barcodes": { + "type": "file", + "description": "A CSV file appended to the Cellranger multi config linking samples to CMO IDs", + "pattern": "*.csv" + } + } + ], + [ + { + "cmo_barcode_assignment": { + "type": "file", + "description": "A CSV file that specifies the barcode-sample assignment in Cell Multiplexing analysis", + "pattern": "*.csv" + } + } + ], + [ + { + "frna_sampleinfo": { + "type": "file", + "description": "Sample information for fixed RNA analysis", + "pattern": "*.csv" + } + } + ], + [ + { + "skip_renaming": { + "type": "boolean", + "description": "Skip renaming" + } + } + ] + ], + "output": [ + { + "config": [ + { + "meta": { + "type": "file", + "description": "The resolved Cellranger multi config used for analysis", + "pattern": "cellranger_multi_config.csv" + } + }, + { + "cellranger_multi_config.csv": { + "type": "file", + "description": "The resolved Cellranger multi config used for analysis", + "pattern": "cellranger_multi_config.csv" + } + } + ] + }, + { + "outs": [ + { + "meta": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger", + "pattern": "${meta.id}/outs/*" + } + }, + { + "**/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger", + "pattern": "${meta.id}/outs/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -23230,45 +29015,65 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj", "licence": [ "10X Genomics EULA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" - } - }, - { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Cell Ranger" - } - } - ], - "output": [ - { - "outs": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", - "pattern": "${meta.id}/outs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" + } + } + ], + [ + { + "reference": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Cell Ranger" + } + } + ] + ], + "output": [ + { + "outs": [ + { + "meta": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "${meta.id}/outs/*" + } + }, + { + "**/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "${meta.id}/outs/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -23310,44 +29115,88 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", "licence": [ "10x Genomics EULA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "lib_csv": { - "type": "file", - "description": "Path to a 3-column CSV file declaring FASTQ paths, sample names and library types of input ATAC and GEX FASTQs.\n" - } - }, - { - "reference": { - "type": "directory", - "description": "Directory containing all the reference indices needed by Cell Ranger ARC" - } - } - ], - "output": [ - { - "outs": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger ARC", - "pattern": "${meta.id}/outs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sample_type": { + "type": "string", + "description": "The type of sample" + } + }, + { + "sub_sample": { + "type": "string", + "description": "The name of sub sample" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ files produced using Cell Ranger ARC", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "reference": { + "type": "directory", + "description": "Directory containing all the reference indices needed by Cell Ranger ARC" + } + } + ] + ], + "output": [ + { + "outs": [ + { + "meta": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger ARC", + "pattern": "${meta.id}/outs/*" + } + }, + { + "${meta.id}/outs/**": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger ARC", + "pattern": "${meta.id}/outs/*" + } + } + ] + }, + { + "lib": [ + { + "${meta.id}_lib.csv": { + "type": "file", + "description": "Library", + "pattern": "*_lib.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -23386,40 +29235,60 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", "licence": [ "10x Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "bcl": { - "type": "file", - "description": "Base call files", - "pattern": "*.bcl.bgzf" + [ + { + "bcl": { + "type": "file", + "description": "Base call files", + "pattern": "*.bcl.bgzf" + } } - }, - { - "csv": { - "type": "file", - "description": "Sample sheet", - "pattern": "*.csv" + ], + [ + { + "csv": { + "type": "file", + "description": "Sample sheet", + "pattern": "*.csv" + } } - } + ] ], "output": [ { - "fastq": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "fastq": [ + { + "${bcl.getSimpleName(": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + }, + { + "/*.fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + } + ] } ], "authors": [ @@ -23451,33 +29320,44 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", "licence": [ "10x Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "gtf": { - "type": "file", - "description": "The reference GTF transcriptome file", - "pattern": "*.gtf" + [ + { + "gtf": { + "type": "file", + "description": "The reference GTF transcriptome file", + "pattern": "*.gtf" + } } - } + ] ], "output": [ { - "gtf": { - "type": "directory", - "description": "The filtered GTF transcriptome file", - "pattern": "*.filtered.gtf" - } + "gtf": [ + { + "*.filtered.gtf": { + "type": "directory", + "description": "The filtered GTF transcriptome file", + "pattern": "*.filtered.gtf" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -23514,60 +29394,89 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc", "licence": [ "10x Genomics EULA" - ] - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf" - } - }, - { - "motifs": { - "type": "file", - "description": "Sequence motif file (e.g., from transcription factors)", - "pattern": "*.txt" - } - }, - { - "reference_config": { - "type": "file", - "description": "JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", - "pattern": "config" - } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder", - "pattern": "str" - } - } - ], - "output": [ - { - "reference": { - "type": "directory", - "description": "Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf" + } + } + ], + [ + { + "motifs": { + "type": "file", + "description": "Sequence motif file (e.g., from transcription factors)", + "pattern": "*.txt" + } + } + ], + [ + { + "reference_config": { + "type": "file", + "description": "JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", + "pattern": "config" + } + } + ], + [ + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder", + "pattern": "str" + } + } + ] + ], + "output": [ + { + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc" + } + } + ] + }, + { + "config": [ + { + "config": { + "type": "file", + "description": "Configuration file" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -23603,44 +29512,64 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", "licence": [ "10x Genomics EULA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively, plus an additional FastQ for the barcodes\n" - } - }, - { - "reference": { - "type": "directory", - "description": "Directory containing all the reference indices needed by Cell Ranger ATAC" - } - } - ], - "output": [ - { - "outs": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger ATAC", - "pattern": "sample-${meta.gem}/outs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively, plus an additional FastQ for the barcodes\n" + } + } + ], + [ + { + "reference": { + "type": "directory", + "description": "Directory containing all the reference indices needed by Cell Ranger ATAC" + } + } + ] + ], + "output": [ + { + "outs": [ + { + "meta": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger ATAC", + "pattern": "sample-${meta.gem}/outs/*" + } + }, + { + "${meta.id}/outs/*": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger ATAC", + "pattern": "sample-${meta.gem}/outs/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -23744,40 +29673,60 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", "licence": [ "10x Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "bcl": { - "type": "file", - "description": "Base call files", - "pattern": "*.bcl.bgzf" + [ + { + "bcl": { + "type": "file", + "description": "Base call files", + "pattern": "*.bcl.bgzf" + } } - }, - { - "csv": { - "type": "file", - "description": "Sample sheet", - "pattern": "*.csv" + ], + [ + { + "csv": { + "type": "file", + "description": "Sample sheet", + "pattern": "*.csv" + } } - } + ] ], "output": [ { - "fastq": { - "type": "file", - "description": "Unaligned FastQ files", - "pattern": "*.fastq.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "fastq": [ + { + "${bcl.getSimpleName(": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + }, + { + "/*.fastq.gz": { + "type": "file", + "description": "Unaligned FastQ files", + "pattern": "*.fastq.gz" + } + } + ] } ], "authors": [ @@ -23880,60 +29829,79 @@ "tool_dev_url": "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac", "licence": [ "10x Genomics EULA" - ] - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf" - } - }, - { - "motifs": { - "type": "file", - "description": "Sequence motif file (e.g., of transcription factors)", - "pattern": "*.txt" - } - }, - { - "reference_config": { - "type": "file", - "description": "JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", - "pattern": "config" - } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder", - "pattern": "str" - } - } - ], - "output": [ - { - "reference": { - "type": "directory", - "description": "Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf" + } + } + ], + [ + { + "motifs": { + "type": "file", + "description": "Sequence motif file (e.g., of transcription factors)", + "pattern": "*.txt" + } + } + ], + [ + { + "reference_config": { + "type": "file", + "description": "JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path", + "pattern": "config" + } + } + ], + [ + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder", + "pattern": "str" + } + } + ] + ], + "output": [ + { + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24050,101 +30018,162 @@ "doi": "10.1093/bioinformatics/btab358", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "A single BAM/SAM/CRAM file, e.g., from CellRanger.", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "The index of the BAM/CRAM file.", - "pattern": "*.{bai,crai}" - } - }, - { - "region_vcf": { - "type": "file", - "description": "A optional vcf file listing all candidate SNPs for genotyping.", - "pattern": "*.{vcf, vcf.gz}" - } - }, - { - "barcode": { - "type": "file", - "description": "A plain file listing all effective cell barcodes.", - "pattern": "*.tsv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "base": { - "type": "file", - "description": "A VCF file listing genotyped SNPs and aggregated AD & DP infomation (without GT).", - "pattern": "*.base.vcf.gz" - } - }, - { - "cell": { - "type": "file", - "description": "A VCF file listing genotyped SNPs and aggregated AD & DP infomation & genotype (GT) information for each cell or sample.", - "pattern": "*.cells.vcf.gz" - } - }, - { - "sample": { - "type": "file", - "description": "A TSV file listing cell barcodes or sample IDs.", - "pattern": "*.tsv" - } - }, - { - "allele_depth": { - "type": "file", - "description": "A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.", - "pattern": "*.tag.AD.mtx" - } - }, - { - "depth_coverage": { - "type": "file", - "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).", - "pattern": "*.tag.DP.mtx" - } - }, - { - "depth_other": { - "type": "file", - "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.", - "pattern": "*.tag.OTH.mtx" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "A single BAM/SAM/CRAM file, e.g., from CellRanger.", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "The index of the BAM/CRAM file.", + "pattern": "*.{bai,crai}" + } + }, + { + "region_vcf": { + "type": "file", + "description": "A optional vcf file listing all candidate SNPs for genotyping.", + "pattern": "*.{vcf, vcf.gz}" + } + }, + { + "barcode": { + "type": "file", + "description": "A plain file listing all effective cell barcodes.", + "pattern": "*.tsv" + } + } + ] + ], + "output": [ + { + "base": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.base.vcf.gz": { + "type": "file", + "description": "A VCF file listing genotyped SNPs and aggregated AD & DP infomation (without GT).", + "pattern": "*.base.vcf.gz" + } + } + ] + }, + { + "cell": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.cells.vcf.gz": { + "type": "file", + "description": "A VCF file listing genotyped SNPs and aggregated AD & DP infomation & genotype (GT) information for each cell or sample.", + "pattern": "*.cells.vcf.gz" + } + } + ] + }, + { + "sample": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.samples.tsv": { + "type": "file", + "description": "A TSV file listing cell barcodes or sample IDs.", + "pattern": "*.tsv" + } + } + ] + }, + { + "allele_depth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tag.AD.mtx": { + "type": "file", + "description": "A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.", + "pattern": "*.tag.AD.mtx" + } + } + ] + }, + { + "depth_coverage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tag.DP.mtx": { + "type": "file", + "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).", + "pattern": "*.tag.DP.mtx" + } + } + ] + }, + { + "depth_other": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tag.OTH.mtx": { + "type": "file", + "description": "A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.", + "pattern": "*.tag.OTH.mtx" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24178,73 +30207,92 @@ "doi": "10.1101/gr.210641.116", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file containing sequences to be used in centrifuge database.", - "pattern": "*.{fasta,fna}" - } - }, - { - "conversion_table": { - "type": "file", - "description": "A tab-separated file with sequence ID to taxonomy ID mapping", - "pattern": "*.{map}" - } - }, - { - "taxonomy_tree": { - "type": "file", - "description": "A \\t|\\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents", - "pattern": "*.{dmp}" - } - }, - { - "name_table": { - "type": "file", - "description": "A '|'-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name", - "pattern": "*.{dmp}" - } - }, - { - "size_table": { - "type": "file", - "description": "Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cf": { - "type": "file", - "description": "Index files for the centrifuge database", - "pattern": "*.{cf}" - } + ], + "identifier": "biotools:centrifuge" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file containing sequences to be used in centrifuge database.", + "pattern": "*.{fasta,fna}" + } + } + ], + [ + { + "conversion_table": { + "type": "file", + "description": "A tab-separated file with sequence ID to taxonomy ID mapping", + "pattern": "*.{map}" + } + } + ], + [ + { + "taxonomy_tree": { + "type": "file", + "description": "A \\t|\\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents", + "pattern": "*.{dmp}" + } + } + ], + [ + { + "name_table": { + "type": "file", + "description": "A '|'-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name", + "pattern": "*.{dmp}" + } + } + ], + [ + { + "size_table": { + "type": "file", + "description": "Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "cf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cf": { + "type": "file", + "description": "Index files for the centrifuge database", + "pattern": "*.{cf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24281,90 +30329,147 @@ "doi": "10.1101/gr.210641.116", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "db": { - "type": "directory", - "description": "Path to directory containing centrifuge database files" - } - }, - { - "save_unaligned": { - "type": "boolean", - "description": "If true unmapped fastq files are saved" - } - }, - { - "save_aligned": { - "type": "boolean", - "description": "If true mapped fastq files are saved" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "File containing a classification summary\n", - "pattern": "*.{report.txt}" - } - }, - { - "results": { - "type": "file", - "description": "File containing classification results\n", - "pattern": "*.{results.txt}" - } - }, - { - "sam": { - "type": "file", - "description": "Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s\n", - "pattern": "*.{sam,tab}" - } - }, - { - "fastq_unmapped": { - "type": "file", - "description": "Unmapped fastq files", - "pattern": "*.unmapped.fastq.gz" - } - }, - { - "fastq_mapped": { - "type": "file", - "description": "Mapped fastq files", - "pattern": "*.mapped.fastq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:centrifuge" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Path to directory containing centrifuge database files" + } + } + ], + [ + { + "save_unaligned": { + "type": "boolean", + "description": "If true unmapped fastq files are saved" + } + } + ], + [ + { + "save_aligned": { + "type": "boolean", + "description": "If true mapped fastq files are saved" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "File containing a classification summary\n", + "pattern": "*.{report.txt}" + } + } + ] + }, + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*results.txt": { + "type": "file", + "description": "File containing classification results\n", + "pattern": "*.{results.txt}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{sam,tab}": { + "type": "file", + "description": "Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s\n", + "pattern": "*.{sam,tab}" + } + } + ] + }, + { + "fastq_mapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapped.fastq{,.1,.2}.gz": { + "type": "file", + "description": "Mapped fastq files", + "pattern": "*.mapped.fastq.gz" + } + } + ] + }, + { + "fastq_unmapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unmapped.fastq{,.1,.2}.gz": { + "type": "file", + "description": "Unmapped fastq files", + "pattern": "*.unmapped.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24413,51 +30518,64 @@ "doi": "10.1101/gr.210641.116", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "File containing the centrifuge classification report", - "pattern": "*.{txt}" - } - }, - { - "db": { - "type": "directory", - "description": "Path to directory containing centrifuge database files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "kreport": { - "type": "file", - "description": "File containing kraken-style report from centrifuge\nout files.\n", - "pattern": "*.{txt}" - } + ], + "identifier": "biotools:centrifuge" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "File containing the centrifuge classification report", + "pattern": "*.{txt}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Path to directory containing centrifuge database files" + } + } + ] + ], + "output": [ + { + "kreport": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing kraken-style report from centrifuge\nout files.\n", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24504,23 +30622,39 @@ "doi": "10.1038/s41592-023-01940-w", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" - } + "database": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" + } + }, + { + "checkm2_db_v${db_version}.dmnd": { + "type": "file", + "description": "CheckM2 database file", + "pattern": "checkm2_db_v*.dmnd" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24552,64 +30686,87 @@ "doi": "10.1038/s41592-023-01940-w", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "dbmeta": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "One or multiple FASTA files of each bin", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "db": { - "type": "file", - "description": "CheckM2 database" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "checkm2_output": { - "type": "directory", - "description": "CheckM2 output directory", - "pattern": "${prefix}/" - } - }, - { - "checkm2_tsv": { - "type": "file", - "description": "CheckM2 summary completeness statistics table", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "One or multiple FASTA files of each bin", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "dbmeta": { + "type": "map", + "description": "Groovy Map containing database information\ne.g. `[ id:'test', version:1 ]`\n" + } + }, + { + "db": { + "type": "file", + "description": "CheckM2 database" + } + } + ] + ], + "output": [ + { + "checkm2_output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "CheckM2 output directory", + "pattern": "${prefix}/" + } + } + ] + }, + { + "checkm2_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}/quality_report.tsv": { + "type": "file", + "description": "CheckM2 summary completeness statistics table", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24647,71 +30804,106 @@ "doi": "10.1101/gr.186072.114", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value", - "pattern": "*.{$fasta_ext}" - } - }, - { - "fasta_ext": { - "type": "string", - "description": "The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)" - } - }, - { - "db": { - "type": "directory", - "description": "Optional directory pointing to checkM database to prevent re-downloading" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "checkm_output": { - "type": "directory", - "description": "CheckM output directory", - "pattern": "*/" - } - }, - { - "checkm_output": { - "type": "file", - "description": "Lineage markfer file", - "pattern": "lineage.ms" - } - }, - { - "checkm_tsv": { - "type": "file", - "description": "CheckM summary completeness statistics table", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:checkm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value", + "pattern": "*.{$fasta_ext}" + } + } + ], + [ + { + "fasta_ext": { + "type": "string", + "description": "The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Optional directory pointing to checkM database to prevent re-downloading" + } + } + ] + ], + "output": [ + { + "checkm_output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "CheckM output directory", + "pattern": "*/" + } + } + ] + }, + { + "marker_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/lineage.ms": { + "type": "file", + "description": "Lineage file", + "pattern": "*.ms" + } + } + ] + }, + { + "checkm_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "CheckM summary completeness statistics table", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24764,71 +30956,94 @@ "doi": "10.1101/gr.186072.114", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "analysis_dir": { - "type": "file", - "description": "Directory containing output of checkm/analyze or checkm/lineage_wf etc.", - "pattern": "*" - } - }, - { - "marker_file": { - "type": "file", - "description": "Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf", - "pattern": "*.ms" - } - }, - { - "coverage_file": { - "type": "file", - "description": "File containing coverage of each sequence (generated by checkm coverage)" - } - }, - { - "exclude_marker_file": { - "type": "file", - "description": "File specifying markers to exclude from marker sets" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)", - "pattern": "*.txt" - } - }, - { - "fasta": { - "type": "file", - "description": "Output in fasta format (only if --out_format 9)", - "pattern": "*.fasta" - } + ], + "identifier": "biotools:checkm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "analysis_dir": { + "type": "file", + "description": "Directory containing output of checkm/analyze or checkm/lineage_wf etc.", + "pattern": "*" + } + }, + { + "marker_file": { + "type": "file", + "description": "Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf", + "pattern": "*.ms" + } + }, + { + "coverage_file": { + "type": "file", + "description": "File containing coverage of each sequence (generated by checkm coverage)" + } + } + ], + [ + { + "exclude_marker_file": { + "type": "file", + "description": "File specifying markers to exclude from marker sets" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)", + "pattern": "*.txt" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fasta": { + "type": "file", + "description": "Output in fasta format (only if --out_format 9)", + "pattern": "*.fasta" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24870,46 +31085,65 @@ "doi": "10.21105/joss.00556", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "run_dir": { - "type": "file", - "description": "Illumina sequencing run directory\nCan be directory or a compressed tar (tar.gz) of the directory\n" - } - }, - { - "checkqc_config": { - "type": "file", - "description": "CheckQC configuration file", - "pattern": "*.{yml,yaml}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "report": { - "type": "file", - "description": "CheckQC report in json format", - "pattern": "*checkqc_report.json" - } - }, - { - "log": { - "type": "file", - "description": "CheckQC log in txt format", - "pattern": "*_log.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "run_dir": { + "type": "file", + "description": "Illumina sequencing run directory\nCan be directory or a compressed tar (tar.gz) of the directory\n" + } + } + ], + [ + { + "checkqc_config": { + "type": "file", + "description": "CheckQC configuration file", + "pattern": "*.{yml,yaml}" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "file", + "description": "CheckQC report in json format", + "pattern": "*checkqc_report.json" + } + }, + { + "*checkqc_report.json": { + "type": "file", + "description": "CheckQC report in json format", + "pattern": "*checkqc_report.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -24953,24 +31187,33 @@ "doi": "10.1038/s41587-020-00774-7", "licence": [ "BSD License" - ] + ], + "identifier": "biotools:checkv" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "checkv_db": [ + { + "${prefix}/*": { + "type": "directory", + "description": "directory pointing to database", + "pattern": "${prefix}/" + } + } + ] }, { - "checkv_db": { - "type": "directory", - "description": "directory pointing to database", - "pattern": "${prefix}/" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25015,86 +31258,149 @@ "doi": "10.1038/s41587-020-00774-7", "licence": [ "BSD License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "db": { - "type": "directory", - "description": "Directory pointing to checkV database" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "quality_summary": { - "type": "file", - "description": "CheckV's main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs", - "pattern": "${prefix}/quality_summary.tsv" - } - }, - { - "completeness": { - "type": "file", - "description": "CheckV's detailed overview table on estimating completeness", - "pattern": "${prefix}/completeness.tsv" - } - }, - { - "contamination": { - "type": "file", - "description": "CheckV's detailed overview table on estimating contamination", - "pattern": "${prefix}/contamination.tsv" - } - }, - { - "complete_genomes": { - "type": "file", - "description": "CheckV's detailed overview table on the identified putative complete genomes", - "pattern": "${prefix}/complete_genomes.tsv" - } - }, - { - "proviruses": { - "type": "file", - "description": "CheckV's extracted proviruses contigs", - "pattern": "${prefix}/proviruses.fna" - } - }, - { - "viruses": { - "type": "file", - "description": "CheckV's extracted virus contigs", - "pattern": "${prefix}/viruses.fna" - } + ], + "identifier": "biotools:checkv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Directory pointing to checkV database" + } + } + ] + ], + "output": [ + { + "quality_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/quality_summary.tsv": { + "type": "file", + "description": "CheckV's main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs", + "pattern": "${prefix}/quality_summary.tsv" + } + } + ] + }, + { + "completeness": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/completeness.tsv": { + "type": "file", + "description": "CheckV's detailed overview table on estimating completeness", + "pattern": "${prefix}/completeness.tsv" + } + } + ] + }, + { + "contamination": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/contamination.tsv": { + "type": "file", + "description": "CheckV's detailed overview table on estimating contamination", + "pattern": "${prefix}/contamination.tsv" + } + } + ] + }, + { + "complete_genomes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/complete_genomes.tsv": { + "type": "file", + "description": "CheckV's detailed overview table on the identified putative complete genomes", + "pattern": "${prefix}/complete_genomes.tsv" + } + } + ] + }, + { + "proviruses": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/proviruses.fna": { + "type": "file", + "description": "CheckV's extracted proviruses contigs", + "pattern": "${prefix}/proviruses.fna" + } + } + ] + }, + { + "viruses": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/viruses.fna": { + "type": "file", + "description": "CheckV's extracted virus contigs", + "pattern": "${prefix}/viruses.fna" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25139,50 +31445,63 @@ "doi": "10.1038/s41587-020-00774-7", "licence": [ "BSD License" - ] + ], + "identifier": "biotools:checkv" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file containing additional sequences for the existing checkv database", - "pattern": "*.{fasta,fna,fa}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file containing additional sequences for the existing checkv database", + "pattern": "*.{fasta,fna,fa}" + } } - }, - { - "db": { - "type": "directory", - "description": "directory pointing to existing checkV database to avoid redownloading the database" + ], + [ + { + "db": { + "type": "directory", + "description": "directory pointing to existing checkV database to avoid redownloading the database" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "checkv_db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', bin:'1' ]\n" + } + }, + { + "${prefix}/*": { + "type": "directory", + "description": "directory pointing to database" + } + } + ] }, { - "checkv_db": { - "type": "directory", - "description": "directory pointing to database" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25215,73 +31534,103 @@ "doi": "10.1099/mgen.0.000166", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "directory", - "description": "One or multiple FASTA files to create schema from", - "pattern": "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" - } - }, - { - "prodigal_tf": { - "type": "file", - "description": "File containing the prodigal training file", - "pattern": "*.ptf" - } - }, - { - "cds": { - "type": "file", - "description": "File containing the prodigal cds file", - "pattern": "*.cds" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "schema": { - "type": "directory", - "description": "Schema directory", - "pattern": "*/" - } - }, - { - "cds_coordinates": { - "type": "file", - "description": "File containing the coordinates of the CDS in the input sample", - "pattern": "*_cds_coordinates.tsv" - } - }, - { - "invalid_cds": { - "type": "file", - "description": "File containing the list of alleles predicted by Prodigal that were excluded", - "pattern": "*_invalid_cds.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "directory", + "description": "One or multiple FASTA files to create schema from", + "pattern": "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" + } + } + ], + [ + { + "prodigal_tf": { + "type": "file", + "description": "File containing the prodigal training file", + "pattern": "*.ptf" + } + } + ], + [ + { + "cds": { + "type": "file", + "description": "File containing the prodigal cds file", + "pattern": "*.cds" + } + } + ] + ], + "output": [ + { + "schema": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "results/$meta.id": { + "type": "directory", + "description": "Schema directory", + "pattern": "*/" + } + } + ] + }, + { + "cds_coordinates": [ + { + "results/cds_coordinates.tsv": { + "type": "file", + "description": "File containing the coordinates of the CDS in the input sample", + "pattern": "*_cds_coordinates.tsv" + } + } + ] + }, + { + "invalid_cds": [ + { + "results/invalid_cds.txt": { + "type": "file", + "description": "File containing the list of alleles predicted by Prodigal that were excluded", + "pattern": "*_invalid_cds.txt" + } + }, + { + "id_cds": { + "type": "file", + "description": "File containing the list of alleles predicted by Prodigal that were excluded", + "pattern": "*_invalid_cds.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25308,7 +31657,8 @@ "zcat": { "description": "zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output.", "documentation": "https://linux.die.net/man/1/zcat", - "args_id": "$args" + "args_id": "$args", + "identifier": "" } }, { @@ -25321,52 +31671,64 @@ "licence": [ "MIT" ], - "args_id": "$args2" + "args_id": "$args2", + "identifier": "" } }, { "gzip": { "description": "Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77).", "documentation": "https://linux.die.net/man/1/gzip", - "args_id": "$args3" + "args_id": "$args3", + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FastQ with reads from long read sequencing e.g. PacBio or ONT", + "pattern": "*.{fastq.gz}" + } } - }, - { - "fastq": { - "type": "file", - "description": "FastQ with reads from long read sequencing e.g. PacBio or ONT", - "pattern": "*.{fastq.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Filtered and trimmed FastQ file", + "pattern": "*.{fastq.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Filtered and trimmed FastQ file", - "pattern": "*.{fastq.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25406,113 +31768,166 @@ "tool_dev_url": "https://github.com/haowenz/chromap", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The fasta reference file.\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information for the index\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Chromap genome index files (*.index)\n" - } - }, - { - "barcodes": { - "type": "file", - "description": "Cell barcode files\n" - } - }, - { - "whitelist": { - "type": "file", - "description": "Cell barcode whitelist file\n" - } - }, - { - "chr_order": { - "type": "file", - "description": "Custom chromosome order\n" - } - }, - { - "pairs_chr_order": { - "type": "file", - "description": "Natural chromosome order for pairs flipping\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed.gz" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "tagAlign": { - "type": "file", - "description": "tagAlign file", - "pattern": "*.tagAlign.gz" - } - }, - { - "pairs": { - "type": "file", - "description": "pairs file", - "pattern": "*.pairs.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The fasta reference file.\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information for the index\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Chromap genome index files (*.index)\n" + } + } + ], + [ + { + "barcodes": { + "type": "file", + "description": "Cell barcode files\n" + } + } + ], + [ + { + "whitelist": { + "type": "file", + "description": "Cell barcode whitelist file\n" + } + } + ], + [ + { + "chr_order": { + "type": "file", + "description": "Custom chromosome order\n" + } + } + ], + [ + { + "pairs_chr_order": { + "type": "file", + "description": "Natural chromosome order for pairs flipping\n" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "BED file", + "pattern": "*.bed.gz" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "tagAlign": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tagAlign.gz": { + "type": "file", + "description": "tagAlign file", + "pattern": "*.tagAlign.gz" + } + } + ] + }, + { + "pairs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairs.gz": { + "type": "file", + "description": "pairs file", + "pattern": "*.pairs.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25557,44 +31972,55 @@ "tool_dev_url": "https://github.com/haowenz/chromap", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta reference file." + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta reference file." + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.index": { + "type": "file", + "description": "Index file of the reference genome", + "pattern": "*.{index}" + } + } + ] }, { - "index": { - "type": "file", - "description": "Index file of the reference genome", - "pattern": "*.{index}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25638,116 +32064,139 @@ "documentation": "https://github.com/Clinical-Genomics/chromograph/blob/master/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta7": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "autozyg": { - "type": "file", - "description": "Bed file containing the regions of autozygosity" - } - }, - { - "coverage": { - "type": "file", - "description": "Wig file containing the coverage information" - } - }, - { - "exome": { - "type": "file", - "description": "Bed file containing the coverage for exome." - } - }, - { - "fracsnp": { - "type": "file", - "description": "Wig file containing the fraction of homozygous SNPs" - } - }, - { - "ideogram": { - "type": "file", - "description": "Bed file containing information necessary for ideogram plots.\nFormat ['chrom', 'start', 'end', 'name', 'gStain']\n" - } - }, - { - "regions": { - "type": "file", - "description": "Bed file containing UPD regions" - } - }, - { - "sites": { - "type": "file", - "description": "Bed file containing UPD sites" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "plots": { - "type": "file", - "description": "Directory containing the plots in png format", - "pattern": "*.png" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "autozyg": { + "type": "file", + "description": "Bed file containing the regions of autozygosity" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage": { + "type": "file", + "description": "Wig file containing the coverage information" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "exome": { + "type": "file", + "description": "Bed file containing the coverage for exome." + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fracsnp": { + "type": "file", + "description": "Wig file containing the fraction of homozygous SNPs" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ideogram": { + "type": "file", + "description": "Bed file containing information necessary for ideogram plots.\nFormat ['chrom', 'start', 'end', 'name', 'gStain']\n" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "Bed file containing UPD regions" + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sites": { + "type": "file", + "description": "Bed file containing UPD sites" + } + } + ] + ], + "output": [ + { + "plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Directory containing the plots in png format", + "pattern": "*.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25785,59 +32234,74 @@ "doi": "10.1101/gr.202895.115", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "junctions": { - "type": "file", - "description": "Reformatted junctions file", - "pattern": "*.{junction}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "gene_annotation": { - "type": "file", - "description": "Reformatted GTF file for CIRCexplorer2", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "txt": { - "type": "file", - "description": "Annotated circRNA TXT file", - "pattern": "*.{txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:CIRCexplorer2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "junctions": { + "type": "file", + "description": "Reformatted junctions file", + "pattern": "*.{junction}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Genome FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "gene_annotation": { + "type": "file", + "description": "Reformatted GTF file for CIRCexplorer2", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Annotated circRNA TXT file", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25875,45 +32339,56 @@ "doi": "10.1101/gr.202895.115", "licence": [ "MIT License" - ] + ], + "identifier": "biotools:CIRCexplorer2" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fusions": { - "type": "file", - "description": "BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) file. Aligner will be autodetected based on file suffix.", - "pattern": "*.{bam,junction,bed,txt}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fusions": { + "type": "file", + "description": "BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) file. Aligner will be autodetected based on file suffix.", + "pattern": "*.{bam,junction,bed,txt}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Standardized fusion junction file suitable for CIRCexplorer2 annotate module.", - "pattern": "*.{bam,cram,sam}" - } + "junction": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -25952,76 +32427,101 @@ "doi": "no DOI available", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.fasta" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "elongation_factor": { - "type": "integer", - "description": "The number of bases that the ends of the target chromosome in the reference genome should be elongated by" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "target": { - "type": "string", - "description": "The name of the chromosome in the reference genome that should be elongated" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.fasta" - } - }, - { - "elongated": { - "type": "file", - "description": "File listing the chromosomes that were elongated", - "pattern": "*_elongated" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "elongation_factor": { + "type": "integer", + "description": "The number of bases that the ends of the target chromosome in the reference genome should be elongated by" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "target": { + "type": "string", + "description": "The name of the chromosome in the reference genome that should be elongated" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_${elongation_factor}.fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.fasta" + } + } + ] + }, + { + "elongated": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*${elongation_factor}_elongated": { + "type": "file", + "description": "File listing the chromosomes that were elongated", + "pattern": "*_elongated" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26060,82 +32560,99 @@ "doi": "10.1186/s13059-016-0918-z", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input elongated genome fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "elongation_factor": { - "type": "integer", - "description": "The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "elongated_chr_list": { - "type": "file", - "description": "File listing the chromosomes that were elongated", - "pattern": "*_elongated" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Realigned BAM file", - "pattern": "*.bam" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input elongated genome fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "elongation_factor": { + "type": "integer", + "description": "The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "elongated_chr_list": { + "type": "file", + "description": "File listing the chromosomes that were elongated", + "pattern": "*_elongated" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_realigned.bam": { + "type": "file", + "description": "Realigned BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26167,80 +32684,141 @@ "doi": "10.1186/s12864-018-5191-y", "licence": [ "GPLv3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Nucleotide sequences in FASTA format", - "pattern": "*.{fasta,fa,fna,faa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Output fasta file for all the bins reported, optional since it will be created when bins can be found", - "pattern": "*.{fasta}" - } - }, - { - "bins": { - "type": "file", - "description": "All bins reported", - "pattern": "*.{binning}" - } - }, - { - "fm": { - "type": "file", - "description": "FM-index output", - "pattern": "*.{fm9}" - } - }, - { - "index": { - "type": "file", - "description": "1st column contains the original name for each read, 2nd column the index used by CLAME", - "pattern": "*.{index}" - } - }, - { - "links": { - "type": "file", - "description": "Histogram links by number of reads", - "pattern": "*.{links}" - } - }, - { - "result": { - "type": "file", - "description": "Adjacency list for the overlap detected by each read", - "pattern": "*.{result}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide sequences in FASTA format", + "pattern": "*.{fasta,fa,fna,faa}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Output fasta file for all the bins reported, optional since it will be created when bins can be found", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "bins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.binning": { + "type": "file", + "description": "All bins reported", + "pattern": "*.{binning}" + } + } + ] + }, + { + "fm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fm9": { + "type": "file", + "description": "FM-index output", + "pattern": "*.{fm9}" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.index": { + "type": "file", + "description": "1st column contains the original name for each read, 2nd column the index used by CLAME", + "pattern": "*.{index}" + } + } + ] + }, + { + "links": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.links": { + "type": "file", + "description": "Histogram links by number of reads", + "pattern": "*.{links}" + } + } + ] + }, + { + "result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.result": { + "type": "file", + "description": "Adjacency list for the overlap detected by each read", + "pattern": "*.{result}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26270,65 +32848,115 @@ "doi": "10.7554/eLife.84034", "licence": [ "GPL v3" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file of crosslinks", + "pattern": "*.{bed,bed.gz}" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "A GTF file of genes to call peaks on", + "pattern": "*.{gtf}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "FAI file corresponding to the reference sequence", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "peaks": [ + { + "meta": { + "type": "file", + "description": "BED file of peaks called by Clippy", + "pattern": "*_broadPeaks.bed.gz" + } + }, + { + "*_Peaks.bed": { + "type": "file", + "description": "BED file of peaks called by Clippy", + "pattern": "*_broadPeaks.bed.gz" + } + } + ] + }, + { + "summits": [ + { + "meta": { + "type": "file", + "description": "BED file of peak summits called by Clippy", + "pattern": "*[0-9].bed.gz" + } + }, + { + "*_Summits.bed": { + "type": "file", + "description": "BED file of peak summits called by Clippy", + "pattern": "*[0-9].bed.gz" + } + } + ] + }, + { + "intergenic_gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_intergenic_regions.gtf": { + "type": "file", + "description": "GTF file of intergenic regions", + "pattern": "*_intergenic_regions.gtf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file of crosslinks", - "pattern": "*.{bed,bed.gz}" - } - }, - { - "gtf": { - "type": "file", - "description": "A GTF file of genes to call peaks on", - "pattern": "*.{gtf}" - } - }, - { - "fai": { - "type": "file", - "description": "FAI file corresponding to the reference sequence", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "peaks": { - "type": "file", - "description": "BED file of peaks called by Clippy", - "pattern": "*_broadPeaks.bed.gz" - } - }, - { - "summits": { - "type": "file", - "description": "BED file of peak summits called by Clippy", - "pattern": "*[0-9].bed.gz" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.txt}" - } - } - ], - "authors": [ - "@marc-jones", - "@CharlotteAnne" + "authors": [ + "@marc-jones", + "@CharlotteAnne" ], "maintainers": [ "@marc-jones", @@ -26358,87 +32986,148 @@ "doi": "10.1371/journal.pcbi.1004041", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "msa": { - "type": "file", - "description": "A multiple seqeunce alignmnet in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - }, - { - "newick": { - "type": "file", - "description": "A Newick formated tree based on multiple sequence alignment", - "pattern": "*.{newick,treefile,dnd}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "emsim": { - "type": "file", - "description": "Bootstrapped values for the three parameters R/theta, nu and delta", - "pattern": "*.emsim.txt" - } - }, - { - "em": { - "type": "file", - "description": "Point estimates for R/theta, nu, delta and the branch lengths", - "pattern": "*.em.txt" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequence reconstructed by maximum likelihood", - "pattern": "*.ML_sequence.fasta" - } - }, - { - "newick": { - "type": "file", - "description": "Tree with all nodes labelled", - "pattern": "*.labelled_tree.newick" - } - }, - { - "pos_ref": { - "type": "file", - "description": "CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta", - "pattern": "*.position_cross_reference.txt" - } - }, - { - "status": { - "type": "file", - "description": "List of reconstructed recombination events", - "pattern": "*.importation_status.txt" - } + ], + "identifier": "biotools:clonalframeml" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "newick": { + "type": "file", + "description": "A Newick formated tree based on multiple sequence alignment", + "pattern": "*.{newick,treefile,dnd}" + } + }, + { + "msa": { + "type": "file", + "description": "A multiple seqeunce alignmnet in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + } + ] + ], + "output": [ + { + "emsim": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.emsim.txt": { + "type": "file", + "description": "Bootstrapped values for the three parameters R/theta, nu and delta", + "pattern": "*.emsim.txt" + } + } + ] + }, + { + "em": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.em.txt": { + "type": "file", + "description": "Point estimates for R/theta, nu, delta and the branch lengths", + "pattern": "*.em.txt" + } + } + ] + }, + { + "status": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.importation_status.txt": { + "type": "file", + "description": "List of reconstructed recombination events", + "pattern": "*.importation_status.txt" + } + } + ] + }, + { + "newick": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.labelled_tree.newick": { + "type": "file", + "description": "Tree with all nodes labelled", + "pattern": "*.labelled_tree.newick" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ML_sequence.fasta": { + "type": "file", + "description": "Sequence reconstructed by maximum likelihood", + "pattern": "*.ML_sequence.fasta" + } + } + ] + }, + { + "pos_ref": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.position_cross_reference.txt": { + "type": "file", + "description": "CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta", + "pattern": "*.position_cross_reference.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26471,71 +33160,87 @@ "doi": "10.1038/msb.2011.75", "licence": [ "GPL v2" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Alignment file, in gzipped fasta format", - "pattern": "*.aln{.gz,}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file, in gzipped fasta format", + "pattern": "*.aln{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26577,45 +33282,56 @@ "doi": "10.1038/msb.2011.75", "licence": [ "GPL v2" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}" + } } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Guide tree file in Newick format", - "pattern": "*.{dnd}" - } + "tree": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.dnd": { + "type": "file", + "description": "Guide tree file in Newick format", + "pattern": "*.{dnd}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26662,66 +33378,77 @@ "tool_dev_url": "https://github.com/SegataLab/cmseq", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "gff": { - "type": "file", - "description": "GFF file used to extract protein-coding genes", - "pattern": "*.gff" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional fasta file to run on a subset of references in the BAM file.", - "pattern": ".{fa,fasta,fas,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "polymut": { - "type": "file", - "description": "Polymut report in `.txt` format.", - "pattern": "*.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + }, + { + "gff": { + "type": "file", + "description": "GFF file used to extract protein-coding genes", + "pattern": "*.gff" + } + }, + { + "fasta": { + "type": "file", + "description": "Optional fasta file to run on a subset of references in the BAM file.", + "pattern": ".{fa,fasta,fas,fna}" + } + } + ] + ], + "output": [ + { + "polymut": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Polymut report in `.txt` format.", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26755,57 +33482,70 @@ "doi": "10.1371/journal.pcbi.1004873", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome FASTA.", - "pattern": "*.fasta" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "exclude_bed": { - "type": "file", - "description": "Additional regions to exclude, in BED format. Can be used multiple times." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "File containing accessible regions.", - "pattern": "*.{bed}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome FASTA.", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "exclude_bed": { + "type": "file", + "description": "Additional regions to exclude, in BED format. Can be used multiple times." + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing accessible regions.", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26841,45 +33581,56 @@ "doi": "10.1371/journal.pcbi.1004873", "licence": [ "Apache-2.0" - ] + ], + "identifier": "biotools:cnvkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "targets": { - "type": "file", - "description": "File containing genomic regions", - "pattern": "*.{bed}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "targets": { + "type": "file", + "description": "File containing genomic regions", + "pattern": "*.{bed}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "File containing off-target regions", - "pattern": "*.{bed}" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing off-target regions", + "pattern": "*.{bed}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -26921,139 +33672,210 @@ "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tumor": { - "type": "file", - "description": "Input tumour sample bam file (or cram)\n" - } - }, - { - "normal": { - "type": "file", - "description": "Input normal sample bam file (or cram)\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Input reference genome fasta index (optional, but recommended for cram_input)\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing information about target file\ne.g. [ id:'test' ]\n" - } - }, - { - "targets": { - "type": "file", - "description": "Input target bed file\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing information about reference file\ne.g. [ id:'test' ]\n" - } - }, - { - "reference": { - "type": "file", - "description": "Input reference cnn-file (only for germline and tumor-only running)\n" - } - }, - { - "panel_of_normals": { - "type": "file", - "description": "Input panel of normals file\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "File containing genomic regions", - "pattern": "*.{bed}" - } - }, - { - "cnn": { - "type": "file", - "description": "File containing coverage information", - "pattern": "*.{cnn}" - } - }, - { - "cnr": { - "type": "file", - "description": "File containing copy number ratio information", - "pattern": "*.{cnr}" - } - }, - { - "cns": { - "type": "file", - "description": "File containing copy number segment information", - "pattern": "*.{cns}" - } - }, - { - "pdf": { - "type": "file", - "description": "File with plot of copy numbers or segments on chromosomes", - "pattern": "*.{pdf}" - } - }, - { - "png": { - "type": "file", - "description": "File with plot of bin-level log2 coverages and segmentation calls", - "pattern": "*.{png}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tumor": { + "type": "file", + "description": "Input tumour sample bam file (or cram)\n" + } + }, + { + "normal": { + "type": "file", + "description": "Input normal sample bam file (or cram)\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Input reference genome fasta index (optional, but recommended for cram_input)\n" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing information about target file\ne.g. [ id:'test' ]\n" + } + }, + { + "targets": { + "type": "file", + "description": "Input target bed file\n" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing information about reference file\ne.g. [ id:'test' ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Input reference cnn-file (only for germline and tumor-only running)\n" + } + } + ], + [ + { + "panel_of_normals": { + "type": "file", + "description": "Input panel of normals file\n" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing genomic regions", + "pattern": "*.{bed}" + } + } + ] + }, + { + "cnn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cnn": { + "type": "file", + "description": "File containing coverage information", + "pattern": "*.{cnn}" + } + } + ] + }, + { + "cnr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cnr": { + "type": "file", + "description": "File containing copy number ratio information", + "pattern": "*.{cnr}" + } + } + ] + }, + { + "cns": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cns": { + "type": "file", + "description": "File containing copy number segment information", + "pattern": "*.{cns}" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "File with plot of copy numbers or segments on chromosomes", + "pattern": "*.{pdf}" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "File with plot of bin-level log2 coverages and segmentation calls", + "pattern": "*.{png}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27111,52 +33933,63 @@ "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cns": { - "type": "file", - "description": "CNVKit CNS file.", - "pattern": "*.cns" - } - }, - { - "vcf": { - "type": "file", - "description": "Germline VCF file for BAF.", - "pattern": "*.vcf{,.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "File containing copy number information in new format.", - "pattern": "*.{bed,vcf,cdt,jtv,seg,interval_count}" - } + ], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cns": { + "type": "file", + "description": "CNVKit CNS file.", + "pattern": "*.cns" + } + }, + { + "vcf": { + "type": "file", + "description": "Germline VCF file for BAF.", + "pattern": "*.vcf{,.gz}" + } + } + ] + ], + "output": [ + { + "cns": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cns": { + "type": "file", + "description": "CNS file.", + "pattern": "*.cns" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27195,45 +34028,55 @@ "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", "licence": [ "Apache-2.0" - ] + ], + "identifier": "biotools:cnvkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cns": { - "type": "file", - "description": "CNVKit CNS file.", - "pattern": "*.cns" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cns": { + "type": "file", + "description": "CNVKit CNS file.", + "pattern": "*.cns" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${suffix}": { + "type": "file", + "description": "Output file" + } + } + ] }, { - "cns": { - "type": "file", - "description": "File containing copy number segment information", - "pattern": "*.{cns}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27273,52 +34116,80 @@ "documentation": "https://cnvkit.readthedocs.io/en/stable/index.html", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cnr": { - "type": "file", - "description": "CNR file", - "pattern": "*.cnr" - } - }, - { - "cns": { - "type": "file", - "description": "CNS file [Optional]", - "pattern": "*.cns" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "txt": { - "type": "file", - "description": "TXT file", - "pattern": "*.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cnr": { + "type": "file", + "description": "CNR file", + "pattern": "*.cnr" + } + }, + { + "cns": { + "type": "file", + "description": "CNS file [Optional]", + "pattern": "*.cns" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file", + "pattern": "*.tsv" + } + } + ] + }, + { + "cnn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cnn": { + "type": "file", + "description": "CNN file", + "pattern": "*.cnn" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27362,53 +34233,62 @@ "doi": "10.1371/journal.pcbi.1004873", "licence": [ "Apache-2.0" - ] + ], + "identifier": "biotools:cnvkit" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "File containing reference genome", - "pattern": "*.{fasta}" + [ + { + "fasta": { + "type": "file", + "description": "File containing reference genome", + "pattern": "*.{fasta}" + } } - }, - { - "targets": { - "type": "file", - "description": "File containing genomic regions", - "pattern": "*.{bed}" + ], + [ + { + "targets": { + "type": "file", + "description": "File containing genomic regions", + "pattern": "*.{bed}" + } } - }, - { - "antitargets": { - "type": "file", - "description": "File containing off-target genomic regions", - "pattern": "*.{bed}" + ], + [ + { + "antitargets": { + "type": "file", + "description": "File containing off-target genomic regions", + "pattern": "*.{bed}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cnn": { - "type": "file", - "description": "File containing a copy-number reference (required for CNV calling in tumor_only mode)", - "pattern": "*.{cnn}" - } + "cnn": [ + { + "*.cnn": { + "type": "file", + "description": "File containing a copy-number reference (required for CNV calling in tumor_only mode)", + "pattern": "*.{cnn}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27452,58 +34332,71 @@ "doi": "10.1371/journal.pcbi.1004873", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "baits": { - "type": "file", - "description": "BED or interval file listing the targeted regions.", - "pattern": "*.{bed}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "annotation": { - "type": "file", - "description": "Use gene models from this file to assign names to the target regions.", - "pattern": "*.{txt,bed,gff3,pil}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "File containing target regions", - "pattern": "*.{bed}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "baits": { + "type": "file", + "description": "BED or interval file listing the targeted regions.", + "pattern": "*.{bed}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "annotation": { + "type": "file", + "description": "Use gene models from this file to assign names to the target regions.", + "pattern": "*.{txt,bed,gff3,pil}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "File containing target regions", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27537,98 +34430,125 @@ "tool_dev_url": "https://github.com/abyzovlab/CNVnator", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.bam" - } - }, - { - "root": { - "type": "file", - "description": "ROOT file", - "pattern": "*.root" - } - }, - { - "fasta": { - "type": "file", - "description": "Path to a directory containing fasta files or a fasta file", - "pattern": "*.fa" - } - }, - { - "fai": { - "type": "file", - "description": "Path to a fasta file index", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "output_meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "root": { - "type": "file", - "description": "A ROOT file", - "pattern": "*.root" - } - }, - { - "tab": { - "type": "file", - "description": "A tab file containing cnvnator calls", - "pattern": "*.tab" - } + ], + "identifier": "biotools:cnvnator" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.bam" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "root": { + "type": "file", + "description": "ROOT file", + "pattern": "*.root" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Path to a directory containing fasta files or a fasta file", + "pattern": "*.fa" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Path to a fasta file index", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "root": [ + { + "output_meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.root": { + "type": "file", + "description": "A ROOT file", + "pattern": "*.root" + } + } + ] + }, + { + "tab": [ + { + "output_meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.tab": { + "type": "file", + "description": "A tab file containing cnvnator calls", + "pattern": "*.tab" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27666,45 +34586,56 @@ "tool_dev_url": "https://github.com/abyzovlab/CNVnator", "licence": [ "MIT" - ] + ], + "identifier": "biotools:cnvnator" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "calls": { - "type": "file", - "description": "A tab file containing CNVnator calls", - "pattern": "*.tab" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "calls": { + "type": "file", + "description": "A tab file containing CNVnator calls", + "pattern": "*.tab" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "CNVnator calls in vcf format", + "pattern": "*.vcf" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "CNVnator calls in vcf format", - "pattern": "*.vcf" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27743,51 +34674,64 @@ "doi": "10.1101/2021.01.27.428472v1", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "pytor": { - "type": "file", - "description": "pytor file containing partitions of read depth histograms using mean-shift method", - "pattern": "*.{pytor}" - } - }, - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "pytor": { - "type": "file", - "description": "pytor files containing cnv calls", - "pattern": "*.{pytor}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "pytor": { + "type": "file", + "description": "pytor file containing partitions of read depth histograms using mean-shift method", + "pattern": "*.{pytor}" + } + } + ], + [ + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" + } + } + ] + ], + "output": [ + { + "pytor": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${pytor.baseName}.pytor": { + "type": "file", + "description": "pytor files containing cnv calls", + "pattern": "*.{pytor}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27820,51 +34764,64 @@ "doi": "10.1101/2021.01.27.428472v1", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "pytor": { - "type": "file", - "description": "pytor file containing read depth data", - "pattern": "*.{pytor}" - } - }, - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "pytor": { - "type": "file", - "description": "pytor file containing read depth histograms binned based on given bin size(s)", - "pattern": "*.{pytor}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "pytor": { + "type": "file", + "description": "pytor file containing read depth data", + "pattern": "*.{pytor}" + } + } + ], + [ + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" + } + } + ] + ], + "output": [ + { + "pytor": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${pytor.baseName}.pytor": { + "type": "file", + "description": "pytor file containing read depth histograms binned based on given bin size(s)", + "pattern": "*.{pytor}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27900,66 +34857,81 @@ "doi": "10.1101/2021.01.27.428472v1", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input_file": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "index": { - "type": "file", - "description": "bam file index", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "specifies reference genome file (only for cram file without reference genome)", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "pytor": { - "type": "file", - "description": "read depth root file in which read depth data binned to 100 base pair bins will be stored.", - "pattern": "*.{pytor}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input_file": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "index": { + "type": "file", + "description": "bam file index", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "specifies reference genome file (only for cram file without reference genome)", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "pytor": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.pytor": { + "type": "file", + "description": "read depth root file in which read depth data binned to 100 base pair bins will be stored.", + "pattern": "*.{pytor}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -27994,51 +34966,64 @@ "doi": "10.1101/2021.01.27.428472v1", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "pytor": { - "type": "file", - "description": "pytor file containing read depth data", - "pattern": "*.{pytor}" - } - }, - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "partitions": { - "type": "file", - "description": "pytor file containing partitions of read depth histograms using mean-shift method", - "pattern": "*.{pytor}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "pytor": { + "type": "file", + "description": "pytor file containing read depth data", + "pattern": "*.{pytor}" + } + } + ], + [ + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" + } + } + ] + ], + "output": [ + { + "pytor": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "${pytor.baseName}.pytor": { + "type": "file", + "description": "pytor file", + "pattern": "*.{pytor}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28073,71 +35058,106 @@ "doi": "10.1101/2021.01.27.428472v1", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "pytor_files": { - "type": "file", - "description": "pytor file containing cnv calls. To merge calls from multiple samples use a list of files.", - "pattern": "*.{pytor}" - } - }, - { - "bin_sizes": { - "type": "string", - "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" - } - }, - { - "output_format": { - "type": "string", - "description": "output format of the cnv calls. Valid entries are \"tsv\", \"vcf\", and \"xls\"" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "tsv file containing cnv calls", - "pattern": "*.{tsv}" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file containing cnv calls", - "pattern": "*.{vcf}" - } - }, - { - "xls": { - "type": "file", - "description": "xls file containing cnv calls", - "pattern": "*.{xls}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cnvpytor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "pytor_files": { + "type": "file", + "description": "pytor file containing cnv calls. To merge calls from multiple samples use a list of files.", + "pattern": "*.{pytor}" + } + } + ], + [ + { + "bin_sizes": { + "type": "string", + "description": "list of binsizes separated by space e.g. \"1000 10000\" and \"1000\"" + } + } + ], + [ + { + "output_format": { + "type": "string", + "description": "output format of the cnv calls. Valid entries are \"tsv\", \"vcf\", and \"xls\"" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "vcf file containing cnv calls", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tsv file containing cnv calls", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "xls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.xls": { + "type": "file", + "description": "xls file containing cnv calls", + "pattern": "*.{xls}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28176,136 +35196,247 @@ "doi": "10.1038/s41564-023-01598-2", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly file (contigs/scaffolds) in FASTA format\n", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" - } - }, - { - "coverage": { - "type": "file", - "description": "TSV file with 2 columns containing 1) the contig/scaffold id and\n2) the coverage depth of the sequence specified in column 1\n", - "pattern": "*.{tsv,txt}" - } - }, - { - "query": { - "type": "file", - "description": "File containing the query contigs that the user wants COBRA to extend. This\ncan be provided in one-column TXT or FASTA format. (The IDs must match the IDs\nin the `--fasta` file exactly)\n", - "pattern": "*.{txt,fasta}" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly\nto the resulting assembly FASTA\n", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "assembler": { - "type": "string", - "description": "The name of the tool used to assemble contigs", - "pattern": "{metaspades,megahit,idba}" - } - }, - { - "mink": { - "type": "integer", - "description": "The minimum kmer size used to assemble contigs", - "pattern": "[0-9]+" - } - }, - { - "maxk": { - "type": "integer", - "description": "The maximum kmer size used to assemble contigs", - "pattern": "[0-9]+" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "extended_assemblies": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs that are already circular\n", - "pattern": "${prefix}/COBRA_category_i_self_circular.fasta.gz" - } - }, - { - "extended_circular": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs that were joined and extended\ninto a circular genome\n", - "pattern": "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz" - } - }, - { - "extended_partial": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs were joined and extended, but\nnot into circular sequences\n", - "pattern": "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz" - } - }, - { - "extended_failed": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs that could not be extended due\nto COBRA rules\n", - "pattern": "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz" - } - }, - { - "orphan_end": { - "type": "file", - "description": "Gzipped FASTA file containing query contigs that do not shared the\n\"expected overlap length\" with other contigs\n", - "pattern": "${prefix}/COBRA_category_iii_orphan_end.fasta.gz" - } - }, - { - "all_assemblies": { - "type": "file", - "description": "Gzipped FASTA file containing all FASTA outputs combined into one file\n", - "pattern": "${prefix}/COBRA_all_assemblies.fasta.gz" - } - }, - { - "joining_summary": { - "type": "file", - "description": "TSV file containing information regarding COBRA's extension results\n", - "pattern": "${prefix}/COBRA_joining_summary.txt" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing the contents of each processing\n", - "pattern": "${prefix}/log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembly file (contigs/scaffolds) in FASTA format\n", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage": { + "type": "file", + "description": "TSV file with 2 columns containing 1) the contig/scaffold id and\n2) the coverage depth of the sequence specified in column 1\n", + "pattern": "*.{tsv,txt}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query": { + "type": "file", + "description": "File containing the query contigs that the user wants COBRA to extend. This\ncan be provided in one-column TXT or FASTA format. (The IDs must match the IDs\nin the `--fasta` file exactly)\n", + "pattern": "*.{txt,fasta}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly\nto the resulting assembly FASTA\n", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "assembler": { + "type": "string", + "description": "The name of the tool used to assemble contigs", + "pattern": "{metaspades,megahit,idba}" + } + } + ], + [ + { + "mink": { + "type": "integer", + "description": "The minimum kmer size used to assemble contigs", + "pattern": "[0-9]+" + } + } + ], + [ + { + "maxk": { + "type": "integer", + "description": "The maximum kmer size used to assemble contigs", + "pattern": "[0-9]+" + } + } + ] + ], + "output": [ + { + "self_circular": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_i_self_circular.fasta.gz": { + "type": "file", + "description": "fasta file", + "pattern": "*/COBRA_category_i_self_circular.fasta.gz" + } + } + ] + }, + { + "extended_circular": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs that were joined and extended\ninto a circular genome\n", + "pattern": "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz" + } + } + ] + }, + { + "extended_partial": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs were joined and extended, but\nnot into circular sequences\n", + "pattern": "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz" + } + } + ] + }, + { + "extended_failed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs that could not be extended due\nto COBRA rules\n", + "pattern": "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz" + } + } + ] + }, + { + "orphan_end": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_category_iii_orphan_end.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing query contigs that do not shared the\n\"expected overlap length\" with other contigs\n", + "pattern": "${prefix}/COBRA_category_iii_orphan_end.fasta.gz" + } + } + ] + }, + { + "all_cobra_assemblies": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_all_assemblies.fasta.gz": { + "type": "file", + "description": "Gzipped FASTA file containing all the assemblies generated by COBRA", + "pattern": "*/COBRA_all_assemblies.fasta.gz" + } + } + ] + }, + { + "joining_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/COBRA_joining_summary.txt": { + "type": "file", + "description": "TSV file containing information regarding COBRA's extension results\n", + "pattern": "${prefix}/COBRA_joining_summary.txt" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/log": { + "type": "file", + "description": "Log file containing the contents of each processing\n", + "pattern": "${prefix}/log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28345,45 +35476,56 @@ "doi": "10.1007/978-3-030-32686-9_21", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz),\n 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (*.mfasta, *.mfastq),\n 4. McCortex files (*.ctx),\n 5. or text files (*.txt).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a *.list file which lists all paths COBS should index.\n", - "pattern": "*.*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz),\n 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (*.mfasta, *.mfastq),\n 4. McCortex files (*.ctx),\n 5. or text files (*.txt).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a *.list file which lists all paths COBS should index.\n", + "pattern": "*.*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "index": { - "type": "file", - "description": "The COBS classic index", - "pattern": "*.index.cobs_classic" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.index.cobs_classic": { + "type": "file", + "description": "The COBS classic index", + "pattern": "*.index.cobs_classic" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28416,45 +35558,56 @@ "doi": "10.1007/978-3-030-32686-9_21", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`),\n 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (`*.mfasta`, `*.mfastq`),\n 4. McCortex files (`*.ctx`),\n 5. or text files (`*.txt`).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a `*.list` file which lists all paths COBS should index.\n", - "pattern": "*.*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "The file or directory to be indexed.\nCOBS can read:\n 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`),\n 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`),\n 3. \"Multi-FASTA\" and \"Multi-FASTQ\" files (`*.mfasta`, `*.mfastq`),\n 4. McCortex files (`*.ctx`),\n 5. or text files (`*.txt`).\nYou can either recursively scan a directory for all files matching any of these files,\nor pass a `*.list` file which lists all paths COBS should index.\n", + "pattern": "*.*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "index": { - "type": "file", - "description": "The COBS compact index", - "pattern": "*.index.cobs_compact" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.index.cobs_compact": { + "type": "file", + "description": "The COBS compact index", + "pattern": "*.index.cobs_compact" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28493,87 +35646,148 @@ "doi": "10.1038/nmeth.3103", "licence": [ "FreeBSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_file": { - "type": "file", - "description": "Subcontig coverage TSV table (typically generated with concoct_coverage_table.py)", - "pattern": "*.tsv" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing subcontigs (typically generated with cutup_fasta.py)", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "args_txt": { - "type": "file", - "description": "File containing execution parameters", - "pattern": "*_args.txt" - } - }, - { - "clustering_csv": { - "type": "file", - "description": "CSV containing information which subcontig is assigned to which cluster", - "pattern": "*_clustering_gt1000.csv" - } - }, - { - "log_txt": { - "type": "file", - "description": "Log file of tool execution", - "pattern": "*_log.txt" - } - }, - { - "original_data_csv": { - "type": "file", - "description": "Original CONCOCT GT1000 output", - "pattern": "*_original_data_gt1000.csv" - } - }, - { - "pca_components_csv": { - "type": "file", - "description": "Untransformed PCA component values", - "pattern": "*_PCA_components_data_gt1000.csv" - } - }, - { - "pca_transformed_csv": { - "type": "file", - "description": "Transformed PCA compontent values", - "pattern": "*_PCA_transformed_data_gt1000.csv" - } + ], + "identifier": "biotools:concoct" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage_file": { + "type": "file", + "description": "Subcontig coverage TSV table (typically generated with concoct_coverage_table.py)", + "pattern": "*.tsv" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing subcontigs (typically generated with cutup_fasta.py)", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "args_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_args.txt": { + "type": "file", + "description": "File containing execution parameters", + "pattern": "*_args.txt" + } + } + ] + }, + { + "clustering_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_clustering_gt1000.csv": { + "type": "file", + "description": "CSV containing information which subcontig is assigned to which cluster", + "pattern": "*_clustering_gt1000.csv" + } + } + ] + }, + { + "log_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_log.txt": { + "type": "file", + "description": "Log file of tool execution", + "pattern": "*_log.txt" + } + } + ] + }, + { + "original_data_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_original_data_gt1000.csv": { + "type": "file", + "description": "Original CONCOCT GT1000 output", + "pattern": "*_original_data_gt1000.csv" + } + } + ] + }, + { + "pca_components_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PCA_components_data_gt1000.csv": { + "type": "file", + "description": "Untransformed PCA component values", + "pattern": "*_PCA_components_data_gt1000.csv" + } + } + ] + }, + { + "pca_transformed_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PCA_transformed_data_gt1000.csv": { + "type": "file", + "description": "Transformed PCA compontent values", + "pattern": "*_PCA_transformed_data_gt1000.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28617,59 +35831,70 @@ "doi": "10.1038/nmeth.3103", "licence": [ "FreeBSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file describing where each contig was cut up (typically output from CONCOCT's cut_up_fasta.py)", - "pattern": "*.bed" - } - }, - { - "bamfiles": { - "type": "file", - "description": "A single or list of BAM files of reads mapped back to original contigs (prior cutting up)", - "pattern": "*.bam" - } - }, - { - "baifiles": { - "type": "file", - "description": "A single or list of BAM index files (.bai) corresponding to BAM", - "pattern": "*.bam" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "Contig coverage table", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:concoct" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file describing where each contig was cut up (typically output from CONCOCT's cut_up_fasta.py)", + "pattern": "*.bed" + } + }, + { + "bamfiles": { + "type": "file", + "description": "A single or list of BAM files of reads mapped back to original contigs (prior cutting up)", + "pattern": "*.bam" + } + }, + { + "baifiles": { + "type": "file", + "description": "A single or list of BAM index files (.bai) corresponding to BAM", + "pattern": "*.bam" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Contig coverage table", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28712,58 +35937,81 @@ "doi": "10.1038/nmeth.3103", "licence": [ "FreeBSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Uncompressed) FASTA file containing contigs", - "pattern": "*.{fasta,fna,fa,fas}" - } - }, - { - "bed": { - "type": "boolean", - "description": "Specify whether to generate a BED file describing where each contig was cut up" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Cut up fasta file in non-overlapping or overlapping parts of equal length.", - "pattern": "*.fasta" - } - }, - { - "bed": { - "type": "file", - "description": "Optional BED File containing locations on original contigs where they were cut up.", - "pattern": "*.bed" - } + ], + "identifier": "biotools:concoct" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Uncompressed) FASTA file containing contigs", + "pattern": "*.{fasta,fna,fa,fas}" + } + } + ], + [ + { + "bed": { + "type": "boolean", + "description": "Specify whether to generate a BED file describing where each contig was cut up" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Cut up fasta file in non-overlapping or overlapping parts of equal length.", + "pattern": "*.fasta" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Optional BED File containing locations on original contigs where they were cut up.", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28808,52 +36056,63 @@ "doi": "10.1038/nmeth.3103", "licence": [ "FreeBSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "original_fasta": { - "type": "file", - "description": "Original input FASTA file to CONOCT cut_up_fasta", - "pattern": "*.{fasta,fna,fa,fas}" - } - }, - { - "csv": { - "type": "boolean", - "description": "Output table of merge_cutup_clustering with new cluster assignments", - "pattern": ".csv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA files containing CONCOCT predicted bin clusters, named numerically by CONCOCT cluster ID in a directory called `fasta_bins`", - "pattern": "*.fa.gz" - } + ], + "identifier": "biotools:concoct" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "original_fasta": { + "type": "file", + "description": "Original input FASTA file to CONOCT cut_up_fasta", + "pattern": "*.{fasta,fna,fa,fas}" + } + }, + { + "csv": { + "type": "boolean", + "description": "Output table of merge_cutup_clustering with new cluster assignments", + "pattern": ".csv" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.fa.gz": { + "type": "file", + "description": "FASTA files containing CONCOCT predicted bin clusters, named numerically by CONCOCT cluster ID in a directory called `fasta_bins`", + "pattern": "*.fa.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28897,45 +36156,56 @@ "doi": "10.1038/nmeth.3103", "licence": [ "FreeBSD" - ] + ], + "identifier": "biotools:concoct" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "clustering_csv": { - "type": "file", - "description": "Input cutup clustering result. Typically *_gt1000.csv from concoct", - "pattern": "*.csv" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "clustering_csv": { + "type": "file", + "description": "Input cutup clustering result. Typically *_gt1000.csv from concoct", + "pattern": "*.csv" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Cluster assignments per contig part with concensus cluster", + "pattern": "*.csv" + } + } + ] }, { - "csv": { - "type": "file", - "description": "Cluster assignments per contig part with concensus cluster", - "pattern": "*.csv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -28974,50 +36244,63 @@ "tool_dev_url": "https://github.com/Ivarz/Conifer", "licence": [ "BSD / BSD-2-Clause" - ] + ], + "identifier": "biotools:conifer" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kraken_result": { + "type": "file", + "description": "Raw Kraken2 standard output file\n" + } } - }, - { - "kraken_result": { - "type": "file", - "description": "Raw Kraken2 standard output file\n" - } - }, - { - "kraken_taxon_db": { - "type": "file", - "description": "Kraken2 taxo.k2d database file" + ], + [ + { + "kraken_taxon_db": { + "type": "file", + "description": "Kraken2 taxo.k2d database file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "score": { - "type": "file", - "description": "Conifer report file containing confidence scores of Kraken2 classified reads.\n", - "pattern": "*.score" - } + "score": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.score": { + "type": "file", + "description": "Conifer report file containing confidence scores of Kraken2 classified reads.\n", + "pattern": "*.score" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29054,52 +36337,70 @@ "doi": "10.1093/bioinformatics/btq635", "licence": [ "GPL >=2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cnvs": { - "type": "file", - "description": "_CNVs file generated by FREEC", - "pattern": "*._CNVs" - } - }, - { - "ratio": { - "type": "file", - "description": "ratio file generated by FREEC", - "pattern": "*.ratio.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "p_value_txt": { - "type": "file", - "description": "CNV file containing p_values for each call", - "pattern": "*.p.value.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cnvs": { + "type": "file", + "description": "_CNVs file generated by FREEC", + "pattern": "*._CNVs" + } + }, + { + "ratio": { + "type": "file", + "description": "ratio file generated by FREEC", + "pattern": "*.ratio.txt" + } + } + ] + ], + "output": [ + { + "p_value_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.p.value.txt": { + "type": "file", + "description": "CNV file containing p_values for each call", + "pattern": "*.p.value.txt" + } + }, + { + "ue_txt": { + "type": "file", + "description": "CNV file containing p_values for each call", + "pattern": "*.p.value.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29140,198 +36441,305 @@ "doi": "10.1093/bioinformatics/btq635", "licence": [ "GPL >=2" - ] - } - } - ], - "input": [ - { - "args": { - "type": "map", - "description": "Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.\nParameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. `sex = meta.sex`:\nFor default values, please check the documentation above.\n\n```\n{\n [\n \"general\" :[\n \"bedgraphoutput\": (optional),\n \"breakpointthreshold\": (optional),\n \"breakpointtype\": (optional),\n \"coefficientofvariation\": (optional),\n \"contamination\": (optional),\n \"contaminationadjustment\": (optional),\n \"degree\": (optional),\n \"forcegccontentnormalization\": (optional),\n \"gccontentprofile\": (optional),\n \"intercept\": (optional),\n \"mincnalength\": (optional),\n \"minmappabilityperwindow\": (optional),\n \"minexpectedgc\": (optional),\n \"maxexpectedgc\": (optional),\n \"minimalsubclonepresence\": (optional),\n \"noisydata\": (optional),\n \"ploidy\": (optional),\n \"printNA\": (optional),\n \"readcountthreshold\": (optional),\n \"sex\": (optional),\n \"step\": (optional),\n \"telocentromeric\": (optional),\n \"uniquematch\": (optional),\n \"window\": (optional)\n ],\n \"control\":[\n \"inputformat\": (required),\n \"mateorientation\": (optional),\n ],\n \"sample\":[\n \"inputformat\": (required),\n \"mateorientation\": (optional),\n ],\n \"BAF\":[\n \"minimalcoverageperposition\": (optional),\n \"minimalqualityperposition\": (optional),\n \"shiftinquality\": (optional)\n ]\n ]\n}\n```\n" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mateFile_normal": { - "type": "file", - "description": "File with mapped reads", - "pattern": "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - } - }, - { - "mateFile_tumor": { - "type": "file", - "description": "File with mapped reads", - "pattern": "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - } - }, - { - "cpn_normal": { - "type": "file", - "description": "Raw copy number profiles (optional)", - "pattern": "*.cpn" - } - }, - { - "cpn_tumor": { - "type": "file", - "description": "Raw copy number profiles (optional)", - "pattern": "*.cpn" - } - }, - { - "minipileup_normal": { - "type": "file", - "description": "miniPileup file from previous run (optional)", - "pattern": "*.pileup" - } - }, - { - "minipileup_tumor": { - "type": "file", - "description": "miniPileup file from previous run (optional)", - "pattern": "*.pileup" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file (optional; required if args 'makePileup' is set)", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "Fasta index", - "pattern": "*.fai" - } - }, - { - "snp_position": { - "type": "file", - "description": "Path to a BED or VCF file with SNP positions to create a mini pileup file from the initial BAM file provided in mateFile (optional)", - "pattern": "*.{bed,vcf}" - } - }, - { - "known_snps": { - "type": "file", - "description": "File with known SNPs", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "known_snps_tbi": { - "type": "file", - "description": "Index of known_snps", - "pattern": "*.tbi" - } - }, - { - "chr_directory": { - "type": "file", - "description": "Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)", - "pattern": "*/" - } - }, - { - "mappability": { - "type": "file", - "description": "Contains information of mappable positions (optional)", - "pattern": "*.gem" - } - }, - { - "target_bed": { - "type": "file", - "description": "Sorted bed file containing capture regions (optional)", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bedgraph": { - "type": "file", - "description": "Bedgraph format for the UCSC genome browser", - "pattern": ".bedgraph" - } - }, - { - "control_cpn": { - "type": "file", - "description": "files with raw copy number profiles", - "pattern": "*_control.cpn" - } - }, - { - "sample_cpn": { - "type": "file", - "description": "files with raw copy number profiles", - "pattern": "*_sample.cpn" - } - }, - { - "gcprofile_cpn": { - "type": "file", - "description": "file with GC-content profile.", - "pattern": "GC_profile.*.cpn" - } - }, - { - "BAF": { - "type": "file", - "description": "file B-allele frequencies for each possibly heterozygous SNP position", - "pattern": "*_BAF.txt" - } - }, - { - "CNV": { - "type": "file", - "description": "file with coordinates of predicted copy number alterations.", - "pattern": "*_CNVs" - } - }, - { - "info": { - "type": "file", - "description": "parsable file with information about FREEC run", - "pattern": "*_info.txt" - } - }, - { - "ratio": { - "type": "file", - "description": "file with ratios and predicted copy number alterations for each window", - "pattern": "*_ratio.txt" - } - }, - { - "config": { - "type": "file", - "description": "Config file used to run Control-FREEC", - "pattern": "config.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mpileup_normal": { + "type": "file", + "description": "miniPileup file" + } + }, + { + "mpileup_tumor": { + "type": "file", + "description": "miniPileup file" + } + }, + { + "cpn_normal": { + "type": "file", + "description": "Raw copy number profiles (optional)", + "pattern": "*.cpn" + } + }, + { + "cpn_tumor": { + "type": "file", + "description": "Raw copy number profiles (optional)", + "pattern": "*.cpn" + } + }, + { + "minipileup_normal": { + "type": "file", + "description": "miniPileup file from previous run (optional)", + "pattern": "*.pileup" + } + }, + { + "minipileup_tumor": { + "type": "file", + "description": "miniPileup file from previous run (optional)", + "pattern": "*.pileup" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference file (optional; required if args 'makePileup' is set)", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Fasta index", + "pattern": "*.fai" + } + } + ], + [ + { + "snp_position": { + "type": "file", + "description": "Path to a BED or VCF file with SNP positions to create a mini pileup file from the initial BAM file provided in mateFile (optional)", + "pattern": "*.{bed,vcf}" + } + } + ], + [ + { + "known_snps": { + "type": "file", + "description": "File with known SNPs", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "known_snps_tbi": { + "type": "file", + "description": "Index of known_snps", + "pattern": "*.tbi" + } + } + ], + [ + { + "chr_directory": { + "type": "file", + "description": "Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)", + "pattern": "*/" + } + } + ], + [ + { + "mappability": { + "type": "file", + "description": "Contains information of mappable positions (optional)", + "pattern": "*.gem" + } + } + ], + [ + { + "target_bed": { + "type": "file", + "description": "Sorted bed file containing capture regions (optional)", + "pattern": "*.bed" + } + } + ], + [ + { + "gccontent_profile": { + "type": "file", + "description": "File with GC-content profile" + } + } + ] + ], + "output": [ + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.BedGraph": { + "type": "file", + "description": "Bedgraph format for the UCSC genome browser", + "pattern": ".bedgraph" + } + } + ] + }, + { + "control_cpn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_control.cpn": { + "type": "file", + "description": "files with raw copy number profiles", + "pattern": "*_control.cpn" + } + } + ] + }, + { + "sample_cpn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_sample.cpn": { + "type": "file", + "description": "files with raw copy number profiles", + "pattern": "*_sample.cpn" + } + } + ] + }, + { + "gcprofile_cpn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "GC_profile.*.cpn": { + "type": "file", + "description": "file with GC-content profile.", + "pattern": "GC_profile.*.cpn" + } + } + ] + }, + { + "BAF": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_BAF.txt": { + "type": "file", + "description": "file B-allele frequencies for each possibly heterozygous SNP position", + "pattern": "*_BAF.txt" + } + } + ] + }, + { + "CNV": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_CNVs": { + "type": "file", + "description": "file with coordinates of predicted copy number alterations.", + "pattern": "*_CNVs" + } + } + ] + }, + { + "info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_info.txt": { + "type": "file", + "description": "parsable file with information about FREEC run", + "pattern": "*_info.txt" + } + } + ] + }, + { + "ratio": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.txt": { + "type": "file", + "description": "file with ratios and predicted copy number alterations for each window", + "pattern": "*_ratio.txt" + } + } + ] + }, + { + "config": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "config.txt": { + "type": "file", + "description": "Config file used to run Control-FREEC", + "pattern": "config.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29372,45 +36780,56 @@ "doi": "10.1093/bioinformatics/btq635", "licence": [ "GPL >=2" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ratio": { - "type": "file", - "description": "ratio file generated by FREEC", - "pattern": "*.ratio.txt" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ratio": { + "type": "file", + "description": "ratio file generated by FREEC", + "pattern": "*.ratio.txt" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file", + "pattern": "*.bed" + } + } + ] }, { - "bed": { - "type": "file", - "description": "Bed file", - "pattern": "*.bed" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29451,45 +36870,56 @@ "doi": "10.1093/bioinformatics/btq635", "licence": [ "GPL >=2" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ratio": { - "type": "file", - "description": "ratio file generated by FREEC", - "pattern": "*.ratio.txt" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ratio": { + "type": "file", + "description": "ratio file generated by FREEC", + "pattern": "*.ratio.txt" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "circos": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.circos.txt": { + "type": "file", + "description": "Txt file", + "pattern": "*.circos.txt" + } + } + ] }, { - "circos": { - "type": "file", - "description": "Txt file", - "pattern": "*.circos.txt" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29530,72 +36960,103 @@ "doi": "10.1093/bioinformatics/btq635", "licence": [ "GPL >=2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ratio": { - "type": "file", - "description": "ratio file generated by FREEC", - "pattern": "*.ratio.txt" - } - }, - { - "baf": { - "type": "file", - "description": ".BAF file generated by FREEC", - "pattern": "*.BAF" - } - }, - { - "ploidy": { - "type": "integer", - "description": "Ploidy value for which graph should be created" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "png_baf": { - "type": "file", - "description": "Image of BAF plot", - "pattern": "*_BAF.png" - } - }, - { - "png_ratio_log2": { - "type": "file", - "description": "Image of ratio log2 plot", - "pattern": "*_ratio.log2.png" - } - }, - { - "png_ratio": { - "type": "file", - "description": "Image of ratio plot", - "pattern": "*_ratio.png" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ratio": { + "type": "file", + "description": "ratio file generated by FREEC", + "pattern": "*.ratio.txt" + } + }, + { + "baf": { + "type": "file", + "description": ".BAF file generated by FREEC", + "pattern": "*.BAF" + } + }, + { + "ploidy": { + "type": "integer", + "description": "Ploidy value for which graph should be created" + } + } + ] + ], + "output": [ + { + "png_baf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_BAF.png": { + "type": "file", + "description": "Image of BAF plot", + "pattern": "*_BAF.png" + } + } + ] + }, + { + "png_ratio_log2": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.log2.png": { + "type": "file", + "description": "Image of ratio log2 plot", + "pattern": "*_ratio.log2.png" + } + } + ] + }, + { + "png_ratio": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.png": { + "type": "file", + "description": "Image of ratio plot", + "pattern": "*_ratio.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29630,66 +37091,97 @@ "doi": "10.1093/bioinformatics/btq635", "licence": [ "GPL >=2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ratio": { - "type": "file", - "description": "ratio file generated by FREEC", - "pattern": "*.ratio.txt" - } - }, - { - "baf": { - "type": "file", - "description": ".BAF file generated by FREEC", - "pattern": "*.BAF" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "png_baf": { - "type": "file", - "description": "Image of BAF plot", - "pattern": "*_BAF.png" - } - }, - { - "png_ratio_log2": { - "type": "file", - "description": "Image of ratio log2 plot", - "pattern": "*_ratio.log2.png" - } - }, - { - "png_ratio": { - "type": "file", - "description": "Image of ratio plot", - "pattern": "*_ratio.png" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ratio": { + "type": "file", + "description": "ratio file generated by FREEC", + "pattern": "*.ratio.txt" + } + }, + { + "baf": { + "type": "file", + "description": ".BAF file generated by FREEC", + "pattern": "*.BAF" + } + } + ] + ], + "output": [ + { + "png_baf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_BAF.png": { + "type": "file", + "description": "Image of BAF plot", + "pattern": "*_BAF.png" + } + } + ] + }, + { + "png_ratio_log2": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.log2.png": { + "type": "file", + "description": "Image of ratio log2 plot", + "pattern": "*_ratio.log2.png" + } + } + ] + }, + { + "png_ratio": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_ratio.png": { + "type": "file", + "description": "Image of ratio plot", + "pattern": "*_ratio.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29726,51 +37218,62 @@ "doi": "10.1093/bioinformatics/btz540", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cool": { - "type": "file", - "description": "Path to COOL file", - "pattern": "*.{cool,mcool}" - } - }, - { - "resolution": { - "type": "integer", - "description": "Resolution" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cool": { - "type": "file", - "description": "Output COOL file balancing weigths", - "pattern": "*.cool" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool,mcool}" + } + }, + { + "resolution": { + "type": "integer", + "description": "Resolution" + } + } + ] + ], + "output": [ + { + "cool": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}": { + "type": "file", + "description": "Output COOL file balancing weigths", + "pattern": "*.cool" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29812,68 +37315,82 @@ "doi": "10.1093/bioinformatics/btz540", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pairs": { - "type": "file", - "description": "Path to contacts (i.e. read pairs) file." - } - }, - { - "index": { - "type": "file", - "description": "Path to index file of the contacts." - } - }, - { - "cool_bin": { - "type": "integer", - "description": "Bins size in bp" - } - }, - { - "chromsizes": { - "type": "file", - "description": "Path to a chromsizes file." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "cool": { - "type": "file", - "description": "Output COOL file path", - "pattern": "*.cool" - } - }, - { - "cool_bin": { - "type": "integer", - "description": "Bins size in bp" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pairs": { + "type": "file", + "description": "Path to contacts (i.e. read pairs) file." + } + }, + { + "index": { + "type": "file", + "description": "Path to index file of the contacts." + } + }, + { + "cool_bin": { + "type": "integer", + "description": "Bins size in bp" + } + } + ], + [ + { + "chromsizes": { + "type": "file", + "description": "Path to a chromsizes file." + } + } + ] + ], + "output": [ + { + "cool": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cool": { + "type": "file", + "description": "Output COOL file path", + "pattern": "*.cool" + } + }, + { + "cool_bin": { + "type": "file", + "description": "Output COOL file path", + "pattern": "*.cool" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29914,46 +37431,61 @@ "doi": "10.1093/bioinformatics/btz540", "licence": [ "BSD-3-Clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Genome assembly FASTA file or folder containing FASTA files (uncompressed).", - "pattern": "*.{fasta,fa}" + [ + { + "fasta": { + "type": "file", + "description": "Genome assembly FASTA file or folder containing FASTA files (uncompressed).", + "pattern": "*.{fasta,fa}" + } } - }, - { - "chromsizes": { - "type": "file", - "description": "Path to a chromsizes file." + ], + [ + { + "chromsizes": { + "type": "file", + "description": "Path to a chromsizes file." + } } - }, - { - "enzyme": { - "type": "string", - "description": "Name of restriction enzyme. e.g. CviQI.", - "documentation": "http://biopython.org/DIST/docs/cookbook/Restriction.html" + ], + [ + { + "enzyme": { + "type": "string", + "description": "Name of restriction enzyme. e.g. CviQI.", + "documentation": "http://biopython.org/DIST/docs/cookbook/Restriction.html" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bed": [ + { + "*.bed": { + "type": "file", + "description": "A genome segmentation of restriction fragments as a BED file.", + "pattern": "*.{bed}" + } + } + ] }, { - "bed": { - "type": "file", - "description": "A genome segmentation of restriction fragments as a BED file.", - "pattern": "*.{bed}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -29992,51 +37524,62 @@ "doi": "10.1093/bioinformatics/btz540", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cool": { - "type": "file", - "description": "Path to COOL file", - "pattern": "*.{cool,mcool}" - } - }, - { - "resolution": { - "type": "integer", - "description": "Resolution" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bedpe": { - "type": "file", - "description": "Output text file", - "pattern": "*.bedpe" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool,mcool}" + } + }, + { + "resolution": { + "type": "integer", + "description": "Resolution" + } + } + ] + ], + "output": [ + { + "bedpe": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedpe": { + "type": "file", + "description": "Output text file", + "pattern": "*.bedpe" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30081,38 +37624,62 @@ "doi": "10.1093/bioinformatics/btz540", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "chromsize": { - "type": "file", - "description": "Path to chromosome size file" - } - }, - { - "cool_bin": { - "type": "integer", - "description": "Resolution (bin size) in base pairs" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "Genome segmentation at a fixed resolution as a BED file.", - "pattern": "*.bed" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chromsizes": { + "type": "file", + "description": "Path to a chromsizes file." + } + }, + { + "cool_bin": { + "type": "integer", + "description": "Resolution (bin size) in base pairs" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "file", + "description": "Genome segmentation at a fixed resolution as a BED file.", + "pattern": "*.bed" + } + }, + { + "*.bed": { + "type": "file", + "description": "Genome segmentation at a fixed resolution as a BED file.", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30153,45 +37720,56 @@ "doi": "10.1093/bioinformatics/btz540", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cool": { - "type": "file", - "description": "Path to COOL file", - "pattern": "*.{cool,mcool}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool,mcool}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "cool": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.cool" + } + } + ] }, { - "cool": { - "type": "file", - "description": "Path to COOL file", - "pattern": "*.cool" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30224,45 +37802,56 @@ "doi": "10.1093/bioinformatics/btz540", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cool": { - "type": "file", - "description": "Path to COOL file", - "pattern": "*.{cool,mcool}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cool": { + "type": "file", + "description": "Path to COOL file", + "pattern": "*.{cool,mcool}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "mcool": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mcool": { + "type": "file", + "description": "Output mcool file", + "pattern": "*.mcool" + } + } + ] }, { - "mcool": { - "type": "file", - "description": "Output mcool file", - "pattern": "*.mcool" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30302,66 +37891,111 @@ "doi": "10.1038/s41592-021-01308-y", "license": [ "MIT License" - ] - } - } - ], - "input": [ - { - "image": { - "type": "file", - "description": "ome.tif/tif file", - "pattern": "*.{ome.tif,tif}" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cores": { - "type": "file", - "description": "Complete/Incomplete tissue cores", - "pattern": "*.{tif}" - } - }, - { - "masks": { - "type": "file", - "description": "Binary masks for the Complete/Incomplete tissue cores", - "pattern": "./masks/*.{tif}" - } - }, - { - "tma_map": { - "type": "file", - "description": "A TMA map showing labels and outlines", - "pattern": "TMA_MAP.tif" - } - }, - { - "centroids": { - "type": "file", - "description": "A text file listing centroids of each core in format Y, X", - "pattern": "centroidsY-X.txt" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "image": { + "type": "file", + "description": "ome.tif/tif file", + "pattern": "*.{ome.tif,tif}" + } + } + ] + ], + "output": [ + { + "cores": [ + { + "meta": { + "type": "file", + "description": "Complete/Incomplete tissue cores", + "pattern": "*.{tif}" + } + }, + { + "*[0-9]*.tif": { + "type": "file", + "description": "Complete/Incomplete tissue cores", + "pattern": "*.{tif}" + } + } + ] + }, + { + "masks": [ + { + "meta": { + "type": "file", + "description": "Binary masks for the Complete/Incomplete tissue cores", + "pattern": "./masks/*.{tif}" + } + }, + { + "./masks/": { + "type": "file", + "description": "Binary masks for the Complete/Incomplete tissue cores", + "pattern": "./masks/*.{tif}" + } + } + ] + }, + { + "tma_map": [ + { + "meta": { + "type": "file", + "description": "A TMA map showing labels and outlines", + "pattern": "TMA_MAP.tif" + } + }, + { + "TMA_MAP.tif": { + "type": "file", + "description": "A TMA map showing labels and outlines", + "pattern": "TMA_MAP.tif" + } + } + ] + }, + { + "centroids": [ + { + "meta": { + "type": "file", + "description": "A text file listing centroids of each core in format Y, X", + "pattern": "centroidsY-X.txt" + } + }, + { + "centroidsY-X.txt": { + "type": "file", + "description": "A text file listing centroids of each core in format Y, X", + "pattern": "centroidsY-X.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30401,45 +38035,56 @@ "tool_dev_url": "https://github.com/sstadick/crabz", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "file": { - "type": "file", - "description": "File to be compressed", - "pattern": "*.*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "file": { + "type": "file", + "description": "File to be compressed", + "pattern": "*.*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "archive": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "The compressed file", + "pattern": "*.gz" + } + } + ] }, { - "archive": { - "type": "file", - "description": "The compressed file", - "pattern": "*.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30471,45 +38116,56 @@ "tool_dev_url": "https://github.com/sstadick/crabz", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "archive": { - "type": "file", - "description": "File to be decompressed", - "pattern": "*.gz" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "archive": { + "type": "file", + "description": "File to be decompressed", + "pattern": "*.gz" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.*": { + "type": "file", + "description": "The decompressed file", + "pattern": "*.*" + } + } + ] }, { - "file": { - "type": "file", - "description": "The decompressed file", - "pattern": "*.*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30543,52 +38199,79 @@ "doi": "10.1186/s12864-018-4989-y", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "count_file": { - "type": "file", - "description": "sgRNA raw counts", - "pattern": "*.tsv" - } - }, - { - "library_file": { - "type": "file", - "description": "sgRNA library", - "pattern": "*.tsv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "norm_count_file": { - "type": "file", - "description": "normalized count file", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:crisprcleanr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "count_file": { + "type": "file", + "description": "sgRNA raw counts", + "pattern": "*.tsv" + } + }, + { + "library_file": { + "type": "file", + "description": "sgRNA library", + "pattern": "*.tsv" + } + } + ], + [ + { + "min_reads": { + "type": "integer", + "description": "Minimum number of reads" + } + } + ], + [ + { + "min_targeted_genes": { + "type": "integer", + "description": "Minimum number of targeted genes" + } + } + ] + ], + "output": [ + { + "norm_count_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_norm_table.tsv": { + "type": "file", + "description": "normalized count file", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30628,78 +38311,123 @@ "doi": "10.1093/bioinformatics/bty608", "licence": [ "multiple BSD style licenses" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "keepbed": { - "type": "file", - "description": "BED file defining regions to keep quality" - } - }, - { - "bedout": { - "type": "boolean", - "description": "set to true to ouput suspicious regions to a BED file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "optional filtered/compressed BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "optional filtered/compressed CRAM file", - "pattern": "*.{cram}" - } - }, - { - "sam": { - "type": "file", - "description": "optional filtered/compressed SAM file", - "pattern": "*.{sam}" - } - }, - { - "bed": { - "type": "file", - "description": "optional suspicious regions BED file", - "pattern": "*{bed}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "keepbed": { + "type": "file", + "description": "BED file defining regions to keep quality" + } + } + ], + [ + { + "bedout": { + "type": "boolean", + "description": "set to true to ouput suspicious regions to a BED file" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "optional filtered/compressed BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "optional filtered/compressed CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "optional filtered/compressed SAM file", + "pattern": "*.{sam}" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "optional suspicious regions BED file", + "pattern": "*{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30731,139 +38459,165 @@ "tool_dev_url": "https://github.com/shenwei356/csvtk", "licence": [ "MIT" - ] + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV formatted files", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "in_format": { + "type": "string", + "description": "Input format (csv, tab, or a delimiting character)", + "pattern": "*" + } + } + ], + [ + { + "out_format": { + "type": "string", + "description": "Output format (csv, tab, or a delimiting character)", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Concatenated CSV/TSV file", + "pattern": "*.{csv,tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "version.yml" + } + } + ] + } + ], + "authors": [ + "@rpetit3" + ], + "maintainers": [ + "@rpetit3" + ] + }, + "pipelines": [ + { + "name": "multiplesequencealign", + "version": "dev" + }, + { + "name": "reportho", + "version": "1.0.1" + } + ] + }, + { + "name": "csvtk_join", + "path": "modules/nf-core/csvtk/join/meta.yml", + "type": "module", + "meta": { + "name": "csvtk_join", + "description": "Join two or more CSV (or TSV) tables by selected fields into a single table", + "keywords": [ + "join", + "tsv", + "csv" + ], + "tools": [ + { + "csvtk": { + "description": "A cross-platform, efficient, practical CSV/TSV toolkit", + "homepage": "http://bioinf.shenwei.me/csvtk", + "documentation": "http://bioinf.shenwei.me/csvtk", + "tool_dev_url": "https://github.com/shenwei356/csvtk", + "licence": [ + "MIT" + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV formatted files", - "pattern": "*.{csv,tsv}" - } - }, - { - "in_format": { - "type": "string", - "description": "Input format (csv, tab, or a delimiting character)", - "pattern": "*" - } - }, - { - "out_format": { - "type": "string", - "description": "Output format (csv, tab, or a delimiting character)", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "version.yml" - } - }, - { - "csv": { - "type": "file", - "description": "Concatenated CSV/TSV file", - "pattern": "*.{csv,tsv}" - } - } - ], - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "multiplesequencealign", - "version": "dev" - }, - { - "name": "reportho", - "version": "1.0.1" - } - ] - }, - { - "name": "csvtk_join", - "path": "modules/nf-core/csvtk/join/meta.yml", - "type": "module", - "meta": { - "name": "csvtk_join", - "description": "Join two or more CSV (or TSV) tables by selected fields into a single table", - "keywords": [ - "join", - "tsv", - "csv" - ], - "tools": [ - { - "csvtk": { - "description": "A cross-platform, efficient, practical CSV/TSV toolkit", - "homepage": "http://bioinf.shenwei.me/csvtk", - "documentation": "http://bioinf.shenwei.me/csvtk", - "tool_dev_url": "https://github.com/shenwei356/csvtk", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV formatted files", - "pattern": "*.{csv,tsv}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV formatted files", + "pattern": "*.{csv,tsv}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "version.yml" - } + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${out_extension}": { + "type": "file", + "description": "Joined CSV/TSV file", + "pattern": "*.{csv,tsv}" + } + } + ] }, { - "csv": { - "type": "file", - "description": "Joined CSV/TSV file", - "pattern": "*.{csv,tsv}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "version.yml" + } + } + ] } ], "authors": [ @@ -30909,59 +38663,74 @@ "tool_dev_url": "https://github.com/shenwei356/csvtk", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "CSV/TSV file", - "pattern": "*.{csv,tsv}" - } - }, - { - "in_format": { - "type": "string", - "description": "Input format (csv, tab, or a delimiting character)", - "pattern": "*" - } - }, - { - "out_format": { - "type": "string", - "description": "Output format (csv, tab, or a delimiting character)", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "split_csv": { - "type": "file", - "description": "Split CSV/TSV file", - "pattern": "*.{csv,tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "CSV/TSV file", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "in_format": { + "type": "string", + "description": "Input format (csv, tab, or a delimiting character)", + "pattern": "*" + } + } + ], + [ + { + "out_format": { + "type": "string", + "description": "Output format (csv, tab, or a delimiting character)", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "split_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${out_extension}": { + "type": "file", + "description": "Split CSV/TSV file", + "pattern": "*.{csv,tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -30997,78 +38766,103 @@ "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing additional fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA-format sequence file", - "pattern": "*.{fasta,fa}" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format annotation file for fasta", - "pattern": "*.gtf" - } - }, - { - "add_fasta": { - "type": "file", - "description": "FASTA-format file of additional sequences", - "pattern": "*.fa" - } - }, - { - "biotype": { - "type": "string", - "description": "Biotype to apply to new GTF entries" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA-format combined sequence file", - "pattern": "*.{fasta,fa}" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format combined annotation file", - "pattern": "*.gtf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA-format sequence file", + "pattern": "*.{fasta,fa}" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for fasta", + "pattern": "*.gtf" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing additional fasta information\n" + } + }, + { + "add_fasta": { + "type": "file", + "description": "FASTA-format file of additional sequences", + "pattern": "*.fa" + } + } + ], + [ + { + "biotype": { + "type": "string", + "description": "Biotype to apply to new GTF entries" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "*/*.fasta": { + "type": "file", + "description": "FASTA-format combined sequence file", + "pattern": "*.{fasta,fa}" + } + } + ] + }, + { + "gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "*/*.gtf": { + "type": "file", + "description": "GTF-format combined annotation file", + "pattern": "*.gtf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31109,40 +38903,55 @@ "documentation": "https://github.com/nf-core/tools", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "versions": { - "type": "file", - "description": "YML file containing software versions", - "pattern": "*.yml" + [ + { + "versions": { + "type": "file", + "description": "YML file containing software versions", + "pattern": "*.yml" + } } - } + ] ], "output": [ { - "yml": { - "type": "file", - "description": "Standard YML file containing software versions", - "pattern": "software_versions.yml" - } + "yml": [ + { + "software_versions.yml": { + "type": "file", + "description": "Standard YML file containing software versions", + "pattern": "software_versions.yml" + } + } + ] }, { - "mqc_yml": { - "type": "file", - "description": "MultiQC custom content YML file containing software versions", - "pattern": "software_versions_mqc.yml" - } + "mqc_yml": [ + { + "software_versions_mqc.yml": { + "type": "file", + "description": "MultiQC custom content YML file containing software versions", + "pattern": "software_versions_mqc.yml" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31331,59 +39140,90 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta,fna,fas}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sizes": { - "type": "file", - "description": "File containing chromosome lengths", - "pattern": "*.{sizes}" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}" - } - }, - { - "gzi": { - "type": "file", - "description": "Optional gzip index file for compressed inputs", - "pattern": "*.gzi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta,fna,fas}" + } + } + ] + ], + "output": [ + { + "sizes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sizes": { + "type": "file", + "description": "File containing chromosome lengths", + "pattern": "*.{sizes}" + } + } + ] + }, + { + "fai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}" + } + } + ] + }, + { + "gzi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gzi": { + "type": "file", + "description": "Optional gzip index file for compressed inputs", + "pattern": "*.gzi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31452,52 +39292,71 @@ { "gtffilter": { "description": "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/gtffilter/main.nf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Filtered GTF file", - "pattern": "*.{gtf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/gtffilter/main.nf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.{gtf}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${suffix}": { + "type": "file", + "description": "Filtered GTF file", + "pattern": "*.{gtf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31531,109 +39390,103 @@ { "matrixfilter": { "description": "filter a matrix based on a minimum value and numbers of samples", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on matrix to be filtered, at a\nminimum an id. e.g. [ id:'test' ]\n" - } - }, - { - "abundance": { - "type": "file", - "description": "Raw TSV or CSV format abundance matrix with features (e.g.\ngenes) by row and observations (e.g. samples) by column. All rownames\nfrom the sample sheet should be present in the columns.\n" - } - }, - { - "samplesheet_meta": { - "type": "map", - "description": "Where samplesheet is provided, aroovy Map containing information on\nsample sheet, at a minimum an id. e.g. [ id:'test' ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Optional CSV or TSV format sample sheet with sample metadata. If\nprovided this is used to infer minimum passing samples from group sizes\npresent (see grouping_variable), but also to validate matrix columns.\nIf not provided, all numeric columns are selected.\n" - } - }, - { - "minimum_abundance": { - "type": "float", - "description": "Minimum abundance value, supplied via task.ext.args as --minimum_abundance\n", - "default": 1 - } - }, - { - "minimum_samples": { - "type": "integer", - "description": "Minimum observations that must pass the threshold to retain\nthe row/ feature (e.g. gene). Supplied via task.ext.args as\n--minimum_samples\n", - "default": 1 - } - }, - { - "minimum_proportion": { - "type": "float", - "description": "A minimum proportion of observations that must pass the threshold.\nSupplied via task.ext.args as --minimum_proportion. Overrides\nminimum_samples\n", - "default": 0 - } - }, - { - "grouping_variable": { - "type": "string", - "description": "Optionally supply a variable from the sample sheet that can be used to\ndefine groups and derive a minimum group size upon which to base\nminimum observation numbers. The rationale being to allow retention of\nfeatures that might be present in only one group. Supplied via\ntask.ext.args as --grouping_variable\n" - } - }, - { - "minimum_proportion_not_na": { - "type": "float", - "description": "A minimum proportion of observations that must have a numeric value (not be NA).\nSupplied via task.ext.args as --minimum_proportion_not_na\n", - "default": 0.5 - } - }, - { - "minimum_samples_not_na": { - "type": "integer", - "description": "Minimum observations that must have a numeric value (not be NA) to retain\nthe row/ feature (e.g. gene). Supplied via task.ext.args as\n--minimum_samples_not_na. Overrides minimum_proportion_not_na\n" - } - }, - { - "most_variant_features": { - "type": "integer", - "description": "Variance filter for the number of row/ feature (e.g. gene) observations returned.\nSupplied via task.ext.args as --most_variant_features\n" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "filtered": { - "type": "file", - "description": "Filtered version of input matrix", - "pattern": "*.filtered.tsv" - } - }, - { - "tests": { - "type": "file", - "description": "Boolean matrix with pass/ fail status for each test on each feature", - "pattern": "*.tests.tsv" - } + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on matrix to be filtered, at a\nminimum an id. e.g. [ id:'test' ]\n" + } + }, + { + "abundance": { + "type": "file", + "description": "Raw TSV or CSV format abundance matrix with features (e.g.\ngenes) by row and observations (e.g. samples) by column. All rownames\nfrom the sample sheet should be present in the columns.\n" + } + } + ], + [ + { + "samplesheet_meta": { + "type": "map", + "description": "Where samplesheet is provided, aroovy Map containing information on\nsample sheet, at a minimum an id. e.g. [ id:'test' ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Optional CSV or TSV format sample sheet with sample metadata. If\nprovided this is used to infer minimum passing samples from group sizes\npresent (see grouping_variable), but also to validate matrix columns.\nIf not provided, all numeric columns are selected.\n" + } + } + ] + ], + "output": [ + { + "filtered": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.filtered.tsv": { + "type": "file", + "description": "Filtered version of input matrix", + "pattern": "*.filtered.tsv" + } + } + ] + }, + { + "tests": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tests.tsv": { + "type": "file", + "description": "Boolean matrix with pass/ fail status for each test on each feature", + "pattern": "*.tests.tsv" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "R_sessionInfo.log": { + "type": "file", + "description": "Log file containing R session information", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31673,24 +39526,33 @@ "tool_dev_url": "https://github.com/ncbi/sra-tools", "licence": [ "Public Domain" - ] + ], + "identifier": "" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "ncbi_settings": [ + { + "*.mkfg": { + "type": "file", + "description": "An NCBI user settings file.", + "pattern": "*.mkfg" + } + } + ] }, { - "ncbi_settings": { - "type": "file", - "description": "An NCBI user settings file.", - "pattern": "*.mkfg" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31724,44 +39586,55 @@ { "custom": { "description": "Make a GSEA class file (.cls) from tabular inputs", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf" + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf", + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata including an id, the sample sheet column\nused to define groups, and optionally a separator to override defaults e.g. [\n id:'test', variable:'treatment', separator:',' ]. The way these values are\npassed to the associated module parameters is then defined via an ext.args\nspecification for the process from the workflow, like: ext.args = { [\n \"separator\": \"\\t\", \"variable\": \"$meta.variable\" ] } ('variable' is\ncompulsory here).\n" - } - }, - { - "samples": { - "type": "file", - "description": "Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column.", - "pattern": "*.{csv,tsv}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata including an id, the sample sheet column\nused to define groups, and optionally a separator to override defaults e.g. [\n id:'test', variable:'treatment', separator:',' ]. The way these values are\npassed to the associated module parameters is then defined via an ext.args\nspecification for the process from the workflow, like: ext.args = { [\n \"separator\": \"\\t\", \"variable\": \"$meta.variable\" ] } ('variable' is\ncompulsory here).\n" + } + }, + { + "samples": { + "type": "file", + "description": "Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column.", + "pattern": "*.{csv,tsv}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata e.g. [ id:'test', variable:'treatment',\nseparator:',' ]\n" - } - }, - { - "cls": { - "type": "file", - "description": "A categorical class format file (.cls) as defined by the Broad\ndocumentation at\nhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats\n" - } + "cls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata e.g. [ id:'test', variable:'treatment',\nseparator:',' ]\n" + } + }, + { + "*.cls": { + "type": "file", + "description": "A categorical class format file (.cls) as defined by the Broad\ndocumentation at\nhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats\n" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31794,45 +39667,56 @@ { "tabulartogseagct": { "description": "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA", - "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseagct/main.nf" + "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseagct/main.nf", + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" - } - }, - { - "tabular": { - "type": "file", - "description": "Tabular (e.g. TSV or CSV file) containing a numeric matrix with features (e.g. genes) by row and samples by column.", - "pattern": "*.{tsv,csv}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" + } + }, + { + "tabular": { + "type": "file", + "description": "Tabular (e.g. TSV or CSV file) containing a numeric matrix with features (e.g. genes) by row and samples by column.", + "pattern": "*.{tsv,csv}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" - } - }, - { - "gct": { - "type": "file", - "description": "GCT format version of input TSV", - "pattern": "*.{gct}" - } + "gct": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing matrix information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gct": { + "type": "file", + "description": "GCT format version of input TSV", + "pattern": "*.{gct}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31869,75 +39753,94 @@ "tool_dev_url": "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "An annotation file of the reference genome in GTF format", - "pattern": "*.gtf" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "quants": { - "type": "directory", - "description": "Paths to subdirectories corresponding to sample-wise runs of Salmon or Kallisto" - } - }, - { - "quant_type": { - "type": "string", - "description": "Quantification type, 'kallisto' or 'salmon'" - } - }, - { - "id": { - "type": "string", - "description": "Gene ID attribute in the GTF file (default= gene_id)" - } - }, - { - "extra": { - "type": "string", - "description": "Extra gene attribute in the GTF file (default= gene_name)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" - } - }, - { - "tx2gene": { - "type": "file", - "description": "A transcript/ gene mapping table in TSV format", - "pattern": "*.tx2gene.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "An annotation file of the reference genome in GTF format", + "pattern": "*.gtf" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "\"quants/*\"": { + "type": "file", + "description": "quants file" + } + } + ], + [ + { + "quant_type": { + "type": "string", + "description": "Quantification type, 'kallisto' or 'salmon'" + } + } + ], + [ + { + "id": { + "type": "string", + "description": "Gene ID attribute in the GTF file (default= gene_id)" + } + } + ], + [ + { + "extra": { + "type": "string", + "description": "Extra gene attribute in the GTF file (default= gene_name)" + } + } + ] + ], + "output": [ + { + "tx2gene": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information related to the GTF file\ne.g. `[ id:'yeast' ]`\n" + } + }, + { + "*tx2gene.tsv": { + "type": "file", + "description": "A transcript/ gene mapping table in TSV format", + "pattern": "*.tx2gene.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -31983,51 +39886,72 @@ "doi": "10.14806/ej.17.1.200", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "cuatadapt log file", - "pattern": "*cutadapt.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cutadapt" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trim.fastq.gz": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "cuatadapt log file", + "pattern": "*cutadapt.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32083,64 +40007,77 @@ "tool_dev_url": "https://github.com/tjiangHIT/cuteSV", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM file", - "pattern": "*.bai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file containing called variants from CuteSV", - "pattern": "*.vcf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:cuteSV" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "Index of BAM file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF file containing called variants from CuteSV", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32182,60 +40119,84 @@ "doi": "10.1093/bioinformatics/btab190", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "OPTIONAL FASTA reference file", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "OPTIONAL FASTA index file from samtools faidx", - "pattern": "*.{fai}" - } - }, - { - "specieslist": { - "type": "file", - "description": "OPTIONAL text file with list of target reference headers", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "directory", - "description": "DamageProfiler results directory", - "pattern": "*/*" - } + ], + "identifier": "biotools:damageprofiler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "OPTIONAL FASTA reference file", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "OPTIONAL FASTA index file from samtools faidx", + "pattern": "*.{fai}" + } + } + ], + [ + { + "specieslist": { + "type": "file", + "description": "OPTIONAL text file with list of target reference headers", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "directory", + "description": "DamageProfiler results directory", + "pattern": "*/*" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "DamageProfiler results directory", + "pattern": "*/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32273,135 +40234,267 @@ "doi": "10.1038/s41564-018-0171-1", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fa.gz,fas.gz,fasta.gz}" - } - }, - { - "bins": { - "type": "file", - "description": "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin", - "pattern": "*.tsv" - } - }, - { - "proteins": { - "type": "file", - "description": "Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)", - "pattern": "*.{fa.gz,fas.gz,fasta.gz}" - } - }, - { - "db_directory": { - "type": "file", - "description": "(optional) Directory of single copy gene database." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "Log file of the run", - "pattern": "*.log" - } - }, - { - "summary": { - "type": "file", - "description": "Summary of output bins including quality and completeness estimates", - "pattern": "*summary.txt" - } - }, - { - "contig2bin": { - "type": "file", - "description": "Scaffolds to bin file of output bins", - "pattern": "*.contig2bin.txt" - } - }, - { - "eval": { - "type": "file", - "description": "Quality and completeness estimates of input bin sets", - "pattern": "*.eval" - } - }, - { - "bins": { - "type": "file", - "description": "Final refined bins in fasta format", - "pattern": "*.fa" - } - }, - { - "pdfs": { - "type": "file", - "description": "Plots showing the amount of high quality bins and score distribution of bins per method", - "pattern": "*.pdf" - } - }, - { - "fasta_proteins": { - "type": "file", - "description": "Output from prodigal if not already supplied", - "pattern": "*.proteins.faa" - } - }, - { - "fasta_archaea_scg": { - "type": "file", - "description": "Results of archaeal single-copy-gene prediction", - "pattern": "*.archaea.scg" - } - }, - { - "fasta_bacteria_scg": { - "type": "file", - "description": "Results of bacterial single-copy-gene prediction", - "pattern": "*.bacteria.scg" - } - }, - { - "b6": { - "type": "file", - "description": "Results in b6 format", - "pattern": "*.b6" - } - }, - { - "seqlength": { - "type": "file", - "description": "Summary of contig lengths", - "pattern": "*.seqlength" - } + ], + "identifier": "biotools:dastool" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contigs": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fa.gz,fas.gz,fasta.gz}" + } + }, + { + "bins": { + "type": "file", + "description": "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin", + "pattern": "*.tsv" + } + } + ], + [ + { + "proteins": { + "type": "file", + "description": "Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)", + "pattern": "*.{fa.gz,fas.gz,fasta.gz}" + } + } + ], + [ + { + "db_directory": { + "type": "file", + "description": "(optional) Directory of single copy gene database." + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of the run", + "pattern": "*.log" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary.tsv": { + "type": "file", + "description": "Summary of output bins including quality and completeness estimates", + "pattern": "*summary.txt" + } + } + ] + }, + { + "contig2bin": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_DASTool_contig2bin.tsv": { + "type": "file", + "description": "Scaffolds to bin file of output bins", + "pattern": "*.contig2bin.txt" + } + } + ] + }, + { + "eval": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.eval": { + "type": "file", + "description": "Quality and completeness estimates of input bin sets", + "pattern": "*.eval" + } + } + ] + }, + { + "bins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_DASTool_bins/*.fa": { + "type": "file", + "description": "Final refined bins in fasta format", + "pattern": "*.fa" + } + } + ] + }, + { + "pdfs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Plots showing the amount of high quality bins and score distribution of bins per method", + "pattern": "*.pdf" + } + } + ] + }, + { + "fasta_proteins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidates.faa": { + "type": "file", + "description": "Output from prodigal if not already supplied", + "pattern": "*.proteins.faa" + } + } + ] + }, + { + "candidates_faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.faa": { + "type": "file", + "description": "FAA file", + "pattern": "*.faa" + } + } + ] + }, + { + "fasta_archaea_scg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.archaea.scg": { + "type": "file", + "description": "Results of archaeal single-copy-gene prediction", + "pattern": "*.archaea.scg" + } + } + ] + }, + { + "fasta_bacteria_scg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bacteria.scg": { + "type": "file", + "description": "Results of bacterial single-copy-gene prediction", + "pattern": "*.bacteria.scg" + } + } + ] + }, + { + "b6": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.b6": { + "type": "file", + "description": "Results in b6 format", + "pattern": "*.b6" + } + } + ] + }, + { + "seqlength": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.seqlength": { + "type": "file", + "description": "Summary of contig lengths", + "pattern": "*.seqlength" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32447,51 +40540,64 @@ "doi": "10.1038/s41564-018-0171-1", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta of list of fasta files recommended to be gathered via with .collect() of bins", - "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - } - }, - { - "extension": { - "type": "string", - "description": "Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastatocontig2bin": { - "type": "file", - "description": "tabular contig2bin file for DAS tool input", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:dastool" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta of list of fasta files recommended to be gathered via with .collect() of bins", + "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + } + } + ], + [ + { + "extension": { + "type": "string", + "description": "Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input." + } + } + ] + ], + "output": [ + { + "fastatocontig2bin": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tabular contig2bin file for DAS tool input", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32537,51 +40643,64 @@ "doi": "10.1038/s41564-018-0171-1", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta or list of fasta files recommended to be gathered via with .collect() of bins", - "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - } - }, - { - "extension": { - "type": "string", - "description": "Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "scaffolds2bin": { - "type": "file", - "description": "tabular scaffolds2bin file for DAS tool input", - "pattern": "*.scaffolds2bin.tsv" - } + ], + "identifier": "biotools:dastool" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta or list of fasta files recommended to be gathered via with .collect() of bins", + "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + } + } + ], + [ + { + "extension": { + "type": "string", + "description": "Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input." + } + } + ] + ], + "output": [ + { + "scaffolds2bin": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tabular scaffolds2bin file for DAS tool input", + "pattern": "*.scaffolds2bin.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32613,46 +40732,50 @@ "tool_dev_url": "https://github.com/datavzrd/datavzrd", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "config_file": { - "type": "file", - "description": "configuration file used for visualisation", - "pattern": "*.{yml,yaml}" - } - }, - { - "table": { - "type": "file", - "description": "file used for visualisation", - "pattern": "*.{tsv,csv}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "report": [ + { + "meta": { + "type": "directory", + "description": "directory with HTML report of provided CSV/TSV files", + "pattern": "/output/" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "directory with HTML report of provided CSV/TSV files", + "pattern": "/output/" + } + } + ] }, { - "report": { - "type": "directory", - "description": "directory with HTML report of provided CSV/TSV files", - "pattern": "/output/" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32688,66 +40811,89 @@ "doi": "10.1093/bioadv/vbac016", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" - } - }, - { - "mat": { - "type": "file", - "description": "Path to the matrix file (e.g. gene/protein expression, etc.).\nShould be in in tab-separated format (`*.tab`)\n", - "pattern": "*.tsv" - } - }, - { - "net": { - "type": "file", - "description": "The prior knowledge network linking the features of the\nexpression matrix to a process/component (e.g. gene set,\ntranscription factor, kinase, etc.)\n", - "pattern": "*.tsv" - } - }, - { - "args": { - "type": "string", - "description": "Keyword arguments passed to `decoupler.decouple()` (see\ndocumentation for more information here:\nhttps://decoupler-py.readthedocs.io/en/latest/generated/decoupler.decouple.html#decoupler.decouple).\nArguments specific for a method must be specified with\nthe method name as a prefix e.g. `'gsea_batch_size'`\n", - "pattern": "{arg: val, ..., method_arg: val}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" - } - }, - { - "dc_estimate": { - "type": "file", - "description": "The file containing the estimation results of the enrichment(s)\n", - "pattern": "*estimate__decoupler.tsv" - } - }, - { - "dc_pvals": { - "type": "file", - "description": "The file containing the p-value associated to the estimation\nresults of the enrichment(s)\n", - "pattern": "*pvals__decoupler.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:decoupler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" + } + }, + { + "mat": { + "type": "file", + "description": "Path to the matrix file (e.g. gene/protein expression, etc.).\nShould be in in tab-separated format (`*.tab`)\n", + "pattern": "*.tsv" + } + } + ], + [ + { + "net": { + "type": "file", + "description": "The prior knowledge network linking the features of the\nexpression matrix to a process/component (e.g. gene set,\ntranscription factor, kinase, etc.)\n", + "pattern": "*.tsv" + } + } + ] + ], + "output": [ + { + "dc_estimate": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" + } + }, + { + "*estimate__decoupler.tsv": { + "type": "file", + "description": "The file containing the estimation results of the enrichment(s)\n", + "pattern": "*estimate__decoupler.tsv" + } + } + ] + }, + { + "dc_pvals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:‘test’, single_end ]\n" + } + }, + { + "*pvals__decoupler.tsv": { + "type": "file", + "description": "The file containing the p-value associated to the estimation\nresults of the enrichment(s)\n", + "pattern": "*pvals__decoupler.tsv" + } + }, + { + "s": { + "type": "file", + "description": "The file containing the p-value associated to the estimation\nresults of the enrichment(s)\n", + "pattern": "*pvals__decoupler.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32782,66 +40928,107 @@ "doi": "10.1186/s13059-016-0918-z", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Deduplicated BAM file", - "pattern": "*_rmdup.bam" - } - }, - { - "json": { - "type": "file", - "description": "JSON file for MultiQC", - "pattern": "*.json" - } - }, - { - "hist": { - "type": "file", - "description": "Histogram data of amount of deduplication", - "pattern": "*.hist" - } - }, - { - "log": { - "type": "file", - "description": "Dedup log information", - "pattern": "*log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_rmdup.bam": { + "type": "file", + "description": "Deduplicated BAM file", + "pattern": "*_rmdup.bam" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file for MultiQC", + "pattern": "*.json" + } + } + ] + }, + { + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "Histogram data of amount of deduplication", + "pattern": "*.hist" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*log": { + "type": "file", + "description": "Dedup log information", + "pattern": "*log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32877,24 +41064,33 @@ "doi": "10.1186/s40168-018-0401-z", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "db/": { + "type": "directory", + "description": "Directory containing database required for deepARG.", + "pattern": "db/" + } + } + ] }, { - "db": { - "type": "directory", - "description": "Directory containing database required for deepARG.", - "pattern": "db/" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -32938,80 +41134,123 @@ "doi": "10.1186/s40168-018-0401-z", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing gene-like sequences", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "model": { - "type": "string", - "description": "Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively", - "pattern": "LS|LS" - } - }, - { - "db": { - "type": "directory", - "description": "Path to a directory containing the deepARG pre-built models", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "daa": { - "type": "file", - "description": "Sequences of ARG-like sequences from DIAMOND alignment", - "pattern": "*.align.daa" - } - }, - { - "daa_tsv": { - "type": "file", - "description": "Alignments scores against ARG-like sequences from DIAMOND alignment", - "pattern": "*.align.daa.tsv" - } - }, - { - "arg": { - "type": "file", - "description": "Table containing sequences with an ARG-like probability of more than specified thresholds", - "pattern": "*.mapping.ARG" - } - }, - { - "potential_arg": { - "type": "file", - "description": "Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection", - "pattern": "*.mapping.potential.ARG" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing gene-like sequences", + "pattern": "*.{fasta,fa,fna}" + } + }, + { + "model": { + "type": "string", + "description": "Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively", + "pattern": "LS|LS" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Path to a directory containing the deepARG pre-built models", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "daa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.align.daa": { + "type": "file", + "description": "Sequences of ARG-like sequences from DIAMOND alignment", + "pattern": "*.align.daa" + } + } + ] + }, + { + "daa_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.align.daa.tsv": { + "type": "file", + "description": "Alignments scores against ARG-like sequences from DIAMOND alignment", + "pattern": "*.align.daa.tsv" + } + } + ] + }, + { + "arg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapping.ARG": { + "type": "file", + "description": "Table containing sequences with an ARG-like probability of more than specified thresholds", + "pattern": "*.mapping.ARG" + } + } + ] + }, + { + "potential_arg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapping.potential.ARG": { + "type": "file", + "description": "Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection", + "pattern": "*.mapping.potential.ARG" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33057,24 +41296,33 @@ "doi": "10.1093/nar/gkz654", "licence": [ "MIT" - ] + ], + "identifier": "biotools:DeepBGC" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "deepbgc_db/": { + "type": "directory", + "description": "Directory containing the DeepBGC database", + "pattern": "deepbgc_db/" + } + } + ] }, { - "deepbgc_db": { - "type": "directory", - "description": "Contains reference database files", - "pattern": "deepbgc_db" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33118,121 +41366,234 @@ "doi": "10.1093/nar/gkz654", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "genome": { - "type": "file", - "description": "FASTA/GenBank/Pfam CSV file", - "pattern": "*.{fasta,fa,fna,gbk,csv}" - } - }, - { - "db": { - "type": "directory", - "description": "Database path" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "readme": { - "type": "file", - "description": "txt file containing description of output files", - "pattern": "*.{txt}" - } - }, - { - "log": { - "type": "file", - "description": "Log output of DeepBGC", - "pattern": "*.{txt}" - } - }, - { - "json": { - "type": "file", - "description": "AntiSMASH JSON file for sideloading", - "pattern": "*.{json}" - } - }, - { - "bgc_gbk": { - "type": "file", - "description": "Sequences and features of all detected BGCs in GenBank format", - "pattern": "*.{bgc.gbk}" - } - }, - { - "bgc_tsv": { - "type": "file", - "description": "Table of detected BGCs and their properties", - "pattern": "*.{bgc.tsv}" - } - }, - { - "full_gbk": { - "type": "file", - "description": "Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features)", - "pattern": "*.{full.gbk}" - } - }, - { - "pfam_tsv": { - "type": "file", - "description": "Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores", - "pattern": "*.{pfam.tsv}" - } - }, - { - "bgc_png": { - "type": "file", - "description": "Detected BGCs plotted by their nucleotide coordinates", - "pattern": "*.{bgc.png}" - } - }, - { - "pr_png": { - "type": "file", - "description": "Precision-Recall curve based on predicted per-Pfam BGC scores", - "pattern": "*.{pr.png}" - } - }, - { - "roc_png": { - "type": "file", - "description": "ROC curve based on predicted per-Pfam BGC scores", - "pattern": "*.{roc.png}" - } - }, - { - "score_png": { - "type": "file", - "description": "BGC detection scores of each Pfam domain in genomic order", - "pattern": "*.{score.png}" - } + ], + "identifier": "biotools:DeepBGC" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "genome": { + "type": "file", + "description": "FASTA/GenBank/Pfam CSV file", + "pattern": "*.{fasta,fa,fna,gbk,csv}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Database path" + } + } + ] + ], + "output": [ + { + "readme": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/README.txt": { + "type": "file", + "description": "txt file containing description of output files", + "pattern": "*.{txt}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/LOG.txt": { + "type": "file", + "description": "Log output of DeepBGC", + "pattern": "*.{txt}" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/${prefix}.antismash.json": { + "type": "file", + "description": "AntiSMASH JSON file for sideloading", + "pattern": "*.{json}" + } + } + ] + }, + { + "bgc_gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/${prefix}.bgc.gbk": { + "type": "file", + "description": "Sequences and features of all detected BGCs in GenBank format", + "pattern": "*.{bgc.gbk}" + } + } + ] + }, + { + "bgc_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/${prefix}.bgc.tsv": { + "type": "file", + "description": "Table of detected BGCs and their properties", + "pattern": "*.{bgc.tsv}" + } + } + ] + }, + { + "full_gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/${prefix}.full.gbk": { + "type": "file", + "description": "Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features)", + "pattern": "*.{full.gbk}" + } + } + ] + }, + { + "pfam_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/${prefix}.pfam.tsv": { + "type": "file", + "description": "Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores", + "pattern": "*.{pfam.tsv}" + } + } + ] + }, + { + "bgc_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/evaluation/${prefix}.bgc.png": { + "type": "file", + "description": "Detected BGCs plotted by their nucleotide coordinates", + "pattern": "*.{bgc.png}" + } + } + ] + }, + { + "pr_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/evaluation/${prefix}.pr.png": { + "type": "file", + "description": "Precision-Recall curve based on predicted per-Pfam BGC scores", + "pattern": "*.{pr.png}" + } + } + ] + }, + { + "roc_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/evaluation/${prefix}.roc.png": { + "type": "file", + "description": "ROC curve based on predicted per-Pfam BGC scores", + "pattern": "*.{roc.png}" + } + } + ] + }, + { + "score_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/evaluation/${prefix}.score.png": { + "type": "file", + "description": "BGC detection scores of each Pfam domain in genomic order", + "pattern": "*.{score.png}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33273,58 +41634,71 @@ "doi": "10.1038/s41587-021-01094-0", "licence": [ "APACHE2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "img": { - "type": "file", - "description": "Multichannel image file", - "pattern": "*.{tiff,tif,h5,hdf5}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "membrane_img": { - "type": "file", - "description": "Optional membrane image to be provided separately.", - "pattern": "*.{tiff,tif,h5,hdf5}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mask": { - "type": "file", - "description": "File containing the mask.", - "pattern": "*.{tif, tiff}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deepcell" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "img": { + "type": "file", + "description": "Multichannel image file", + "pattern": "*.{tiff,tif,h5,hdf5}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "membrane_img": { + "type": "file", + "description": "Optional membrane image to be provided separately.", + "pattern": "*.{tiff,tif,h5,hdf5}" + } + } + ] + ], + "output": [ + { + "mask": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tif": { + "type": "file", + "description": "File containing the mask.", + "pattern": "*.{tif, tiff}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33368,73 +41742,124 @@ "doi": "10.1101/2022.04.08.487609", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Database of sequences in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Predicted topologies (inside, outside, TMhelix) in general Feature Format Version 3", - "pattern": "biolib_results/TMRs.gff3" - } - }, - { - "line3": { - "type": "file", - "description": "Predicted topologies and information of protein sequences in three lines (name, sequence, topology)", - "pattern": "biolib_results/predicted_topologies.3line" - } - }, - { - "md": { - "type": "file", - "description": "Markdown results file", - "pattern": "biolib_results/deeptmhmm_results.md" - } - }, - { - "csv": { - "type": "file", - "description": "CSV file with per-residue predictions for the likelihood of each amino acid being in structural regions such as Beta-sheet, Periplasm, Membrane, Inside, Outside or Signal (only when querying against genomic fasta)", - "pattern": "biolib_results/*_probs.csv" - } - }, - { - "png": { - "type": "file", - "description": "Most likely topology probability line plots (only when querying against genomic fasta)", - "pattern": "biolib_results/plot.png" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Database of sequences in FASTA format", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ] + ], + "output": [ + { + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "biolib_results/TMRs.gff3": { + "type": "file", + "description": "Predicted topologies (inside, outside, TMhelix) in general Feature Format Version 3", + "pattern": "biolib_results/TMRs.gff3" + } + } + ] + }, + { + "line3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "biolib_results/predicted_topologies.3line": { + "type": "file", + "description": "Predicted topologies and information of protein sequences in three lines (name, sequence, topology)", + "pattern": "biolib_results/predicted_topologies.3line" + } + } + ] + }, + { + "md": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "biolib_results/deeptmhmm_results.md": { + "type": "file", + "description": "Markdown results file", + "pattern": "biolib_results/deeptmhmm_results.md" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "biolib_results/*_probs.csv": { + "type": "file", + "description": "CSV file with per-residue predictions for the likelihood of each amino acid being in structural regions such as Beta-sheet, Periplasm, Membrane, Inside, Outside or Signal (only when querying against genomic fasta)", + "pattern": "biolib_results/*_probs.csv" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "biolib_results/plot.png": { + "type": "file", + "description": "Most likely topology probability line plots (only when querying against genomic fasta)", + "pattern": "biolib_results/plot.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33467,73 +41892,98 @@ "doi": "10.1093/nar/gkw257", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM file was created with (required with CRAM input)", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference file (optional, but recommended)", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bigWig": { - "type": "file", - "description": "BigWig file", - "pattern": "*.bigWig" - } - }, - { - "bedgraph": { - "type": "file", - "description": "Bedgraph file", - "pattern": "*.bedgraph" - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference file the CRAM file was created with (required with CRAM input)", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference file (optional, but recommended)", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "bigwig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bigWig": { + "type": "file", + "description": "BigWig file", + "pattern": "*.bigWig" + } + } + ] + }, + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedgraph": { + "type": "file", + "description": "Bedgraph file", + "pattern": "*.bedgraph" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33580,59 +42030,82 @@ "doi": "10.1093/nar/gku365", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bigwig": { - "type": "file", - "description": "bigwig file containing genomic scores", - "pattern": "*.{bw,bigwig}" - } - }, - { - "bed": { - "type": "file", - "description": "bed file containing genomic regions", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "gzipped matrix file needed by the plotHeatmap and plotProfile\ndeeptools utilities\n", - "pattern": "*.{computeMatrix.mat.gz}" - } - }, - { - "table": { - "type": "file", - "description": "tabular file containing the scores of the generated matrix\n", - "pattern": "*.{computeMatrix.vals.mat.tab}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bigwig": { + "type": "file", + "description": "bigwig file containing genomic scores", + "pattern": "*.{bw,bigwig}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "bed file containing genomic regions", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mat.gz": { + "type": "file", + "description": "gzipped matrix file needed by the plotHeatmap and plotProfile\ndeeptools utilities\n", + "pattern": "*.{computeMatrix.mat.gz}" + } + } + ] + }, + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mat.tab": { + "type": "file", + "description": "tabular file containing the scores of the generated matrix\n", + "pattern": "*.{computeMatrix.vals.mat.tab}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33685,58 +42158,69 @@ "doi": "10.1093/nar/gku365", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "One or more BAM files", - "pattern": "*.{bam}" - } - }, - { - "bais": { - "type": "file", - "description": "Corresponding BAM file indexes", - "pattern": "*.bam.bai" - } - }, - { - "labels": { - "type": "string", - "description": "User specified labels instead of default labels (file names)." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "compressed numpy array of read coverage data used by plotCorrelation and plotPCA\ndeeptool utilities\n", - "pattern": "all_bam.bamSummary.npz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "One or more BAM files", + "pattern": "*.{bam}" + } + }, + { + "bais": { + "type": "file", + "description": "Corresponding BAM file indexes", + "pattern": "*.bam.bai" + } + }, + { + "labels": { + "type": "string", + "description": "User specified labels instead of default labels (file names)." + } + } + ] + ], + "output": [ + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.npz": { + "type": "file", + "description": "compressed numpy array of read coverage data used by plotCorrelation and plotPCA\ndeeptool utilities\n", + "pattern": "all_bam.bamSummary.npz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33779,66 +42263,91 @@ "doi": "10.1093/nar/gku365", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "compressed matrix file produced by\nmutlibamsummary or multibigwigsummary\n", - "pattern": "*.{npz}" - } - }, - { - "method": { - "type": "string", - "description": "Correlation coefficient to use for heatmap or scatterplot generation\n", - "pattern": "{spearman,pearson}" - } - }, - { - "plot_type": { - "type": "string", - "description": "Type of output plot to display sample correlation\n", - "pattern": "{heatmap,scatterplot}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotCorrelation.pdf}" - } - }, - { - "matrix": { - "type": "file", - "description": "Tab-separated file containing a matrix of pairwise correlations\n", - "pattern": "*.{plotCorrelation.mat.tab}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "matrix": { + "type": "file", + "description": "compressed matrix file produced by\nmutlibamsummary or multibigwigsummary\n", + "pattern": "*.{npz}" + } + } + ], + [ + { + "method": { + "type": "string", + "description": "Correlation coefficient to use for heatmap or scatterplot generation\n", + "pattern": "{spearman,pearson}" + } + } + ], + [ + { + "plot_type": { + "type": "string", + "description": "Type of output plot to display sample correlation\n", + "pattern": "{heatmap,scatterplot}" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Output figure containing resulting plot\n", + "pattern": "*.{plotCorrelation.pdf}" + } + } + ] + }, + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "Tab-separated file containing a matrix of pairwise correlations\n", + "pattern": "*.{plotCorrelation.mat.tab}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33881,66 +42390,97 @@ "doi": "10.1093/nar/gku365", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "One or more BAM files", - "pattern": "*.{bam}" - } - }, - { - "bais": { - "type": "file", - "description": "Corresponding BAM file indexes", - "pattern": "*.bam.bai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotFingerprint.pdf}" - } - }, - { - "matrix": { - "type": "file", - "description": "Output file summarizing the read counts per bin\n", - "pattern": "*.{plotFingerprint.raw.txt}" - } - }, - { - "metrics": { - "type": "file", - "description": "file containing BAM file quality metrics\n", - "pattern": "*.{qcmetrics.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "BAM files", + "pattern": "*.bam" + } + }, + { + "bais": { + "type": "file", + "description": "Corresponding BAM file indexes", + "pattern": "*.bam.bai" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Output figure containing resulting plot\n", + "pattern": "*.{plotFingerprint.pdf}" + } + } + ] + }, + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.raw.txt": { + "type": "file", + "description": "Output file summarizing the read counts per bin\n", + "pattern": "*.{plotFingerprint.raw.txt}" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.qcmetrics.txt": { + "type": "file", + "description": "file containing BAM file quality metrics\n", + "pattern": "*.{qcmetrics.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -33995,52 +42535,72 @@ "doi": "10.1093/nar/gku365", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "gzipped matrix file produced by deeptools_\ncomputematrix deeptools utility\n", - "pattern": "*.{mat.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotHeatmap.pdf}" - } - }, - { - "matrix": { - "type": "file", - "description": "File containing the matrix of values\nused to generate the heatmap\n", - "pattern": "*.{plotHeatmap.mat.tab}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "matrix": { + "type": "file", + "description": "gzipped matrix file produced by deeptools_\ncomputematrix deeptools utility\n", + "pattern": "*.{mat.gz}" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Output figure containing resulting plot\n", + "pattern": "*.{plotHeatmap.pdf}" + } + } + ] + }, + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "Output table" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -34091,52 +42651,73 @@ "doi": "10.1093/nar/gku365", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "compressed matrix file produced by\nmutlibamsummary or multibigwigsummary\n", - "pattern": "*.{npz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotPCA.pdf}" - } - }, - { - "tab": { - "type": "file", - "description": "Tab file containing data used to generate the PCA plot\n", - "pattern": "*.{plotPCA.tab}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "matrix": { + "type": "file", + "description": "compressed matrix file produced by\nmutlibamsummary or multibigwigsummary\n", + "pattern": "*.{npz}" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Output figure containing resulting plot\n", + "pattern": "*.{plotPCA.pdf}" + } + } + ] + }, + { + "tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "Tab file containing data used to generate the PCA plot\n", + "pattern": "*.{plotPCA.tab}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -34179,58 +42760,79 @@ "doi": "10.1093/nar/gku365", "licence": [ "GPL v3" - ] - } + ], + "identifier": "biotools:deeptools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "matrix": { + "type": "file", + "description": "gzipped matrix file produced by deeptools_\ncomputematrix deeptools utility\n", + "pattern": "*.{mat.gz}" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Output figure containing resulting plot\n", + "pattern": "*.{plotProfile.pdf}" + } + } + ] + }, + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "Output table", + "pattern": "*.tab" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "gzipped matrix file produced by deeptools_\ncomputematrix deeptools utility\n", - "pattern": "*.{mat.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pdf": { - "type": "file", - "description": "Output figure containing resulting plot\n", - "pattern": "*.{plotProfile.pdf}" - } - }, - { - "matrix": { - "type": "file", - "description": "File containing the matrix of values\nused to generate the profile\n", - "pattern": "*.{plotProfile.mat.tab}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@edmundmiller", - "@drpatelh", - "@joseespinosa" + "authors": [ + "@edmundmiller", + "@drpatelh", + "@joseespinosa" ], "maintainers": [ "@edmundmiller", @@ -34271,118 +42873,180 @@ "doi": "10.1038/nbt.4235", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.bam/cram" - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.bai/crai" - } - }, - { - "interval": { - "type": "file", - "description": "Interval file for targeted regions", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gzi": { - "type": "file", - "description": "GZI index of reference fasta file", - "pattern": "*.gzi" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "par_bed": { - "type": "file", - "description": "BED file containing PAR regions", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "gvcf": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.txt}" - } + ], + "identifier": "biotools:deepvariant" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.bam/cram" + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.bai/crai" + } + }, + { + "intervals": { + "type": "file", + "description": "file containing intervals" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gzi": { + "type": "file", + "description": "GZI index of reference fasta file", + "pattern": "*.gzi" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "par_bed": { + "type": "file", + "description": "BED file containing PAR regions", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index of compressed VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "gvcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.g.vcf.gz": { + "type": "file", + "description": "Compressed GVCF file", + "pattern": "*.g.vcf.gz" + } + } + ] + }, + { + "gvcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.g.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index of compressed GVCF file", + "pattern": "*.g.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -34431,38 +43095,55 @@ "doi": "10.1038/nbt.4235", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "biotools:deepvariant" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "make_examples_tfrecords": { - "type": "file", - "description": "The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process", - "pattern": "*.gz" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "make_examples_tfrecords": { + "type": "file", + "description": "The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process", + "pattern": "*.gz" + } } - } + ] ], "output": [ { - "call_variants_tfrecords": { - "type": "list", - "description": "Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls.\n" - } + "call_variants_tfrecords": [ + { + "meta": { + "type": "list", + "description": "Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls.\n" + } + }, + { + "${prefix}.call-*-of-*.tfrecord.gz": { + "type": "list", + "description": "Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls.\n" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -34498,110 +43179,145 @@ "doi": "10.1038/nbt.4235", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.bam/cram" - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.bai/crai" - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file for targeted regions", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gzi": { - "type": "file", - "description": "GZI index of reference fasta file" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n", - "pattern": "*.gzi" - } - }, - { - "par_bed": { - "type": "file", - "description": "BED file containing PAR regions", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "examples": { - "type": "list", - "description": "Tuple containing sample metadata and examples that can be used for calling\n" - } - }, - { - "gvcf": { - "type": "list", - "description": "Tuple containing sample metadata and the GVCF data in tfrecord format\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing the DeepVariant software version", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deepvariant" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.bam/cram" + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.bai/crai" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file for targeted regions", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gzi": { + "type": "file", + "description": "GZI index of reference fasta file" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n", + "pattern": "*.gzi" + } + }, + { + "par_bed": { + "type": "file", + "description": "BED file containing PAR regions", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "examples": [ + { + "meta": { + "type": "list", + "description": "Tuple containing sample metadata and examples that can be used for calling\n" + } + }, + { + "${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}": { + "type": "list", + "description": "Tuple containing sample metadata and examples that can be used for calling\n" + } + } + ] + }, + { + "gvcf": [ + { + "meta": { + "type": "list", + "description": "Tuple containing sample metadata and the GVCF data in tfrecord format\n" + } + }, + { + "${prefix}.gvcf.tfrecord-*-of-*.gz": { + "type": "list", + "description": "Tuple containing sample metadata and the GVCF data in tfrecord format\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing the DeepVariant software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -34637,112 +43353,159 @@ "doi": "10.1038/nbt.4235", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variant_calls_tfrecord_files": { - "type": "file", - "description": "One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS\n", - "pattern": "*.tfrecord.gz" - } - }, - { - "gvcf_tfrecords": { - "type": "file", - "description": "Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output\n", - "pattern": "*.gz" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gzi": { - "type": "file", - "description": "GZI index of reference fasta file", - "pattern": "*.gzi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Index for VCF", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "gvcf": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz" - } - }, - { - "gvcf_tbi": { - "type": "file", - "description": "Index for GVCF", - "pattern": "*.g.vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deepvariant" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "variant_calls_tfrecord_files": { + "type": "file", + "description": "One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS\n", + "pattern": "*.tfrecord.gz" + } + }, + { + "gvcf_tfrecords": { + "type": "file", + "description": "Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output\n", + "pattern": "*.gz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gzi": { + "type": "file", + "description": "GZI index of reference fasta file", + "pattern": "*.gzi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf.gz.tbi": { + "type": "file", + "description": "Index for VCF", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "gvcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.g.vcf.gz": { + "type": "file", + "description": "Compressed GVCF file", + "pattern": "*.g.vcf.gz" + } + } + ] + }, + { + "gvcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.g.vcf.gz.tbi": { + "type": "file", + "description": "Index for GVCF", + "pattern": "*.g.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -34778,118 +43541,180 @@ "doi": "10.1038/nbt.4235", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.bam/cram" - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.bai/crai" - } - }, - { - "interval": { - "type": "file", - "description": "Interval file for targeted regions", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gzi": { - "type": "file", - "description": "GZI index of reference fasta file", - "pattern": "*.gzi" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "par_bed": { - "type": "file", - "description": "BED file containing PAR regions", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "gvcf": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.txt}" - } + ], + "identifier": "biotools:deepvariant" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.bam/cram" + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.bai/crai" + } + }, + { + "intervals": { + "type": "file", + "description": "file containing intervals" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gzi": { + "type": "file", + "description": "GZI index of reference fasta file", + "pattern": "*.gzi" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "par_bed": { + "type": "file", + "description": "BED file containing PAR regions", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index file of compressed VCF", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "gvcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.g.vcf.gz": { + "type": "file", + "description": "Compressed GVCF file", + "pattern": "*.g.vcf.gz" + } + } + ] + }, + { + "gvcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.g.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index file of compressed GVCF", + "pattern": "*.g.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -34924,106 +43749,131 @@ "doi": "10.1093/bioinformatics/bts378", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "vcf": { - "type": "file", - "description": "A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped", - "pattern": "*.{vcf.gz,bcf}" - } - }, - { - "vcf_index": { - "type": "file", - "description": "The index of the BCF/VCF file", - "pattern": "*.{tbi,csi}" - } - }, - { - "exclude_bed": { - "type": "file", - "description": "An optional bed file containing regions to exclude from the called VCF", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file to identify split-reads", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bcf": { - "type": "file", - "description": "Called variants in BCF/VCF format. Specify either \"bcf\" or \"vcf\" in ext.suffix to define the output type", - "pattern": "*.{bcf,vcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "A generated csi index that matches the bcf output (not generated for vcf files)", - "pattern": "*.{bcf.csi}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + }, + { + "vcf": { + "type": "file", + "description": "A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped", + "pattern": "*.{vcf.gz,bcf}" + } + }, + { + "vcf_index": { + "type": "file", + "description": "The index of the BCF/VCF file", + "pattern": "*.{tbi,csi}" + } + }, + { + "exclude_bed": { + "type": "file", + "description": "An optional bed file containing regions to exclude from the called VCF", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file to identify split-reads", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "bcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{bcf,vcf.gz}": { + "type": "file", + "description": "Called variants in BCF/VCF format. Specify either \"bcf\" or \"vcf\" in ext.suffix to define the output type", + "pattern": "*.{bcf,vcf.gz}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{csi,tbi}": { + "type": "file", + "description": "A generated csi index that matches the bcf output (not generated for vcf files)", + "pattern": "*.{bcf.csi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35058,82 +43908,111 @@ "doi": "10.1038/s41467-019-10756-2", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input_raw_gene_bc_matrices_h5": { - "type": "string", - "description": "Path to file containing input raw RNA expression matrix in 10x hdf5 format\npattern: \"*.{h5}\"\n" - } - }, - { - "input_hto_csv_file": { - "type": "string", - "description": "Path to file containing input HTO (antibody tag) count matrix in CSV format.\n", - "pattern": "*.{csv}" - } - }, - { - "output_name": { - "type": "string", - "description": "Output name. All outputs will use it as the prefix.\n" - } - }, - { - "generate_gender_plot": { - "type": "string", - "description": "Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names.\n" - } - }, - { - "genome": { - "type": "string", - "description": "Reference genome name. If not provided, the tools infers it from the expression matrix file\n" - } - }, - { - "generate_diagnostic_plots": { - "type": "string", - "description": "Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "zarr": { - "type": "file", - "description": "RNA expression matrix with demultiplexed sample identities in Zarr format.\n", - "pattern": "*_demux.zarr.zip" - } - }, - { - "out_zarr": { - "type": "file", - "description": "DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA.\n", - "pattern": "*.out.demuxEM.zarr.zip" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input_raw_gene_bc_matrices_h5": { + "type": "string", + "description": "Path to file containing input raw RNA expression matrix in 10x hdf5 format\npattern: \"*.{h5}\"\n" + } + }, + { + "input_hto_csv_file": { + "type": "string", + "description": "Path to file containing input HTO (antibody tag) count matrix in CSV format.\n", + "pattern": "*.{csv}" + } + } + ], + [ + { + "output_name": { + "type": "string", + "description": "Output name. All outputs will use it as the prefix.\n" + } + } + ], + [ + { + "generate_gender_plot": { + "type": "string", + "description": "Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names.\n" + } + } + ], + [ + { + "genome": { + "type": "string", + "description": "Reference genome name. If not provided, the tools infers it from the expression matrix file\n" + } + } + ], + [ + { + "generate_diagnostic_plots": { + "type": "string", + "description": "Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions.\n" + } + } + ] + ], + "output": [ + { + "zarr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*_demux.zarr.zip": { + "type": "file", + "description": "RNA expression matrix with demultiplexed sample identities in Zarr format.\n", + "pattern": "*_demux.zarr.zip" + } + } + ] + }, + { + "out_zarr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.out.demuxEM.zarr.zip": { + "type": "file", + "description": "DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA.\n", + "pattern": "*.out.demuxEM.zarr.zip" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35173,148 +44052,260 @@ "doi": "10.1186/s13059-014-0550-8", "licence": [ "LGPL >=3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata\n" - } - }, - { - "counts": { - "type": "file", - "description": "Raw TSV or CSV format expression matrix as output from the nf-core\nRNA-seq workflow\n" - } - }, - { - "meta3": { - "type": "file", - "description": "Meta map describing control genes, e.g. [ id: 'ERCC' ]\n" - } - }, - { - "control_genes_file": { - "type": "file", - "description": "Text file listing control genes, one per line\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the transcript\nlengths file\n" - } - }, - { - "transcript_lengths_file": { - "type": "file", - "description": "Optional file of transcript lengths, with the same sample columns as\ncounts. If supplied, lengths will be supplied to DESeq2 to correct for\ndifferences in average transcript lengths across samples.\n" - } - } - ], - "output": [ - { - "results": { - "type": "file", - "description": "TSV-format table of differential expression information as output by DESeq2", - "pattern": "deseq2.results.tsv" - } - }, - { - "dispersion_plot": { - "type": "file", - "description": "DESeq2 dispersion plot", - "pattern": "deseq2.dispersion.png" - } - }, - { - "rdata": { - "type": "file", - "description": "Serialised DESeq2 object", - "pattern": "dds.rld.rds" - } - }, - { - "size_factors": { - "type": "file", - "description": "Size factors", - "pattern": "deseq2.sizefactors.tsv" - } - }, - { - "normalised_counts": { - "type": "file", - "description": "TSV-format counts matrix, normalised to size factors", - "pattern": "normalised_counts.tsv" - } - }, - { - "rlog_counts": { - "type": "file", - "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `rlog()`.\n", - "pattern": "rlog.tsv" - } - }, - { - "vst_counts": { - "type": "file", - "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `vst()`.\n", - "pattern": "vst_counts.tsv" - } - }, - { - "model": { - "type": "file", - "description": "TXT-format DESeq2 model", - "pattern": "deseq2.model.tsv" - } - }, - { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:deseq2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "contrast_variable": { + "type": "string", + "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" + } + }, + { + "reference": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" + } + }, + { + "target": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata\n" + } + }, + { + "counts": { + "type": "file", + "description": "Raw TSV or CSV format expression matrix as output from the nf-core\nRNA-seq workflow\n" + } + } + ], + [ + { + "meta3": { + "type": "file", + "description": "Meta map describing control genes, e.g. [ id: 'ERCC' ]\n" + } + }, + { + "control_genes_file": { + "type": "file", + "description": "Text file listing control genes, one per line\n" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the transcript\nlengths file\n" + } + }, + { + "transcript_lengths_file": { + "type": "file", + "description": "Optional file of transcript lengths, with the same sample columns as\ncounts. If supplied, lengths will be supplied to DESeq2 to correct for\ndifferences in average transcript lengths across samples.\n" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "file", + "description": "TSV-format table of differential expression information as output by DESeq2", + "pattern": "deseq2.results.tsv" + } + }, + { + "*.deseq2.results.tsv": { + "type": "file", + "description": "TSV-format table of differential expression information as output by DESeq2", + "pattern": "deseq2.results.tsv" + } + } + ] + }, + { + "dispersion_plot": [ + { + "meta": { + "type": "file", + "description": "DESeq2 dispersion plot", + "pattern": "deseq2.dispersion.png" + } + }, + { + "*.deseq2.dispersion.png": { + "type": "file", + "description": "DESeq2 dispersion plot", + "pattern": "deseq2.dispersion.png" + } + } + ] + }, + { + "rdata": [ + { + "meta": { + "type": "file", + "description": "Serialised DESeq2 object", + "pattern": "dds.rld.rds" + } + }, + { + "*.dds.rld.rds": { + "type": "file", + "description": "Serialised DESeq2 object", + "pattern": "dds.rld.rds" + } + } + ] + }, + { + "size_factors": [ + { + "meta": { + "type": "file", + "description": "Size factors", + "pattern": "deseq2.sizefactors.tsv" + } + }, + { + "*.deseq2.sizefactors.tsv": { + "type": "file", + "description": "Size factors", + "pattern": "deseq2.sizefactors.tsv" + } + } + ] + }, + { + "normalised_counts": [ + { + "meta": { + "type": "file", + "description": "TSV-format counts matrix, normalised to size factors", + "pattern": "normalised_counts.tsv" + } + }, + { + "*.normalised_counts.tsv": { + "type": "file", + "description": "TSV-format counts matrix, normalised to size factors", + "pattern": "normalised_counts.tsv" + } + } + ] + }, + { + "rlog_counts": [ + { + "meta": { + "type": "file", + "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `rlog()`.\n", + "pattern": "rlog.tsv" + } + }, + { + "*.rlog.tsv": { + "type": "file", + "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `rlog()`.\n", + "pattern": "rlog.tsv" + } + } + ] + }, + { + "vst_counts": [ + { + "meta": { + "type": "file", + "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `vst()`.\n", + "pattern": "vst_counts.tsv" + } + }, + { + "*.vst.tsv": { + "type": "file", + "description": "Optional, TSV-format counts matrix, normalised to size factors, with\nvariance stabilisation applied via `vst()`.\n", + "pattern": "vst_counts.tsv" + } + } + ] + }, + { + "model": [ + { + "meta": { + "type": "file", + "description": "TXT-format DESeq2 model", + "pattern": "deseq2.model.tsv" + } + }, + { + "*.deseq2.model.txt": { + "type": "file", + "description": "TXT-format DESeq2 model", + "pattern": "deseq2.model.tsv" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35358,113 +44349,190 @@ "doi": "10.1038/s41592-021-01101-x", "licence": [ "GPL v3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing query sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "file", - "description": "File of the indexed DIAMOND database", - "pattern": "*.dmnd" - } - }, - { - "out_ext": { - "type": "string", - "description": "Specify the type of output file to be generated. `blast` corresponds to\nBLAST pairwise format. `xml` corresponds to BLAST xml format.\n`txt` corresponds to to BLAST tabular format. `tsv` corresponds to\ntaxonomic classification format.\n", - "pattern": "blast|xml|txt|daa|sam|tsv|paf" - } - }, - { - "blast_columns": { - "type": "string", - "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused for in conjunction with the 'txt' out_ext option (--outfmt 6). Options:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "blast": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{blast}" - } - }, - { - "xml": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{xml}" - } - }, - { - "txt": { - "type": "file", - "description": "File containing hits in tabular BLAST format.", - "pattern": "*.{txt}" - } - }, - { - "daa": { - "type": "file", - "description": "File containing hits DAA format", - "pattern": "*.{daa}" - } - }, - { - "sam": { - "type": "file", - "description": "File containing aligned reads in SAM format", - "pattern": "*.{sam}" - } - }, - { - "tsv": { - "type": "file", - "description": "Tab separated file containing taxonomic classification of hits", - "pattern": "*.{tsv}" - } - }, - { - "paf": { - "type": "file", - "description": "File containing aligned reads in pairwise mapping format format", - "pattern": "*.{paf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing query sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "file", + "description": "File of the indexed DIAMOND database", + "pattern": "*.dmnd" + } + } + ], + [ + { + "out_ext": { + "type": "string", + "description": "Specify the type of output file to be generated. `blast` corresponds to\nBLAST pairwise format. `xml` corresponds to BLAST xml format.\n`txt` corresponds to to BLAST tabular format. `tsv` corresponds to\ntaxonomic classification format.\n", + "pattern": "blast|xml|txt|daa|sam|tsv|paf" + } + } + ], + [ + { + "blast_columns": { + "type": "string", + "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused for in conjunction with the 'txt' out_ext option (--outfmt 6). Options:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" + } + } + ] + ], + "output": [ + { + "blast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.blast": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{blast}" + } + } + ] + }, + { + "xml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{xml}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing hits in tabular BLAST format.", + "pattern": "*.{txt}" + } + } + ] + }, + { + "daa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.daa": { + "type": "file", + "description": "File containing hits DAA format", + "pattern": "*.{daa}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "File containing aligned reads in SAM format", + "pattern": "*.{sam}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab separated file containing taxonomic classification of hits", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "paf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "File containing aligned reads in pairwise mapping format format", + "pattern": "*.{paf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35501,120 +44569,207 @@ "doi": "10.1038/s41592-021-01101-x", "licence": [ "GPL v3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing query sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "db": { - "type": "file", - "description": "File of the indexed DIAMOND database", - "pattern": "*.dmnd" - } - }, - { - "out_ext": { - "type": "string", - "description": "Specify the type of output file to be generated. `blast` corresponds to\nBLAST pairwise format. `xml` corresponds to BLAST xml format.\n`txt` corresponds to to BLAST tabular format. `tsv` corresponds to\ntaxonomic classification format.\n", - "pattern": "blast|xml|txt|daa|sam|tsv|paf" - } - }, - { - "blast_columns": { - "type": "string", - "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused for in conjunction with the 'txt' out_ext option (--outfmt 6). Options:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "blast": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{blast}" - } - }, - { - "xml": { - "type": "file", - "description": "File containing blastp hits", - "pattern": "*.{xml}" - } - }, - { - "txt": { - "type": "file", - "description": "File containing hits in tabular BLAST format.", - "pattern": "*.{txt}" - } - }, - { - "daa": { - "type": "file", - "description": "File containing hits DAA format", - "pattern": "*.{daa}" - } - }, - { - "sam": { - "type": "file", - "description": "File containing aligned reads in SAM format", - "pattern": "*.{sam}" - } - }, - { - "tsv": { - "type": "file", - "description": "Tab separated file containing taxonomic classification of hits", - "pattern": "*.{tsv}" - } - }, - { - "paf": { - "type": "file", - "description": "File containing aligned reads in pairwise mapping format format", - "pattern": "*.{paf}" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing stdout information", - "pattern": "*.{log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing query sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing db information\ne.g. [ id:'test2', single_end:false ]\n" + } + }, + { + "db": { + "type": "file", + "description": "File of the indexed DIAMOND database", + "pattern": "*.dmnd" + } + } + ], + [ + { + "out_ext": { + "type": "string", + "description": "Specify the type of output file to be generated. `blast` corresponds to\nBLAST pairwise format. `xml` corresponds to BLAST xml format.\n`txt` corresponds to to BLAST tabular format. `tsv` corresponds to\ntaxonomic classification format.\n", + "pattern": "blast|xml|txt|daa|sam|tsv|paf" + } + } + ], + [ + { + "blast_columns": { + "type": "string", + "description": "Optional space separated list of DIAMOND tabular BLAST output keywords\nused for in conjunction with the 'txt' out_ext option (--outfmt 6). Options:\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n" + } + } + ] + ], + "output": [ + { + "blast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.blast": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{blast}" + } + } + ] + }, + { + "xml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "File containing blastp hits", + "pattern": "*.{xml}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing hits in tabular BLAST format.", + "pattern": "*.{txt}" + } + } + ] + }, + { + "daa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.daa": { + "type": "file", + "description": "File containing hits DAA format", + "pattern": "*.{daa}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "File containing aligned reads in SAM format", + "pattern": "*.{sam}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab separated file containing taxonomic classification of hits", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "paf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "File containing aligned reads in pairwise mapping format format", + "pattern": "*.{paf}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stdout information", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35659,45 +44814,56 @@ "doi": "10.1038/s41592-021-01101-x", "licence": [ "GPL v3-or-later" - ] + ], + "identifier": "biotools:diamond" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "db": { - "type": "file", - "description": "The input sequence database. Supported formats are FASTA and DIAMOND (.dmnd) format.", - "pattern": "*.{dmnd,fa,faa,fasta}(.gz)" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "db": { + "type": "file", + "description": "The input sequence database. Supported formats are FASTA and DIAMOND (.dmnd) format.", + "pattern": "*.{dmnd,fa,faa,fasta}(.gz)" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "a 2-column tabular file with the representative accession as the first column and the member sequence accession as the second column", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "a 2-column tabular file with the representative accession as the first column and the member sequence accession as the second column", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35731,66 +44897,83 @@ "doi": "10.1038/s41592-021-01101-x", "licence": [ "GPL v3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "taxonmap": { - "type": "file", - "description": "Optional mapping file of NCBI protein accession numbers to taxon ids (gzip compressed), required for taxonomy functionality.", - "pattern": "*.gz" - } - }, - { - "taxonnodes": { - "type": "file", - "description": "Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality.", - "pattern": "*.dmp" - } - }, - { - "taxonnames": { - "type": "file", - "description": "Optional NCBI taxonomy names.dmp file, required for taxonomy functionality.", - "pattern": "*.dmp" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "db": { - "type": "file", - "description": "File of the indexed DIAMOND database", - "pattern": "*.dmnd" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:diamond" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "taxonmap": { + "type": "file", + "description": "Optional mapping file of NCBI protein accession numbers to taxon ids (gzip compressed), required for taxonomy functionality.", + "pattern": "*.gz" + } + } + ], + [ + { + "taxonnodes": { + "type": "file", + "description": "Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality.", + "pattern": "*.dmp" + } + } + ], + [ + { + "taxonnames": { + "type": "file", + "description": "Optional NCBI taxonomy names.dmp file, required for taxonomy functionality.", + "pattern": "*.dmp" + } + } + ] + ], + "output": [ + { + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dmnd": { + "type": "file", + "description": "File of the indexed DIAMOND database", + "pattern": "*.dmnd" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35832,64 +45015,179 @@ "tool_dev_url": "https://github.com/Illumina/dragmap#basic-command-line-usage", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hashmap": { - "type": "file", - "description": "DRAGMAP hash table", - "pattern": "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta reference files", - "pattern": "*.{fa,fasta,fna}" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hashmap": { + "type": "file", + "description": "DRAGMAP hash table", + "pattern": "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta reference files", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "sort_bam": { + "type": "boolean", + "description": "Sort the BAM file" + } + } + ] + ], + "output": [ + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "Output SAM file containing read alignments", + "pattern": "*.{sam}" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file containing read alignments", + "pattern": "*.{cram}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "Index file for CRAM file", + "pattern": "*.{crai}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Index file for CRAM file", + "pattern": "*.{csi}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -35936,44 +45234,55 @@ "tool_dev_url": "https://github.com/Illumina/dragmap#basic-command-line-usage", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hashmap": { - "type": "file", - "description": "DRAGMAP hash table", - "pattern": "*.{cmp,.bin,.txt}" - } + "hashmap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dragmap": { + "type": "file", + "description": "DRAGMAP hash table", + "pattern": "*.{cmp,.bin,.txt}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36018,155 +45327,217 @@ "documentation": "https://github.com/rpetit3/dragonflye/blob/main/README.md", "licence": [ "GPL v2" - ] + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shortreads": { + "type": "file", + "description": "Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome.\n", + "pattern": "*.fastq.gz" + } + }, + { + "longreads": { + "type": "file", + "description": "Input Nanopore FASTQ file", + "pattern": "*.fastq.gz" + } + } + ] + ], + "output": [ + { + "contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "The final assembly produced by Dragonflye", + "pattern": "*.fa" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dragonflye.log": { + "type": "file", + "description": "Full log file for bug reporting", + "pattern": "dragonflye.log" + } + } + ] + }, + { + "raw_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "{flye,miniasm,raven}.fasta": { + "type": "file", + "description": "Raw assembly produced by the assembler (Flye, Miniasm, or Raven)", + "pattern": "{flye,miniasm,raven}.fasta" + } + } + ] + }, + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "{flye,miniasm,raven}-unpolished.gfa": { + "type": "file", + "description": "Assembly graph produced by Miniasm, or Raven", + "pattern": "{flye,miniasm,raven}-unpolished.gfa" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "flye-info.txt": { + "type": "file", + "description": "Assembly information output by Flye", + "pattern": "flye-info.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@rpetit3" + ], + "maintainers": [ + "@rpetit3" + ] + }, + "pipelines": [ + { + "name": "bacass", + "version": "2.3.1" + } + ] + }, + { + "name": "dshbio_exportsegments", + "path": "modules/nf-core/dshbio/exportsegments/meta.yml", + "type": "module", + "meta": { + "name": "dshbio_exportsegments", + "description": "Export assembly segment sequences in GFA 1.0 format to FASTA format", + "keywords": [ + "gfa", + "assembly", + "segment" + ], + "tools": [ + { + "dshbio": { + "description": "Reads, features, variants, assemblies, alignments, genomic range trees, pangenome\ngraphs, and a bunch of random command line tools for bioinformatics. LGPL version 3\nor later.\n", + "homepage": "https://github.com/heuermh/dishevelled-bio", + "documentation": "https://github.com/heuermh/dishevelled-bio", + "licence": [ + "LGPL-3.0-or-later" + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "shortreads": { - "type": "file", - "description": "Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome.\n", - "pattern": "*.fastq.gz" - } - }, - { - "longreads": { - "type": "file", - "description": "Input Nanopore FASTQ file", - "pattern": "*.fastq.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "contigs": { - "type": "file", - "description": "The final assembly produced by Dragonflye", - "pattern": "*.fa" - } - }, - { - "log": { - "type": "file", - "description": "Full log file for bug reporting", - "pattern": "dragonflye.log" - } - }, - { - "raw_contigs": { - "type": "file", - "description": "Raw assembly produced by the assembler (Flye, Miniasm, or Raven)", - "pattern": "{flye,miniasm,raven}.fasta" - } - }, - { - "txt": { - "type": "file", - "description": "Assembly information output by Flye", - "pattern": "flye-info.txt" - } - }, - { - "gfa": { - "type": "file", - "description": "Assembly graph produced by Miniasm, or Raven", - "pattern": "{flye,miniasm,raven}-unpolished.gfa" - } - } - ], - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.3.1" - } - ] - }, - { - "name": "dshbio_exportsegments", - "path": "modules/nf-core/dshbio/exportsegments/meta.yml", - "type": "module", - "meta": { - "name": "dshbio_exportsegments", - "description": "Export assembly segment sequences in GFA 1.0 format to FASTA format", - "keywords": [ - "gfa", - "assembly", - "segment" - ], - "tools": [ - { - "dshbio": { - "description": "Reads, features, variants, assemblies, alignments, genomic range trees, pangenome\ngraphs, and a bunch of random command line tools for bioinformatics. LGPL version 3\nor later.\n", - "homepage": "https://github.com/heuermh/dishevelled-bio", - "documentation": "https://github.com/heuermh/dishevelled-bio", - "licence": [ - "LGPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Assembly segments in uncompressed or compressed GFA 1.0 format", - "pattern": "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Assembly segments in uncompressed or compressed GFA 1.0 format", + "pattern": "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly segment sequences in gzipped FASTA format", - "pattern": "*.{fa.gz}" - } + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "Assembly segment sequences in gzipped FASTA format", + "pattern": "*.{fa.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36197,45 +45568,56 @@ "documentation": "https://github.com/heuermh/dishevelled-bio", "licence": [ "LGPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Features in gzipped BED format", - "pattern": "*.{bed.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Features in gzipped BED format", + "pattern": "*.{bed.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Features in gzipped BED format", - "pattern": "*.{bed.gz}" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Features in gzipped BED format", + "pattern": "*.{bed.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36266,45 +45648,56 @@ "documentation": "https://github.com/heuermh/dishevelled-bio", "licence": [ "LGPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Features in gzipped GFF3 format", - "pattern": "*.{gff3.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff3": { + "type": "file", + "description": "Features in gzipped GFF3 format", + "pattern": "*.{gff3.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Features in gzipped GFF3 format", - "pattern": "*.{gff3.gz}" - } + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gff3.gz": { + "type": "file", + "description": "Features in gzipped GFF3 format", + "pattern": "*.{gff3.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36335,45 +45728,56 @@ "documentation": "https://github.com/heuermh/dishevelled-bio", "licence": [ "LGPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Features in gzipped BED format to split", - "pattern": "*.{bed.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Features in gzipped BED format to split", + "pattern": "*.{bed.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Features in split gzipped BED formatted files", - "pattern": "*.{bed.gz}" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed.gz": { + "type": "file", + "description": "Features in split gzipped BED formatted files", + "pattern": "*.{bed.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36404,45 +45808,56 @@ "documentation": "https://github.com/heuermh/dishevelled-bio", "licence": [ "LGPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Features in gzipped GFF3 format to split", - "pattern": "*.{gff3.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff3": { + "type": "file", + "description": "Features in gzipped GFF3 format to split", + "pattern": "*.{gff3.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Features in split gzipped GFF3 formatted files", - "pattern": "*.{gff3.gz}" - } + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gff3.gz": { + "type": "file", + "description": "Features in split gzipped GFF3 formatted files", + "pattern": "*.{gff3.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36476,73 +45891,99 @@ "doi": "10.1093/gigascience/giz040", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "aligment_file": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "aligment_file_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "sv_variants": { - "type": "file", - "description": "A variants file containing structural variants", - "pattern": "*.{vcf,bcf}(.gz)?" - } - }, - { - "snp_variants": { - "type": "file", - "description": "A variants file containing SNPs", - "pattern": "*.{vcf,bcf}(.gz)?" - } - }, - { - "snp_variants": { - "type": "file", - "description": "The index of the variants file containing SNPs", - "pattern": "*.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The output VCF", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment_file": { + "type": "file", + "description": "file containing alignments" + } + }, + { + "alignement_index": { + "type": "file", + "description": "index of alignment file" + } + }, + { + "sv_variants": { + "type": "file", + "description": "A variants file containing structural variants", + "pattern": "*.{vcf,bcf}(.gz)?" + } + }, + { + "snp_variants": { + "type": "file", + "description": "A variants file containing SNPs", + "pattern": "*.{vcf,bcf}(.gz)?" + } + }, + { + "snp_variants_index": { + "type": "file", + "description": "index of snp variants file" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Index of fasta file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The output VCF", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36575,100 +46016,173 @@ "doi": "10.1186/s12859-016-1276-2", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'human' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Genomic features annotation in GTF or SAF", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "scatter2d": { - "type": "file", - "description": "PDF duplication rate against total read count plot", - "pattern": "*_duprateExpDens.pdf" - } - }, - { - "boxplot": { - "type": "file", - "description": "PDF duplication rate ~ total reads per kilobase (RPK) boxplot\n", - "pattern": "*_duprateExpBoxplot.pdf" - } - }, - { - "hist": { - "type": "file", - "description": "PDF expression histogram\n", - "pattern": "*.pdf" - } - }, - { - "dupmatrix": { - "type": "file", - "description": "Text file containing tags falling on the features described in the GTF\nfile\n", - "pattern": "*_dupMatrix.txt" - } - }, - { - "intercept_slope": { - "type": "file", - "description": "Text file containing intercept and slope from dupRadar modelling\n", - "pattern": "*_intercept_slope.txt" - } - }, - { - "multiqc": { - "type": "file", - "description": "dupRadar files for passing to MultiQC\n", - "pattern": "*_multiqc.txt" - } - }, - { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:dupradar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'human' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Genomic features annotation in GTF or SAF", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "scatter2d": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_duprateExpDens.pdf": { + "type": "file", + "description": "PDF duplication rate against total read count plot", + "pattern": "*_duprateExpDens.pdf" + } + } + ] + }, + { + "boxplot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_duprateExpBoxplot.pdf": { + "type": "file", + "description": "PDF duplication rate ~ total reads per kilobase (RPK) boxplot\n", + "pattern": "*_duprateExpBoxplot.pdf" + } + } + ] + }, + { + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_expressionHist.pdf": { + "type": "file", + "description": "PDF expression histogram\n", + "pattern": "*.pdf" + } + } + ] + }, + { + "dupmatrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_dupMatrix.txt": { + "type": "file", + "description": "Text file containing tags falling on the features described in the GTF\nfile\n", + "pattern": "*_dupMatrix.txt" + } + } + ] + }, + { + "intercept_slope": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_intercept_slope.txt": { + "type": "file", + "description": "Text file containing intercept and slope from dupRadar modelling\n", + "pattern": "*_intercept_slope.txt" + } + } + ] + }, + { + "multiqc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_mqc.txt": { + "type": "file", + "description": "dupRadar files for passing to MultiQC\n", + "pattern": "*_multiqc.txt" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36707,79 +46221,102 @@ "doi": "10.1093/nar/gkac039", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.bam" - } - }, - { - "index": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with identified structural variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "The index of the BCF/VCF file", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.bam" + } + }, + { + "index": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}" + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with identified structural variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample1' ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the BCF/VCF file", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36812,59 +46349,90 @@ "tool_dev_url": "https://github.com/phac-nml/ecoli_serotyping", "licence": [ "Apache 2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA formatted assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "ectyper log output", - "pattern": "*.log" - } - }, - { - "tsv": { - "type": "file", - "description": "ectyper serotyping results in TSV format", - "pattern": "*.tsv" - } - }, - { - "txt": { - "type": "file", - "description": "Allele report generated from BLAST results", - "pattern": "*.tst" - } + ], + "identifier": "biotools:ectyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA formatted assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "ectyper log output", + "pattern": "*.log" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "ectyper serotyping results in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Allele report generated from BLAST results", + "pattern": "*.tst" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -36897,158 +46465,210 @@ "doi": "10.1093/molbev/msab293", "licence": [ "AGPL v3" - ] + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Database of sequences in FASTA format", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ], + [ + { + "eggnog_db": { + "type": "file", + "description": "The eggnog database file (e.g. eggnog-mapper/data/eggnog.db)", + "pattern": "*.db" + } + } + ], + [ + { + "eggnog_data_dir": { + "type": "directory", + "description": "Directory containing eggnog database files (e.g. eggnog-mapper/data)", + "pattern": "*" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing database information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "eggnog_diamond_db": { + "type": "file", + "description": "The eggnog Diamond protein database file (e.g. eggnog-mapper/data/eggnog_proteins.dmnd)", + "pattern": "*.dmnd" + } + } + ] + ], + "output": [ + { + "annotations": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.emapper.annotations": { + "type": "file", + "description": "TSV with the results from the annotation phase", + "pattern": "*.emapper.annotations" + } + } + ] + }, + { + "orthologs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.emapper.seed_orthologs": { + "type": "file", + "description": "TSV with the results from parsing the hits, linking queries with seed orthologs (with commented metadata)", + "pattern": "*.emapper.seed_orthologs" + } + } + ] + }, + { + "hits": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.emapper.hits": { + "type": "file", + "description": "TSV with the results from the Diamond search phase", + "pattern": "*.emapper.hits" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@vagkaratzas" + ], + "maintainers": [ + "@vagkaratzas", + "@gallvp" + ] + } + }, + { + "name": "eido_convert", + "path": "modules/nf-core/eido/convert/meta.yml", + "type": "module", + "meta": { + "name": "eido_convert", + "description": "Convert any PEP project or Nextflow samplesheet to any format", + "keywords": [ + "eido", + "convert", + "PEP", + "format", + "samplesheet" + ], + "tools": [ + { + "eido": { + "description": "Convert any PEP project or Nextflow samplesheet to any format", + "homepage": "http://eido.databio.org/en/latest/", + "documentation": "http://eido.databio.org/en/latest/", + "doi": "10.1093/gigascience/giab077", + "licence": [ + "BSD-2-Clause" + ], + "identifier": "biotools:eido-python-package" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + [ + { + "samplesheet": { + "type": "file", + "description": "Nextflow samplesheet or PEP project", + "pattern": "*.{yaml,yml,csv}" + } } - }, - { - "fasta": { - "type": "file", - "description": "Database of sequences in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + ], + [ + { + "format": { + "type": "string", + "description": "Extension of an output file" + } } - }, - { - "eggnog_db": { - "type": "file", - "description": "The eggnog database file (e.g. eggnog-mapper/data/eggnog.db)", - "pattern": "*.db" + ], + [ + { + "pep_input_base_dir": { + "type": "file", + "description": "Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory." + } } - }, + ] + ], + "output": [ { - "eggnog_data_dir": { - "type": "directory", - "description": "Directory containing eggnog database files (e.g. eggnog-mapper/data)", - "pattern": "*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] }, { - "meta2": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "eggnog_diamond_db": { - "type": "file", - "description": "The eggnog Diamond protein database file (e.g. eggnog-mapper/data/eggnog_proteins.dmnd)", - "pattern": "*.dmnd" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "annotations": { - "type": "file", - "description": "TSV with the results from the annotation phase", - "pattern": "*.emapper.annotations" - } - }, - { - "orthologs": { - "type": "file", - "description": "TSV with the results from parsing the hits, linking queries with seed orthologs (with commented metadata)", - "pattern": "*.emapper.seed_orthologs" - } - }, - { - "hits": { - "type": "file", - "description": "TSV with the results from the Diamond search phase", - "pattern": "*.emapper.hits" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@vagkaratzas" - ], - "maintainers": [ - "@vagkaratzas", - "@gallvp" - ] - } - }, - { - "name": "eido_convert", - "path": "modules/nf-core/eido/convert/meta.yml", - "type": "module", - "meta": { - "name": "eido_convert", - "description": "Convert any PEP project or Nextflow samplesheet to any format", - "keywords": [ - "eido", - "convert", - "PEP", - "format", - "samplesheet" - ], - "tools": [ - { - "eido": { - "description": "Convert any PEP project or Nextflow samplesheet to any format", - "homepage": "http://eido.databio.org/en/latest/", - "documentation": "http://eido.databio.org/en/latest/", - "doi": "10.1093/gigascience/giab077", - "licence": [ - "BSD-2-Clause" - ] - } - } - ], - "input": [ - { - "samplesheet": { - "type": "file", - "description": "Nextflow samplesheet or PEP project", - "pattern": "*.{yaml,yml,csv}" - } - }, - { - "format": { - "type": "string", - "description": "Extension of an output file" - } - }, - { - "pep_input_base_dir": { - "type": "file", - "description": "Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory." - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "samplesheet_converted": { - "type": "file", - "description": "PEP project or samplesheet converted to csv file" - } + "samplesheet_converted": [ + { + "${prefix}.${format}": { + "type": "file", + "description": "PEP project or samplesheet converted to csv file" + } + } + ] } ], "authors": [ @@ -37082,46 +46702,61 @@ "doi": "10.1093/gigascience/giab077", "licence": [ "BSD-2-Clause" - ] + ], + "identifier": "biotools:eido-python-package" } } ], "input": [ - { - "samplesheet": { - "type": "file", - "description": "Samplesheet or PEP file to be validated", - "pattern": "*.{yaml,yml,csv}" + [ + { + "samplesheet": { + "type": "file", + "description": "Samplesheet or PEP file to be validated", + "pattern": "*.{yaml,yml,csv}" + } } - }, - { - "schema": { - "type": "file", - "description": "Schema that the samplesheet will be validated against", - "pattern": "*.{yaml,yml}" + ], + [ + { + "schema": { + "type": "file", + "description": "Schema that the samplesheet will be validated against", + "pattern": "*.{yaml,yml}" + } } - }, - { - "pep_input_base_dir": { - "type": "file", - "description": "Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory." + ], + [ + { + "pep_input_base_dir": { + "type": "file", + "description": "Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory." + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] }, { - "log": { - "type": "file", - "description": "File containing validation log.", - "pattern": "*.log" - } + "log": [ + { + "*.log": { + "type": "file", + "description": "File containing validation log.", + "pattern": "*.log" + } + } + ] } ], "authors": [ @@ -37154,66 +46789,87 @@ "tool_dev_url": "https://github.com/TCLamnidis/EigenStratDatabaseTools", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "geno": { - "type": "file", - "description": "An Eigenstrat formatted genotype file", - "pattern": "*.{geno}" - } - }, - { - "snp": { - "type": "file", - "description": "An Eigenstrat formatted snp file", - "pattern": "*.{snp}" - } - }, - { - "ind": { - "type": "file", - "description": "An Eigenstrat formatted individual file", - "pattern": "*.{ind}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "A TSV table with the number of covered SNPs per individual.", - "pattern": "*.{tsv}" - } - }, - { - "json": { - "type": "file", - "description": "A json table with the number of covered SNPs per individual.", - "pattern": "*.{json}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "geno": { + "type": "file", + "description": "An Eigenstrat formatted genotype file", + "pattern": "*.{geno}" + } + }, + { + "snp": { + "type": "file", + "description": "An Eigenstrat formatted snp file", + "pattern": "*.{snp}" + } + }, + { + "ind": { + "type": "file", + "description": "An Eigenstrat formatted individual file", + "pattern": "*.{ind}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV table with the number of covered SNPs per individual.", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "A json table with the number of covered SNPs per individual.", + "pattern": "*.{json}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37249,66 +46905,106 @@ "doi": "10.1038/s41436-018-0350-8", "licence": [ "GNU General Public v3 or later (GPL v3+)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "MT BAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "MT BAM/SAM index file", - "pattern": "*.{bai,sai}" - } - }, - { - "ref_gb": { - "type": "file", - "description": "mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb will be used", - "pattern": "*.{gb}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "csv file containing deletions", - "pattern": "*.{csv}" - } - }, - { - "circos": { - "type": "file", - "description": "png file with circos plot of mt", - "pattern": "*.{png}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "MT BAM/SAM file", + "pattern": "*.{bam,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "MT BAM/SAM index file", + "pattern": "*.{bai,sai}" + } + } + ], + [ + { + "ref_gb": { + "type": "file", + "description": "mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb will be used", + "pattern": "*.{gb}" + } + } + ] + ], + "output": [ + { + "deletions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*deletions.csv": { + "type": "file", + "description": "csv file with deletion information", + "pattern": "*deletions.csv" + } + } + ] + }, + { + "genes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*genes.csv": { + "type": "file", + "description": "csv file with gene information", + "pattern": "*genes.csv" + } + } + ] + }, + { + "circos": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "png file with circos plot of mt", + "pattern": "*.{png}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37349,166 +47045,269 @@ "doi": "10.1371/journal.pone.0244471", "licence": [ "AGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input SAM/BAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "run_haplotypecaller": { - "type": "boolean", - "description": "Run variant calling on the input files. Needed to generate gvcf output." - } - }, - { - "run_bqsr": { - "type": "boolean", - "description": "Run BQSR on the input files. Needed to generate recall metrics." - } - }, - { - "reference_sequences": { - "type": "file", - "description": "Optional SAM header to replace existing header.", - "pattern": "*.sam" - } - }, - { - "filter_regions_bed": { - "type": "file", - "description": "Optional BED file containing regions to filter.", - "pattern": "*.bed" - } - }, - { - "reference_elfasta": { - "type": "file", - "description": "Elfasta file, required for BQSR and variant calling.", - "pattern": "*.elfasta" - } - }, - { - "known_sites_elsites": { - "type": "file", - "description": "Optional elsites file containing known SNPs for BQSR.", - "pattern": "*.elsites" - } - }, - { - "target_regions_bed": { - "type": "file", - "description": "Optional BED file containing target regions for BQSR and variant calling.", - "pattern": "*.bed" - } - }, - { - "intermediate_bqsr_tables": { - "type": "file", - "description": "Optional list of BQSR tables, used when parsing files created by `elprep split`", - "pattern": "*.table" - } - }, - { - "bqsr_tables_only": { - "type": "boolean", - "description": "Write intermediate BQSR tables, used when parsing files created by `elprep split`." - } - }, - { - "get_activity_profile": { - "type": "boolean", - "description": "Get the activity profile calculated by the haplotypecaller to the given file in IGV format." - } - }, - { - "get_assembly_regions": { - "type": "boolean", - "description": "Get the assembly regions calculated by haplotypecaller to the speficied file in IGV format." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted, markdup, optionally BQSR BAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "logs": { - "type": "list", - "description": "Runtime log files", - "pattern": "elprep-*.log" - } - }, - { - "metrics": { - "type": "file", - "description": "Optional duplicate metrics file generated by elprep", - "pattern": "*.{metrics.txt}" - } - }, - { - "recall": { - "type": "file", - "description": "Optional recall metrics file generated by elprep", - "pattern": "*.{recall}" - } - }, - { - "gvcf": { - "type": "file", - "description": "Optional GVCF output file", - "pattern": "*.{vcf.gz}" - } - }, - { - "table": { - "type": "file", - "description": "Optional intermediate BQSR table output file", - "pattern": "*.{table}" - } - }, - { - "activity_profile": { - "type": "file", - "description": "Optional activity profile output file", - "pattern": "*.{activity_profile.igv}" - } - }, - { - "assembly_regions": { - "type": "file", - "description": "Optional activity regions output file", - "pattern": "*.{assembly_regions.igv}" - } + ], + "identifier": "biotools:elprep" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input SAM/BAM file", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "run_haplotypecaller": { + "type": "boolean", + "description": "Run variant calling on the input files. Needed to generate gvcf output." + } + } + ], + [ + { + "run_bqsr": { + "type": "boolean", + "description": "Run BQSR on the input files. Needed to generate recall metrics." + } + } + ], + [ + { + "reference_sequences": { + "type": "file", + "description": "Optional SAM header to replace existing header.", + "pattern": "*.sam" + } + } + ], + [ + { + "filter_regions_bed": { + "type": "file", + "description": "Optional BED file containing regions to filter.", + "pattern": "*.bed" + } + } + ], + [ + { + "reference_elfasta": { + "type": "file", + "description": "Elfasta file, required for BQSR and variant calling.", + "pattern": "*.elfasta" + } + } + ], + [ + { + "known_sites_elsites": { + "type": "file", + "description": "Optional elsites file containing known SNPs for BQSR.", + "pattern": "*.elsites" + } + } + ], + [ + { + "target_regions_bed": { + "type": "file", + "description": "Optional BED file containing target regions for BQSR and variant calling.", + "pattern": "*.bed" + } + } + ], + [ + { + "intermediate_bqsr_tables": { + "type": "file", + "description": "Optional list of BQSR tables, used when parsing files created by `elprep split`", + "pattern": "*.table" + } + } + ], + [ + { + "bqsr_tables_only": { + "type": "boolean", + "description": "Write intermediate BQSR tables, used when parsing files created by `elprep split`." + } + } + ], + [ + { + "get_activity_profile": { + "type": "boolean", + "description": "Get the activity profile calculated by the haplotypecaller to the given file in IGV format." + } + } + ], + [ + { + "get_assembly_regions": { + "type": "boolean", + "description": "Get the assembly regions calculated by haplotypecaller to the speficied file in IGV format." + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/**.{bam,sam}": { + "type": "file", + "description": "Sorted, markdup, optionally BQSR BAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ] + }, + { + "logs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "logs/elprep/elprep*": { + "type": "list", + "description": "Runtime log files", + "pattern": "elprep-*.log" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Optional duplicate metrics file generated by elprep", + "pattern": "*.{metrics.txt}" + } + } + ] + }, + { + "recall": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recall": { + "type": "file", + "description": "Optional recall metrics file generated by elprep", + "pattern": "*.{recall}" + } + } + ] + }, + { + "gvcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Optional GVCF output file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "Optional intermediate BQSR table output file", + "pattern": "*.{table}" + } + } + ] + }, + { + "activity_profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.activity_profile.igv": { + "type": "file", + "description": "Optional activity profile output file", + "pattern": "*.{activity_profile.igv}" + } + } + ] + }, + { + "assembly_regions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.assembly_regions.igv": { + "type": "file", + "description": "Optional activity regions output file", + "pattern": "*.{assembly_regions.igv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37541,45 +47340,56 @@ "doi": "10.1371/journal.pone.0244471", "licence": [ "AGPL v3" - ] + ], + "identifier": "biotools:elprep" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "List of BAM/SAM chunks to merge", - "pattern": "*.{bam,sam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List of BAM/SAM chunks to merge", + "pattern": "*.{bam,sam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/**.{bam,sam}": { + "type": "file", + "description": "Merged BAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Merged BAM/SAM file", - "pattern": "*.{bam,sam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37612,45 +47422,56 @@ "doi": "10.1371/journal.pone.0244471", "licence": [ "AGPL v3" - ] + ], + "identifier": "biotools:elprep" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "List of BAM/SAM files", - "pattern": "*.{bam,sam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List of BAM/SAM files", + "pattern": "*.{bam,sam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/**.{bam,sam}": { + "type": "file", + "description": "List of split BAM/SAM files", + "pattern": "*.{bam,sam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "List of split BAM/SAM files", - "pattern": "*.{bam,sam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37685,45 +47506,56 @@ "doi": "10.1016/s0168-9525(00)02024-2 ", "licence": [ "GPL" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Multiple sequence alignment (unzipped)", - "pattern": "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Multiple sequence alignment (unzipped)", + "pattern": "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "consensus": { - "type": "file", - "description": "Consensus sequence calculated from multiple sequence alignment", - "pattern": "*.fa" - } + "consensus": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Consensus sequence calculated from multiple sequence alignment", + "pattern": "*.fa" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37756,45 +47588,56 @@ "doi": "10.1016/s0168-9525(00)02024-2 ", "licence": [ "GPL" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "sequences": { - "type": "file", - "description": "Input sequences", - "pattern": "*.{fasta,fna,fa,fst,aln,phy}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "sequences": { + "type": "file", + "description": "Input sequences", + "pattern": "*.{fasta,fna,fa,fst,aln,phy}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "revseq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.${sequences.name - ~/.*\\./}": { + "type": "file", + "description": "File with reverse complemented sequences", + "pattern": "*.{fasta,fna,fa,fst,aln,phy}" + } + } + ] }, { - "revseq": { - "type": "file", - "description": "File with reverse complemented sequences", - "pattern": "*.{fasta,fna,fa,fst,aln,phy}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37831,51 +47674,64 @@ "doi": "10.1016/s0168-9525(00)02024-2 ", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequence": { - "type": "file", - "description": "Input sequence query", - "pattern": "*.{gff,em,gb,refseq,pir,swiss,sw,txt}" - } - }, - { - "out_ext": { - "type": "string", - "description": "File extension of the output file. Unless otherwise set by a flag in `ext.args`, the extension dictates the output file format." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "outseq": { - "type": "file", - "description": "Converted sequence file", - "pattern": "*" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequence": { + "type": "file", + "description": "Input sequence query", + "pattern": "*.{gff,em,gb,refseq,pir,swiss,sw,txt}" + } + } + ], + [ + { + "out_ext": { + "type": "string", + "description": "File extension of the output file. Unless otherwise set by a flag in `ext.args`, the extension dictates the output file format." + } + } + ] + ], + "output": [ + { + "outseq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${out_ext}": { + "type": "file", + "description": "Converted sequence file", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37907,45 +47763,56 @@ "tool_dev_url": "https://github.com/MDU-PHL/emmtyper", "licence": [ "GNU General Public v3 (GPL v3)" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited result file", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited result file", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -37979,56 +47846,67 @@ "doi": "10.7717/peerj.10947", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "stats_raw": { - "type": "file", - "description": "output of samtools flagstat in a txt file, assumes no quality filtering nor duplicate removal performed" - } - }, - { - "stats_qualityfiltered": { - "type": "file", - "description": "output of samtools flagstat in a txt file, assumes some form of quality or length filtering has been performed, must be provided with at least one of the options -r or -d" - } - }, - { - "stats_deduplicated": { - "type": "file", - "description": "output of samtools flagstat in a txt file, whereby duplicate removal has been performed on the input reads" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "file with the endogenous DNA calculation tailored for multiQC", - "pattern": "*_mqc.json" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "stats_raw": { + "type": "file", + "description": "output of samtools flagstat in a txt file, assumes no quality filtering nor duplicate removal performed" + } + }, + { + "stats_qualityfiltered": { + "type": "file", + "description": "output of samtools flagstat in a txt file, assumes some form of quality or length filtering has been performed, must be provided with at least one of the options -r or -d" + } + }, + { + "stats_deduplicated": { + "type": "file", + "description": "output of samtools flagstat in a txt file, whereby duplicate removal has been performed on the input reads" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_mqc.json": { + "type": "file", + "description": "file with the endogenous DNA calculation tailored for multiQC", + "pattern": "*_mqc.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38059,50 +47937,68 @@ "documentation": "https://www.ensembl.org/info/docs/tools/vep/script/index.html", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "string", - "description": "Genome assembly\n" - } - }, - { - "species": { - "type": "string", - "description": "Specie\n" - } - }, - { - "cache_version": { - "type": "string", - "description": "cache version\n" - } - } - ], - "output": [ - { - "cache": { - "type": "file", - "description": "cache", - "pattern": "*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "string", + "description": "Genome assembly\n" + } + }, + { + "species": { + "type": "string", + "description": "Specie\n" + } + }, + { + "cache_version": { + "type": "string", + "description": "cache version\n" + } + } + ] + ], + "output": [ + { + "cache": [ + { + "meta": { + "type": "file", + "description": "cache", + "pattern": "*" + } + }, + { + "prefix": { + "type": "file", + "description": "cache", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38144,51 +48040,64 @@ "documentation": "https://www.ensembl.org/info/docs/tools/vep/script/index.html", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "VCF/TAB file annotated with vep", - "pattern": "*.{vcf,tab,tsv,txt}" - } - }, - { - "feature_file": { - "type": "file", - "description": "File containing features on separate lines. To be used with --filter option." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "VCF/TAB file", - "pattern": "*.{vcf,tab,txt,tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "VCF/TAB file annotated with vep", + "pattern": "*.{vcf,tab,tsv,txt}" + } + } + ], + [ + { + "feature_file": { + "type": "file", + "description": "File containing features on separate lines. To be used with --filter option." + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF/TAB file", + "pattern": "*.{vcf,tab,txt,tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38226,108 +48135,164 @@ "documentation": "https://www.ensembl.org/info/docs/tools/vep/script/index.html", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf to annotate\n" - } - }, - { - "custom_extra_files": { - "type": "file", - "description": "extra sample-specific files to be used with the `--custom` flag to be configured with ext.args\n(optional)\n" - } - }, - { - "genome": { - "type": "string", - "description": "which genome to annotate with\n" - } - }, - { - "species": { - "type": "string", - "description": "which species to annotate with\n" - } - }, - { - "cache_version": { - "type": "integer", - "description": "which version of the cache to annotate with\n" - } - }, - { - "cache": { - "type": "file", - "description": "path to VEP cache (optional)\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference FASTA file (optional)\n", - "pattern": "*.{fasta,fa}" - } - }, - { - "extra_files": { - "type": "file", - "description": "path to file(s) needed for plugins (optional)\n" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "annotated vcf (optional)\n", - "pattern": "*.ann.vcf.gz" - } - }, - { - "tab": { - "type": "file", - "description": "tab file with annotated variants (optional)\n", - "pattern": "*.ann.tab.gz" - } - }, - { - "json": { - "type": "file", - "description": "json file with annotated variants (optional)\n", - "pattern": "*.ann.json.gz" - } - }, - { - "report": { - "type": "file", - "description": "VEP report file", - "pattern": "*.html" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf to annotate\n" + } + }, + { + "custom_extra_files": { + "type": "file", + "description": "extra sample-specific files to be used with the `--custom` flag to be configured with ext.args\n(optional)\n" + } + } + ], + [ + { + "genome": { + "type": "string", + "description": "which genome to annotate with\n" + } + } + ], + [ + { + "species": { + "type": "string", + "description": "which species to annotate with\n" + } + } + ], + [ + { + "cache_version": { + "type": "integer", + "description": "which version of the cache to annotate with\n" + } + } + ], + [ + { + "cache": { + "type": "file", + "description": "path to VEP cache (optional)\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference FASTA file (optional)\n", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "extra_files": { + "type": "file", + "description": "path to file(s) needed for plugins (optional)\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "annotated vcf (optional)\n", + "pattern": "*.ann.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "annotated vcf (optional)\n", + "pattern": "*.ann.vcf.gz" + } + } + ] + }, + { + "tab": [ + { + "meta": { + "type": "file", + "description": "tab file with annotated variants (optional)\n", + "pattern": "*.ann.tab.gz" + } + }, + { + "*.tab.gz": { + "type": "file", + "description": "tab file with annotated variants (optional)\n", + "pattern": "*.ann.tab.gz" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "file", + "description": "json file with annotated variants (optional)\n", + "pattern": "*.ann.json.gz" + } + }, + { + "*.json.gz": { + "type": "file", + "description": "json file with annotated variants (optional)\n", + "pattern": "*.ann.json.gz" + } + } + ] + }, + { + "report": [ + { + "*.html": { + "type": "file", + "description": "VEP report file", + "pattern": "*.html" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38384,50 +48349,63 @@ "doi": "10.1016/S0076-6879(96)66012-1", "licence": [ "PUBLIC DOMAIN" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "database": { - "type": "string", - "description": "Value must be a valid Entrez database name." + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "term": { + "type": "string", + "description": "Entrez text query. All special characters must be URL encoded.\nSpaces may be replaced by '+' signs.\n" + } } - }, - { - "term": { - "type": "string", - "description": "Entrez text query. All special characters must be URL encoded.\nSpaces may be replaced by '+' signs.\n" + ], + [ + { + "database": { + "type": "string", + "description": "Value must be a valid Entrez database name." + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "xml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "XML file containing search results", + "pattern": "*.xml" + } + } + ] }, { - "result_xml": { - "type": "file", - "description": "Query result text in XML format", - "pattern": "*.xml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38463,56 +48441,69 @@ "doi": "10.1016/S0076-6879(96)66012-1", "licence": [ "PUBLIC DOMAIN" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "database": { - "type": "string", - "description": "Value must be a valid Entrez database name ('assembly', etc)." - } - }, - { - "uid": { - "type": "string", - "description": "Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file" - } - }, - { - "uids_file": { - "type": "file", - "description": "Text file containing multiple UIDs. Cannot be used at the same time as uid." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "xml": { - "type": "file", - "description": "Query result in XML format", - "pattern": "*.xml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "uid": { + "type": "string", + "description": "Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file" + } + }, + { + "uids_file": { + "type": "file", + "description": "Text file containing multiple UIDs. Cannot be used at the same time as uid." + } + } + ], + [ + { + "database": { + "type": "string", + "description": "Value must be a valid Entrez database name ('assembly', etc)." + } + } + ] + ], + "output": [ + { + "xml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "Query result in XML format", + "pattern": "*.xml" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38547,62 +48538,79 @@ "doi": "10.1016/S0076-6879(96)66012-1", "licence": [ "PUBLIC DOMAIN" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "xml_input": { - "type": "file", - "description": "XML text file containing query results from database." - } - }, - { - "pattern": { - "type": "string", - "description": "String in xml_input that encloses element to search." - } - }, - { - "element": { - "type": "string", - "description": "Space-delimited strings that will be converted to columns." - } - }, - { - "sep": { - "type": "string", - "description": "Separator/delimiter between columns (for instance \",\" or \"\\t\")." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "xtract_table": { - "type": "file", - "description": "TXT file containing columns searched from element.", - "pattern": "*.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "xml_input": { + "type": "file", + "description": "XML text file containing query results from database." + } + } + ], + [ + { + "pattern": { + "type": "string", + "description": "String in xml_input that encloses element to search." + } + } + ], + [ + { + "element": { + "type": "string", + "description": "Space-delimited strings that will be converted to columns." + } + } + ], + [ + { + "sep": { + "type": "string", + "description": "Separator/delimiter between columns (for instance \",\" or \"\\t\")." + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Text file", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38635,86 +48643,115 @@ "doi": "10.1093/sysbio/syy054", "licence": [ "GNU Affero General Public License v3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "queryaln": { - "type": "file", - "description": "aligned query sequences in any supported format including phylip and fasta, may be gzipped", - "pattern": "*" - } - }, - { - "referencealn": { - "type": "file", - "description": "reference alignment in any supported format including phylip and fasta, may be gzipped", - "pattern": "*" - } - }, - { - "referencetree": { - "type": "file", - "description": "newick file containing the reference tree in which query sequences will be placed", - "pattern": "*" - } - }, - { - "bfastfile": { - "type": "file", - "description": "file argument to the --bfast parameter", - "pattern": "*" - } - }, - { - "binaryfile": { - "type": "file", - "description": "file argument to the --binary parameter", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "epang": { - "type": "directory", - "description": "directory in which EPA-NG was run" - } - }, - { - "jplace": { - "type": "file", - "description": "gzipped file with placement information", - "pattern": "*.jplace.gz" - } - }, - { - "log": { - "type": "file", - "description": "log file from placement", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "queryaln": { + "type": "file", + "description": "aligned query sequences in any supported format including phylip and fasta, may be gzipped", + "pattern": "*" + } + }, + { + "referencealn": { + "type": "file", + "description": "reference alignment in any supported format including phylip and fasta, may be gzipped", + "pattern": "*" + } + }, + { + "referencetree": { + "type": "file", + "description": "newick file containing the reference tree in which query sequences will be placed", + "pattern": "*" + } + } + ], + [ + { + "bfastfile": { + "type": "file", + "description": "file argument to the --bfast parameter", + "pattern": "*" + } + } + ], + [ + { + "binaryfile": { + "type": "file", + "description": "file argument to the --binary parameter", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "epang": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "./.": { + "type": "directory", + "description": "directory in which EPA-NG was run" + } + } + ] + }, + { + "jplace": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.epa_result.jplace.gz": { + "type": "file", + "description": "gzipped file with placement information", + "pattern": "*.jplace.gz" + } + } + ] + }, + { + "log": [ + { + "*.epa_info.log": { + "type": "file", + "description": "log file from placement", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38757,57 +48794,78 @@ "doi": "10.1093/sysbio/syy054", "licence": [ "GNU Affero General Public License v3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "refaln": { - "type": "file", - "description": "reference alignment in any supported format including phylip and fasta, may be gzipped", - "pattern": "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" - } - }, - { - "fullaln": { - "type": "file", - "description": "full alignment in any supported format to split into reference and query alignments", - "pattern": "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query": { - "type": "file", - "description": "query sequence alignment in gzipped fasta format" - } - }, - { - "reference": { - "type": "file", - "description": "reference sequence alignment in gzipped fasta format" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "refaln": { + "type": "file", + "description": "reference alignment in any supported format including phylip and fasta, may be gzipped", + "pattern": "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" + } + }, + { + "fullaln": { + "type": "file", + "description": "full alignment in any supported format to split into reference and query alignments", + "pattern": "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" + } + } + ] + ], + "output": [ + { + "query": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*query.fasta.gz": { + "type": "file", + "description": "query sequence alignment in gzipped fasta format" + } + } + ] + }, + { + "reference": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*reference.fasta.gz": { + "type": "file", + "description": "reference sequence alignment in gzipped fasta format" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38850,66 +48908,94 @@ "doi": "10.1534/genetics.118.301120", "licence": [ "Free for Academic Use" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "e_config": { - "type": "file", - "description": "config file for est-sfs", - "pattern": "*.txt" - } - }, - { - "data": { - "type": "file", - "description": "input data file for est-sfs", - "pattern": "*.txt" - } - }, - { - "seed": { - "type": "file", - "description": "text file containing random number seed", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sfs_out": { - "type": "file", - "description": "output file consists of the comma-separated estimated uSFS vector", - "pattern": "*.txt" - } - }, - { - "pvalues_out": { - "type": "file", - "description": "this file contains the estimated ancestral state probabilities for each site", - "pattern": "*.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "e_config": { + "type": "file", + "description": "config file for est-sfs", + "pattern": "*.txt" + } + }, + { + "data": { + "type": "file", + "description": "input data file for est-sfs", + "pattern": "*.txt" + } + }, + { + "seed": { + "type": "file", + "description": "text file containing random number seed", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "sfs_out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}_sfs.txt": { + "type": "file", + "description": "output file consists of the comma-separated estimated uSFS vector", + "pattern": "*.txt" + } + } + ] + }, + { + "pvalues_out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}_pvalues.txt": { + "type": "file", + "description": "this file contains the estimated ancestral state probabilities for each site", + "pattern": "*.txt" + } + }, + { + "ues_out": { + "type": "file", + "description": "this file contains the estimated ancestral state probabilities for each site", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -38944,52 +49030,73 @@ "doi": "10.7490/f1000research.1112594.1 ", "licence": [ "Don Gilbert, gilbertd At indiana edu, 2018" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Transcript assembly in fasta format", - "pattern": "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "dropset": { - "type": "directory", - "description": "Directory containing dropped transcripts and associated files", - "pattern": "dropset" - } - }, - { - "okayset": { - "type": "directory", - "description": "Directory containing included transcripts and associated files", - "pattern": "okayset" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Transcript assembly in fasta format", + "pattern": "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}" + } + } + ] + ], + "output": [ + { + "dropset": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "dropset": { + "type": "directory", + "description": "Directory containing dropped transcripts and associated files", + "pattern": "dropset" + } + } + ] + }, + { + "okayset": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "okayset": { + "type": "directory", + "description": "Directory containing included transcripts and associated files", + "pattern": "okayset" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39030,105 +49137,142 @@ "doi": "10.1093/bioinformatics/btz431", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fna,fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Reference genome index", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "variant_catalog": { - "type": "file", - "description": "JSON file with repeat expansion sites to genotype", - "pattern": "*.json" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF with repeat expansions", - "pattern": "*.vcf.gz" - } - }, - { - "json": { - "type": "file", - "description": "JSON with repeat expansions", - "pattern": "*.json.gz" - } + ], + "identifier": "biotools:ExpansionHunter" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome", + "pattern": "*.{fna,fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Reference genome index", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "variant_catalog": { + "type": "file", + "description": "JSON file with repeat expansion sites to genotype", + "pattern": "*.json" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF with repeat expansions", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" + } + }, + { + "*.json.gz": { + "type": "file", + "description": "JSON with repeat expansions", + "pattern": "*.json.gz" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', gender:'female' ]\n" + } + }, + { + "*_realigned.bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39166,71 +49310,86 @@ "tool_dev_url": "https://github.com/Illumina/ExpansionHunterDenovo", "licence": [ "Apache License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "manifest": { - "type": "file", - "description": "A tab-delimited file containing the sample name, whether it's case or control\nand the paths to the corresponding STR profiles.\nSee here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files\n", - "pattern": "*.{tsv,txt}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "merged_profiles": { - "type": "file", - "description": "The merged STR profiles", - "pattern": "*.multisample_profile.json" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "manifest": { + "type": "file", + "description": "A tab-delimited file containing the sample name, whether it's case or control\nand the paths to the corresponding STR profiles.\nSee here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files\n", + "pattern": "*.{tsv,txt}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "merged_profiles": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.multisample_profile.json": { + "type": "file", + "description": "The merged STR profiles", + "pattern": "*.multisample_profile.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39265,92 +49424,127 @@ "tool_dev_url": "https://github.com/Illumina/ExpansionHunterDenovo", "licence": [ "Apache License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment_file": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "alignment_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The FASTA reference file", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA reference file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "locus_tsv": { - "type": "file", - "description": "The locus TSV file", - "pattern": "*.tsv" - } - }, - { - "motif_tsv": { - "type": "file", - "description": "The motif TSV file", - "pattern": "*.tsv" - } - }, - { - "str_profile": { - "type": "file", - "description": "The JSON file containing the STR profile", - "pattern": "*.json" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment_file": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "alignment_index": { + "type": "file", + "description": "Index of the BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The FASTA reference file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA reference file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "locus_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.locus.tsv": { + "type": "file", + "description": "The locus TSV file", + "pattern": "*.tsv" + } + } + ] + }, + { + "motif_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.motif.tsv": { + "type": "file", + "description": "The motif TSV file", + "pattern": "*.tsv" + } + } + ] + }, + { + "str_profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.str_profile.json": { + "type": "file", + "description": "The JSON file containing the STR profile", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39382,58 +49576,72 @@ "documentation": "https://falco.readthedocs.io/", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "html": { - "type": "file", - "description": "FastQC like report", - "pattern": "*_{fastqc_report.html}" - } - }, - { - "txt": { - "type": "file", - "description": "falco report data", - "pattern": "*_{data.txt}" - } - }, - { - "txt": { - "type": "file", - "description": "falco summary file", - "pattern": "*_{summary.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:falco-rna" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "FastQC like report", + "pattern": "*_{fastqc_report.html}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "falco report data", + "pattern": "*_{data.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39476,64 +49684,79 @@ "doi": "10.1038/srep33964", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is handled by passing '-gz' to FAMSA along with any other options specified in task.ext.args." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false", - "pattern": "*.aln{.gz,}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:famsa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is handled by passing '-gz' to FAMSA along with any other options specified in task.ext.args." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false", + "pattern": "*.aln{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39574,45 +49797,56 @@ "doi": "10.1038/srep33964", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:famsa" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Guide tree file in Newick format", - "pattern": "*.{dnd}" - } + "tree": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.dnd": { + "type": "file", + "description": "Guide tree file in Newick format", + "pattern": "*.{dnd}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39654,86 +49888,157 @@ "doi": "10.1186/s12859-014-0366-2", "licence": [ "GPLv3 License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for\nsingle-end and paired-end data, respectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "The trimmed/modified fastq reads", - "pattern": "*trimmed.fastq.gz" - } - }, - { - "reads_fail": { - "type": "file", - "description": "Reads that failed the preprocessing (Optional with --discard args setting)", - "pattern": "*discard.fastq.gz" - } - }, - { - "reads_unpaired": { - "type": "file", - "description": "Reads without matching mates in paired-end files (Optional)", - "pattern": "*trimmed.unpaired.fastq.gz" - } - }, - { - "stats": { - "type": "file", - "description": "trimming/qc text stats file", - "pattern": "*.stats.txt" - } - }, - { - "debug": { - "type": "directory", - "description": "trimming/qc files from --debug option", - "pattern": "./debug" - } - }, - { - "statspdf": { - "type": "file", - "description": "trimming/qc pdf report file", - "pattern": "*_qc_report.pdf" - } - }, - { - "log": { - "type": "file", - "description": "fastq log file", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for\nsingle-end and paired-end data, respectively.\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trimmed.fastq.gz": { + "type": "file", + "description": "The trimmed/modified fastq reads", + "pattern": "*trimmed.fastq.gz" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats.txt": { + "type": "file", + "description": "trimming/qc text stats file", + "pattern": "*.stats.txt" + } + } + ] + }, + { + "debug": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "./debug": { + "type": "directory", + "description": "trimming/qc files from --debug option", + "pattern": "./debug" + } + } + ] + }, + { + "statspdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_qc_report.pdf": { + "type": "file", + "description": "trimming/qc pdf report file", + "pattern": "*_qc_report.pdf" + } + } + ] + }, + { + "reads_fail": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.discard.fastq.gz": { + "type": "file", + "description": "Reads that failed the preprocessing (Optional with --discard args setting)", + "pattern": "*discard.fastq.gz" + } + } + ] + }, + { + "reads_unpaired": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.trimmed.unpaired.fastq.gz": { + "type": "file", + "description": "Reads without matching mates in paired-end files (Optional)", + "pattern": "*trimmed.unpaired.fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "fastq log file", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39771,149 +50076,302 @@ "tool_dev_url": "https://github.com/fannyhb/fargene", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)", - "pattern": "*.{fasta}" - } - }, - { - "hmm_model": { - "type": "string", - "description": "name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "log file", - "pattern": "*.{log}" - } - }, - { - "txt": { - "type": "file", - "description": "analysis summary text file", - "pattern": "*.{txt}" - } - }, - { - "hmm": { - "type": "file", - "description": "output from hmmsearch (both single gene annotations + contigs)", - "pattern": "*.{out}" - } - }, - { - "hmm_genes": { - "type": "file", - "description": "output from hmmsearch (single gene annotations only)", - "pattern": "retrieved-*.{out}" - } - }, - { - "orfs": { - "type": "file", - "description": "open reading frames (ORFs)", - "pattern": "*.{fasta}" - } - }, - { - "orfs_amino": { - "type": "file", - "description": "protein translation of open reading frames (ORFs)", - "pattern": "*.{fasta}" - } - }, - { - "contigs": { - "type": "file", - "description": "(complete) contigs that passed the final full-length classification", - "pattern": "*.{fasta}" - } - }, - { - "contigs_pept": { - "type": "file", - "description": "parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences", - "pattern": "*.{fasta}" - } - }, - { - "filtered": { - "type": "file", - "description": "sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene", - "pattern": "*.{fasta}" - } - }, - { - "filtered_pept": { - "type": "file", - "description": "sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located", - "pattern": "*.{fasta}" - } - }, - { - "fragments": { - "type": "file", - "description": "All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files", - "pattern": "*.{fastq}" - } - }, - { - "trimmed": { - "type": "file", - "description": "The quality controlled retrieved fragments from each input file.", - "pattern": "*.{fasta}" - } - }, - { - "spades": { - "type": "directory", - "description": "The output from the SPAdes assembly", - "pattern": "spades_assembly" - } - }, - { - "metagenome": { - "type": "file", - "description": "The FASTQ to FASTA converted input files from metagenomic reads.", - "pattern": "*.{fasta}" - } - }, - { - "tmp": { - "type": "file", - "description": "The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.", - "pattern": "*.{fasta}" - } + ], + "identifier": "biotools:fargene" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "hmm_model": { + "type": "string", + "description": "name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/results_summary.txt": { + "type": "file", + "description": "analysis summary text file", + "pattern": "*.{txt}" + } + } + ] + }, + { + "hmm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/hmmsearchresults/*.out": { + "type": "file", + "description": "output from hmmsearch (both single gene annotations + contigs)", + "pattern": "*.{out}" + } + } + ] + }, + { + "hmm_genes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/hmmsearchresults/retrieved-*.out": { + "type": "file", + "description": "output from hmmsearch (single gene annotations only)", + "pattern": "retrieved-*.{out}" + } + } + ] + }, + { + "orfs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/predicted-orfs.fasta": { + "type": "file", + "description": "open reading frames (ORFs)", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "orfs_amino": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/predicted-orfs-amino.fasta": { + "type": "file", + "description": "protein translation of open reading frames (ORFs)", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/retrieved-contigs.fasta": { + "type": "file", + "description": "(complete) contigs that passed the final full-length classification", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "contigs_pept": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/retrieved-contigs-peptides.fasta": { + "type": "file", + "description": "parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "filtered": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/*filtered.fasta": { + "type": "file", + "description": "sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "filtered_pept": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/predictedGenes/*filtered-peptides.fasta": { + "type": "file", + "description": "sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "fragments": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/retrievedFragments/all_retrieved_*.fastq": { + "type": "file", + "description": "All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files", + "pattern": "*.{fastq}" + } + } + ] + }, + { + "trimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/retrievedFragments/trimmedReads/*.fasta": { + "type": "file", + "description": "The quality controlled retrieved fragments from each input file.", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "spades": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/spades_assembly/*": { + "type": "directory", + "description": "The output from the SPAdes assembly", + "pattern": "spades_assembly" + } + } + ] + }, + { + "metagenome": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/tmpdir/*.fasta": { + "type": "file", + "description": "The FASTQ to FASTA converted input files from metagenomic reads.", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "tmp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/tmpdir/*.out": { + "type": "file", + "description": "The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -39952,52 +50410,65 @@ "doi": "10.1038/s41467-018-07641-9", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query": { - "type": "file", - "description": "Fasta file(s) to be queried", - "pattern": "*.fasta" - } - }, - { - "reference": { - "type": "file", - "description": "Fasta file(s) to be used as reference for the query", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ani": { - "type": "file", - "description": "Results of the query", - "pattern": "*.ani.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:fastani" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query": { + "type": "file", + "description": "Fasta file(s) to be queried", + "pattern": "*.fasta" + } + } + ], + [ + { + "reference": { + "type": "file", + "description": "Fasta file(s) to be used as reference for the query", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "ani": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ani.txt": { + "type": "file", + "description": "Results of the query", + "pattern": "*.ani.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40030,52 +50501,73 @@ "doi": "10.5281/zenodo.5002710", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" - } - }, - { - "success_log": { - "type": "file", - "description": "Log file for successful validation", - "pattern": "*.success.log" - } - }, - { - "error_log": { - "type": "file", - "description": "Log file for failed validation", - "pattern": "*.error.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "success_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.success.log": { + "type": "file", + "description": "Log file for successful validation", + "pattern": "*.success.log" + } + } + ] + }, + { + "error_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing file information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.error.log": { + "type": "file", + "description": "Log file for failed validation", + "pattern": "*.error.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40106,73 +50598,124 @@ "homepage": "https://github.com/tolkit/fasta_windows", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "freq": { - "type": "file", - "description": "TSV file with frequencies and statistics", - "pattern": "*.{tsv}" - } - }, - { - "mononuc": { - "type": "file", - "description": "TSV file with mononucleotide counts", - "pattern": "*.{tsv}" - } - }, - { - "dinuc": { - "type": "file", - "description": "TSV file with dinucleotide counts", - "pattern": "*.{tsv}" - } - }, - { - "trinuc": { - "type": "file", - "description": "TSV file with trinucleotide counts", - "pattern": "*.{tsv}" - } - }, - { - "tetranuc": { - "type": "file", - "description": "TSV file with tetranucleotide counts", - "pattern": "*.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta,fna}" + } + } + ] + ], + "output": [ + { + "freq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_freq_windows.tsv": { + "type": "file", + "description": "TSV file with frequencies and statistics", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "mononuc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_mononuc_windows.tsv": { + "type": "file", + "description": "TSV file with mononucleotide counts", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "dinuc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_dinuc_windows.tsv": { + "type": "file", + "description": "TSV file with dinucleotide counts", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "trinuc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_trinuc_windows.tsv": { + "type": "file", + "description": "TSV file with trinucleotide counts", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "tetranuc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fw_out/*_tetranuc_windows.tsv": { + "type": "file", + "description": "TSV file with tetranucleotide counts", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40203,58 +50746,89 @@ "tool_dev_url": "https://github.com/thegenemyers/FASTK", "licence": [ "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hist": { - "type": "file", - "description": "Histogram of k-mers", - "pattern": "*.hist" - } - }, - { - "ktab": { - "type": "file", - "description": "A sorted table of all canonical k‑mers along with their counts.", - "pattern": "*.ktab" - } - }, - { - "prof": { - "type": "file", - "description": "A k‑mer count profile of each sequence in the input data set.", - "pattern": "*.prof" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ] + ], + "output": [ + { + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "Histogram of k-mers", + "pattern": "*.hist" + } + } + ] + }, + { + "ktab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ktab*\", hidden: true": { + "type": "file", + "description": "A sorted table of all canonical k‑mers along with their counts.", + "pattern": "*.ktab" + } + } + ] + }, + { + "prof": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{prof,pidx}*\", hidden: true": { + "type": "file", + "description": "A k‑mer count profile of each sequence in the input data set.", + "pattern": "*.prof" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40292,45 +50866,56 @@ "tool_dev_url": "https://github.com/thegenemyers/FASTK", "license": [ "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "histogram": { - "type": "file", - "description": "A FastK histogram file", - "pattern": "*.hist" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "histogram": { + "type": "file", + "description": "A FastK histogram file", + "pattern": "*.hist" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "A formatted histogram file", + "pattern": "*.hist" + } + } + ] }, { - "hist": { - "type": "file", - "description": "A formatted histogram file", - "pattern": "*.hist" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40368,73 +50953,101 @@ "tool_dev_url": "https://github.com/thegenemyers/FASTK", "license": [ "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastk_hist": { - "type": "file", - "description": "A histogram files from the program FastK", - "pattern": "*.hist" - } - }, - { - "fastk_ktab": { - "type": "file", - "description": "Histogram ktab files from the program FastK (option -t)", - "pattern": "*.ktab*" - } - }, - { - "fastk_prof": { - "type": "file", - "description": "Histogram profile files from the program FastK (option -p)", - "pattern": "*.{prof,pidx}*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastk_hist": { - "type": "file", - "description": "A histogram files from the program FastK", - "pattern": "*.hist" - } - }, - { - "fastk_ktab": { - "type": "file", - "description": "Histogram ktab files from the program FastK (option -t)", - "pattern": "*.ktab*" - } - }, - { - "fastk_prof": { - "type": "file", - "description": "Histogram profile files from the program FastK (option -p)", - "pattern": "*.{prof,pidx}*" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hist": { + "type": "file", + "description": "FastK histogram file" + } + }, + { + "ktab": { + "type": "file", + "description": "FastK ktab file" + } + }, + { + "prof": { + "type": "file", + "description": "FastK prof file" + } + } + ] + ], + "output": [ + { + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "FastK histogram file", + "pattern": "*.hist" + } + } + ] + }, + { + "ktab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ktab*\", hidden: true": { + "type": "file", + "description": "FastK ktab file", + "pattern": "*.ktab" + } + } + ] + }, + { + "prof": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{prof,pidx}*\", hidden: true": { + "type": "file", + "description": "FastK prof file", + "pattern": "*.{prof,pidx}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40475,67 +51088,117 @@ "licence": [ "GPL v3" ], - "args_id": "$args" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "A Groovy map containing sample information,\ne.g. [ id: \"test\" ]\n" - } - }, - { - "infile": { - "type": "file", - "description": "MSA or distance matrix in Phylip format", - "pattern": "*" - } - }, - { - "topo": { - "type": "file", - "description": "Initial tree topology in Newick format", - "pattern": "*.{nwk,dnd}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "nwk": { - "type": "file", - "description": "Final phylogeny in Newick format", - "pattern": "*.nwk" - } - }, - { - "stats": { - "type": "file", - "description": "A text file with the statistics of the phylogeny", - "pattern": "*_stat.txt" - } - }, - { - "matrix": { - "type": "file", - "description": "Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten", - "pattern": "*.matrix.phy" - } - }, - { - "bootstrap": { - "type": "file", - "description": "A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten", - "pattern": "*.bootstrap" - } + "args_id": "$args", + "identifier": "biotools:fastme" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "A Groovy map containing sample information,\ne.g. [ id: \"test\" ]\n" + } + }, + { + "infile": { + "type": "file", + "description": "MSA or distance matrix in Phylip format", + "pattern": "*" + } + }, + { + "initial_tree": { + "type": "file", + "description": "Initial tree" + } + } + ] + ], + "output": [ + { + "nwk": [ + { + "meta": { + "type": "file", + "description": "Final phylogeny in Newick format", + "pattern": "*.nwk" + } + }, + { + "*.nwk": { + "type": "file", + "description": "Final phylogeny in Newick format", + "pattern": "*.nwk" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "file", + "description": "A text file with the statistics of the phylogeny", + "pattern": "*_stat.txt" + } + }, + { + "*_stat.txt": { + "type": "file", + "description": "A text file with the statistics of the phylogeny", + "pattern": "*_stat.txt" + } + } + ] + }, + { + "matrix": [ + { + "meta": { + "type": "file", + "description": "Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten", + "pattern": "*.matrix.phy" + } + }, + { + "*.matrix.phy": { + "type": "file", + "description": "Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten", + "pattern": "*.matrix.phy" + } + } + ] + }, + { + "bootstrap": [ + { + "meta": { + "type": "file", + "description": "A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten", + "pattern": "*.bootstrap" + } + }, + { + "*.bootstrap": { + "type": "file", + "description": "A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten", + "pattern": "*.bootstrap" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40572,104 +51235,173 @@ "doi": "10.1093/bioinformatics/bty560", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively. If you wish to run interleaved paired-end data, supply as single-end data\nbut with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.\n" - } - }, - { - "adapter_fasta": { - "type": "file", - "description": "File in FASTA format containing possible adapters to remove.", - "pattern": "*.{fasta,fna,fas,fa}" - } - }, - { - "discard_trimmed_pass": { - "type": "boolean", - "description": "Specify true to not write any reads that pass trimming thresholds. | This can be used to use fastp for the output report only." - } - }, - { - "save_trimmed_fail": { - "type": "boolean", - "description": "Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`" - } - }, - { - "save_merged": { - "type": "boolean", - "description": "Specify true to save all merged reads to a file ending in `*.merged.fastq.gz`" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "The trimmed/modified/unmerged fastq reads", - "pattern": "*fastp.fastq.gz" - } - }, - { - "json": { - "type": "file", - "description": "Results in JSON format", - "pattern": "*.json" - } - }, - { - "html": { - "type": "file", - "description": "Results in HTML format", - "pattern": "*.html" - } - }, - { - "log": { - "type": "file", - "description": "fastq log file", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads_fail": { - "type": "file", - "description": "Reads the failed the preprocessing", - "pattern": "*fail.fastq.gz" - } - }, - { - "reads_merged": { - "type": "file", - "description": "Reads that were successfully merged", - "pattern": "*.{merged.fastq.gz}" - } + ], + "identifier": "biotools:fastp" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively. If you wish to run interleaved paired-end data, supply as single-end data\nbut with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.\n" + } + } + ], + [ + { + "adapter_fasta": { + "type": "file", + "description": "File in FASTA format containing possible adapters to remove.", + "pattern": "*.{fasta,fna,fas,fa}" + } + } + ], + [ + { + "discard_trimmed_pass": { + "type": "boolean", + "description": "Specify true to not write any reads that pass trimming thresholds. | This can be used to use fastp for the output report only." + } + } + ], + [ + { + "save_trimmed_fail": { + "type": "boolean", + "description": "Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`" + } + } + ], + [ + { + "save_merged": { + "type": "boolean", + "description": "Specify true to save all merged reads to a file ending in `*.merged.fastq.gz`" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastp.fastq.gz": { + "type": "file", + "description": "The trimmed/modified/unmerged fastq reads", + "pattern": "*fastp.fastq.gz" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Results in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "Results in HTML format", + "pattern": "*.html" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "fastq log file", + "pattern": "*.log" + } + } + ] + }, + { + "reads_fail": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fail.fastq.gz": { + "type": "file", + "description": "Reads the failed the preprocessing", + "pattern": "*fail.fastq.gz" + } + } + ] + }, + { + "reads_merged": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.merged.fastq.gz": { + "type": "file", + "description": "Reads that were successfully merged", + "pattern": "*.{merged.fastq.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -40777,51 +51509,72 @@ "documentation": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/", "licence": [ "GPL-2.0-only" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "html": { - "type": "file", - "description": "FastQC report", - "pattern": "*_{fastqc.html}" - } - }, - { - "zip": { - "type": "file", - "description": "FastQC report archive", - "pattern": "*_{fastqc.zip}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:fastqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "FastQC report", + "pattern": "*_{fastqc.html}" + } + } + ] + }, + { + "zip": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.zip": { + "type": "file", + "description": "FastQC report archive", + "pattern": "*_{fastqc.zip}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41101,45 +51854,56 @@ "tool_dev_url": "https://github.com/rpetit3/fastq-scan", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fastq.gz,fq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ file", + "pattern": "*.{fastq.gz,fq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON formatted file of summary statistics", + "pattern": "*.json" + } + } + ] }, { - "json": { - "type": "file", - "description": "JSON formatted file of summary statistics", - "pattern": "*.json" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41173,38 +51937,51 @@ "doi": "10.5281/zenodo.5838377", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "genome_names": { - "type": "string", - "description": "List of names for each index" + [ + { + "genome_names": { + "type": "string", + "description": "List of names for each index" + } } - }, - { - "indexes": { - "type": "directory", - "description": "Bowtie2 genome directories containing index files" + ], + [ + { + "indexes": { + "type": "directory", + "description": "Bowtie2 genome directories containing index files" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "database": [ + { + "FastQ_Screen_Genomes": { + "type": "directory", + "description": "fastq screen database folder containing config file and index folders", + "pattern": "FastQ_Screen_Genomes" + } + } + ] }, { - "database": { - "type": "directory", - "description": "fastq screen database folder containing config file and index folders", - "pattern": "FastQ_Screen_Genomes" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41238,73 +52015,115 @@ "doi": "10.5281/zenodo.5838377", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "database": { - "type": "directory", - "description": "fastq screen database folder containing config file and index folders", - "pattern": "FastQ_Screen_Genomes" - } - } - ], - "output": [ - { - "fastq_screen": { - "type": "directory", - "description": "Output fastq_screen file containing png, html, txt and no_hits_fastq files", - "pattern": "*.{_fq_screen}" - } - }, - { - "png": { - "type": "file", - "description": "PNG file with graphical representation of alignments", - "pattern": "*.png" - } - }, - { - "html": { - "type": "file", - "description": "HTML file containing mapping results as a table and graphical representation", - "pattern": "*.html" - } - }, - { - "txt": { - "type": "file", - "description": "TXT file containing alignment statistics", - "pattern": "*.txt" - } - }, - { - "no_hits_fastq": { - "type": "file", - "description": "FastQ file containing reads that did not align to any database (optional)", - "pattern": "*_nohits.fastq" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "database": { + "type": "directory", + "description": "fastq screen database folder containing config file and index folders", + "pattern": "FastQ_Screen_Genomes" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.txt": { + "type": "file", + "description": "TXT file containing alignment statistics", + "pattern": "*.txt" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.png": { + "type": "file", + "description": "PNG file with graphical representation of alignments", + "pattern": "*.png" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML file containing mapping results as a table and graphical representation", + "pattern": "*.html" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "FastQ file containing reads that did not align to any database (optional)", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41333,33 +52152,44 @@ "documentation": "http://www.microbesonline.org/fasttree/#Usage", "licence": [ "GPL v2" - ] + ], + "identifier": "biotools:fasttree" } } ], "input": [ - { - "alignment": { - "type": "file", - "description": "A FASTA format multiple sequence alignment file", - "pattern": "*.{fasta,fas,fa,mfa}" + [ + { + "alignment": { + "type": "file", + "description": "A FASTA format multiple sequence alignment file", + "pattern": "*.{fasta,fas,fa,mfa}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "phylogeny": [ + { + "*.tre": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{tre}" + } + } + ] }, { - "phylogeny": { - "type": "file", - "description": "A phylogeny in Newick format", - "pattern": "*.{tre}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41392,45 +52222,56 @@ "tool_dev_url": "https://github.com/agordon/fastx_toolkit", "licence": [ "AGPL" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Decompressed FASTA/FASTQ input file", - "pattern": "*.{fastq,fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Decompressed FASTA/FASTQ input file", + "pattern": "*.{fastq,fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.fasta": { + "type": "file", + "description": "Collapsed FASTA file", + "pattern": "*.fasta" + } + } + ] }, { - "fasta": { - "type": "file", - "description": "Collapsed FASTA file", - "pattern": "*.fasta" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41464,72 +52305,123 @@ "tool_dev_url": "https://github.com/ncbi/fcs", "licence": [ "United States Government Work" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "assembly fasta file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cleaned_assembly": { - "type": "file", - "description": "Cleaned assembly in fasta format", - "pattern": "*.{cleaned_sequences.fa.gz}" - } - }, - { - "adaptor_report": { - "type": "file", - "description": "Report of identified adaptors", - "pattern": "*.{fcs_adaptor_report.txt}" - } - }, - { - "log": { - "type": "file", - "description": "Log file", - "pattern": "*.{fcs_adaptor.log}" - } - }, - { - "pipeline_args": { - "type": "file", - "description": "Run arguments", - "pattern": "*.{pipeline_args.yaml}" - } - }, - { - "skipped_trims": { - "type": "file", - "description": "Skipped trim information", - "pattern": "*.{skipped_trims.jsonl}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "assembly fasta file" + } + } + ] + ], + "output": [ + { + "cleaned_assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cleaned_sequences.fa.gz": { + "type": "file", + "description": "Cleaned assembly in fasta format", + "pattern": "*.{cleaned_sequences.fa.gz}" + } + } + ] + }, + { + "adaptor_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fcs_adaptor_report.txt": { + "type": "file", + "description": "Report of identified adaptors", + "pattern": "*.{fcs_adaptor_report.txt}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fcs_adaptor.log": { + "type": "file", + "description": "Log file", + "pattern": "*.{fcs_adaptor.log}" + } + } + ] + }, + { + "pipeline_args": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pipeline_args.yaml": { + "type": "file", + "description": "Run arguments", + "pattern": "*.{pipeline_args.yaml}" + } + } + ] + }, + { + "skipped_trims": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.skipped_trims.jsonl": { + "type": "file", + "description": "Skipped trim information", + "pattern": "*.{skipped_trims.jsonl}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41564,57 +52456,80 @@ "tool_dev_url": "https://github.com/ncbi/fcs", "license": [ "United States Government Work" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'6973' ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "assembly fasta file" - } - }, - { - "database": { - "type": "file", - "description": "Files of the database downloaded from the ncbi server, https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/. All files of one db should be downloaded and given to the process as channel.collect(). The link contains 2 databases, test-only and all. Use all for pipeline usage and test-only for tests." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'9606' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fcs_gx_report": { - "type": "file", - "description": "Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)", - "pattern": "*.fcs_gx_report.txt" - } - }, - { - "taxonomy_report": { - "type": "file", - "description": "Report containing the contig identifier and mapped contaminant species", - "pattern": "*.taxonomy.rpt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'6973' ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "assembly fasta file" + } + } + ], + [ + { + "gxdb": { + "type": "file", + "description": "The NCBI GenBank database to search against." + } + } + ] + ], + "output": [ + { + "fcs_gx_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'9606' ]\n" + } + }, + { + "out/*.fcs_gx_report.txt": { + "type": "file", + "description": "Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)", + "pattern": "*.fcs_gx_report.txt" + } + } + ] + }, + { + "taxonomy_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'9606' ]\n" + } + }, + { + "out/*.taxonomy.rpt": { + "type": "file", + "description": "Report containing the contig identifier and mapped contaminant species", + "pattern": "*.taxonomy.rpt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41651,32 +52566,43 @@ "doi": "10.1101/2022.05.18.492548", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "ids": { - "type": "list", - "description": "List of supported database ids e.g. SRA / GEO / ENA" + [ + { + "ids": { + "type": "list", + "description": "List of supported database ids e.g. SRA / GEO / ENA" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "json": [ + { + "*.json": { + "type": "file", + "description": "JSON file containing metadata for ids", + "pattern": "*.{json}" + } + } + ] }, { - "json": { - "type": "file", - "description": "JSON file containing metadata for ids", - "pattern": "*.{json}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41708,57 +52634,72 @@ "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file, grouped by UMI", - "pattern": "*.{bam,sam}" - } - }, - { - "min_reads": { - "type": "string", - "description": "Minimum number of raw/original reads to build each consensus read. Can be a space delimited list of 1-3 values. See fgbio documentation for more details." - } - }, - { - "min_baseq": { - "type": "integer", - "description": "Ignore bases in raw reads that have Q below this value" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "consensus BAM file", - "pattern": "*.bam" - } + ], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "grouped_bam": { + "type": "file", + "description": "Grouped BAM file", + "pattern": "*.bam" + } + } + ], + [ + { + "min_reads": { + "type": "string", + "description": "Minimum number of raw/original reads to build each consensus read. Can be a space delimited list of 1-3 values. See fgbio documentation for more details." + } + } + ], + [ + { + "min_baseq": { + "type": "integer", + "description": "Ignore bases in raw reads that have Q below this value" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "consensus BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41789,57 +52730,72 @@ "documentation": "http://fulcrumgenomics.github.io/fgbio/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, collapse:false ]\n" - } - }, - { - "grouped_bam": { - "type": "file", - "description": "The input SAM or BAM file, grouped by UMIs\n", - "pattern": "*.{bam,sam}" - } - }, - { - "min_reads": { - "type": "integer", - "description": "Minimum number of original reads to build each consensus read." - } - }, - { - "min_baseq": { - "type": "integer", - "description": "Ignore bases in raw reads that have Q below this value." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output SAM or BAM file to write consensus reads.\n", - "pattern": "*.{bam,sam}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, collapse:false ]\n" + } + }, + { + "grouped_bam": { + "type": "file", + "description": "The input SAM or BAM file, grouped by UMIs\n", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "min_reads": { + "type": "integer", + "description": "Minimum number of original reads to build each consensus read." + } + } + ], + [ + { + "min_baseq": { + "type": "integer", + "description": "Ignore bases in raw reads that have Q below this value." + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output SAM or BAM file to write consensus reads.\n", + "pattern": "*.{bam,sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -41878,7 +52834,8 @@ "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", "licence": [ "MIT" - ] + ], + "identifier": "biotools:fgbio" } }, { @@ -41889,87 +52846,150 @@ "tool_dev_url": "https://github.com/tidyverse/ggplot2", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "grouped_bam": { - "type": "file", - "description": "It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order.", - "pattern": "*.bam" - } - }, - { - "interval_list": { - "type": "file", - "description": "Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html", - "pattern": "*.{tsv|txt|interval_list}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "family_sizes": { - "type": "file", - "description": "Metrics on the frequency of different types of families of different sizes", - "pattern": "*.txt" - } - }, - { - "duplex_family_sizes": { - "type": "file", - "description": "Metrics on the frequency of duplex tag families by the number of observations from each strand", - "pattern": "*.txt" - } - }, - { - "duplex_yield_metrics": { - "type": "file", - "description": "Summary QC metrics produced using 5%, 10%, 15%...100% of the data", - "pattern": "*.txt" - } - }, - { - "umi_counts": { - "type": "file", - "description": "Metrics on the frequency of observations of UMIs within reads and tag families", - "pattern": "*.txt" - } - }, - { - "duplex_qc": { - "type": "file", - "description": "A series of plots generated from the preceding metrics files for visualization", - "pattern": "*.pdf" - } - }, - { - "duplex_umi_counts": { - "type": "file", - "description": "Metrics on the frequency of observations of duplex UMIs within reads and tag families.", - "pattern": "*.txt" - } + ], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "grouped_bam": { + "type": "file", + "description": "It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order.", + "pattern": "*.bam" + } + } + ], + [ + { + "interval_list": { + "type": "file", + "description": "Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html", + "pattern": "*.{tsv|txt|interval_list}" + } + } + ] + ], + "output": [ + { + "family_sizes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.family_sizes.txt": { + "type": "file", + "description": "Metrics on the frequency of different types of families of different sizes", + "pattern": "*.txt" + } + } + ] + }, + { + "duplex_family_sizes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_family_sizes.txt": { + "type": "file", + "description": "Metrics on the frequency of duplex tag families by the number of observations from each strand", + "pattern": "*.txt" + } + } + ] + }, + { + "duplex_yield_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_yield_metrics.txt": { + "type": "file", + "description": "Summary QC metrics produced using 5%, 10%, 15%...100% of the data", + "pattern": "*.txt" + } + } + ] + }, + { + "umi_counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.umi_counts.txt": { + "type": "file", + "description": "Metrics on the frequency of observations of UMIs within reads and tag families", + "pattern": "*.txt" + } + } + ] + }, + { + "duplex_qc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_qc.pdf": { + "type": "file", + "description": "A series of plots generated from the preceding metrics files for visualization", + "pattern": "*.pdf" + } + } + ] + }, + { + "duplex_umi_counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "**.duplex_umi_counts.txt": { + "type": "file", + "description": "Metrics on the frequency of observations of duplex UMIs within reads and tag families.", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42001,46 +53021,73 @@ "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "reads": { - "type": "file", - "description": "pair of reads to be converted into BAM file", - "pattern": "*.{fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.yml}" - } - }, - { - "bam": { - "type": "file", - "description": "Unaligned, unsorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Unaligned, unsorted CRAM file", - "pattern": "*.{cram}" - } + ], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "pair of reads to be converted into BAM file", + "pattern": "*.{fastq.gz}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Unaligned, unsorted BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Unaligned, unsorted CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42084,76 +53131,95 @@ "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file containing genomic sequence information", - "pattern": "*.bam" - } - }, - { - "min_reads": { - "type": "integer", - "description": "Minimum number of reads required to keep a consensus read" - } - }, - { - "min_baseq": { - "type": "file", - "description": "Minimum base quality to consider" - } - }, - { - "max_base_error_rate": { - "type": "file", - "description": "Maximum base error rate for a position before it is replaced with an N." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Filtered consensus BAM file", - "pattern": "*.bam" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file containing genomic sequence information", + "pattern": "*.bam" + } + } + ], + [ + { + "min_reads": { + "type": "integer", + "description": "Minimum number of reads required to keep a consensus read" + } + } + ], + [ + { + "min_baseq": { + "type": "file", + "description": "Minimum base quality to consider" + } + } + ], + [ + { + "max_base_error_rate": { + "type": "file", + "description": "Maximum base error rate for a position before it is replaced with an N." + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Filtered consensus BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42185,64 +53251,87 @@ "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file. Note: the MQ tag is required on reads with mapped mates (!)\n", - "pattern": "*.bam" - } - }, - { - "strategy": { - "type": "string", - "enum": [ - "Identity", - "Edit", - "Adjacency", - "Paired" ], - "description": "Reguired argument: defines the UMI assignment strategy.\nMust be chosen among: Identity, Edit, Adjacency, Paired.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "UMI-grouped BAM", - "pattern": "*.bam" - } - }, - { - "histogram": { - "type": "file", - "description": "A text file containing the tag family size counts", - "pattern": "*.txt" - } + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file. Note: the MQ tag is required on reads with mapped mates (!)\n", + "pattern": "*.bam" + } + } + ], + [ + { + "strategy": { + "type": "string", + "enum": [ + "Identity", + "Edit", + "Adjacency", + "Paired" + ], + "description": "Reguired argument: defines the UMI assignment strategy.\nMust be chosen among: Identity, Edit, Adjacency, Paired.\n" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "UMI-grouped BAM", + "pattern": "*.bam" + } + } + ] + }, + { + "histogram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*histogram.txt": { + "type": "file", + "description": "A text file containing the tag family size counts", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42279,45 +53368,56 @@ "documentation": "http://fulcrumgenomics.github.io/fgbio/", "licence": [ "MIT" - ] + ], + "identifier": "biotools:fgbio" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, collapse:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "The input SAM or BAM file to be sorted.\n", - "pattern": "*.{bam,sam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, collapse:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "The input SAM or BAM file to be sorted.\n", + "pattern": "*.{bam,sam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output SAM or BAM file.\n", - "pattern": "*.{bam,sam}" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output SAM or BAM file.\n", + "pattern": "*.{bam,sam}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42357,84 +53457,101 @@ "tool_dev_url": "https://github.com/fulcrumgenomics/fgbio", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mapped_bam": { - "type": "file", - "description": "mapped BAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "unmapped_bam": { - "type": "file", - "description": "unmapped BAM file", - "pattern": "*.bam" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'GRCh38' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file containing genomic sequence information", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'GRCh38' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "dict file containing a sequence dictionary for the fasta file", - "pattern": "*.{dict}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Zipped BAM file", - "pattern": "*.bam" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:fgbio" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "unmapped_bam": { + "type": "file", + "description": "unmapped BAM file", + "pattern": "*.bam" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mapped_bam": { + "type": "file", + "description": "mapped BAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'GRCh38' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file containing genomic sequence information", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'GRCh38' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "dict file containing a sequence dictionary for the fasta file", + "pattern": "*.{dict}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Zipped BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42468,59 +53585,80 @@ "tool_dev_url": "https://github.com/rrwick/Filtlong", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "shortreads": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" - } - }, - { - "longreads": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Filtered (compressed) fastq file", - "pattern": "*.fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Standard error logging file containing summary statistics", - "pattern": "*.log" - } + ], + "identifier": "biotools:filtlong" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shortreads": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" + } + }, + { + "longreads": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Filtered (compressed) fastq file", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Standard error logging file containing summary statistics", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42559,59 +53697,90 @@ "doi": "10.1093/bioinformatics/btr507", "licence": [ "GPL v3+" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 2; i.e., paired-end data.\n", - "pattern": "*fastq.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "merged": { - "type": "file", - "description": "The merged fastq reads", - "pattern": ".extendedFrags.fastq.gz" - } - }, - { - "notcombined": { - "type": "file", - "description": "Not combined reads from flash", - "pattern": ".notCombined_*.fastq.gz" - } - }, - { - "histogram": { - "type": "file", - "description": "HistogramNumeric histogram of merged read lengths.", - "pattern": ".hist" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 2; i.e., paired-end data.\n", + "pattern": "*fastq.gz" + } + } + ] + ], + "output": [ + { + "merged": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.extendedFrags.fastq.gz": { + "type": "file", + "description": "The merged fastq reads", + "pattern": ".extendedFrags.fastq.gz" + } + } + ] + }, + { + "notcombined": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.notCombined_*.fastq.gz": { + "type": "file", + "description": "Not combined reads from flash", + "pattern": ".notCombined_*.fastq.gz" + } + } + ] + }, + { + "histogram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.hist": { + "type": "file", + "description": "HistogramNumeric histogram of merged read lengths.", + "pattern": ".hist" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42646,87 +53815,150 @@ "doi": "10.1038/s41592-020-00971-x", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.", - "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" - } - }, - { - "mode": { - "type": "string", - "description": "Flye mode depending on the input data (source and error rate)", - "pattern": "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembled FASTA file", - "pattern": "*.fasta.gz" - } - }, - { - "gfa": { - "type": "file", - "description": "Repeat graph in gfa format", - "pattern": "*.gfa.gz" - } - }, - { - "gv": { - "type": "file", - "description": "Repeat graph in gv format", - "pattern": "*.gv.gz" - } - }, - { - "txt": { - "type": "file", - "description": "Extra information and statistics about resulting contigs", - "pattern": "*.txt" - } - }, - { - "log": { - "type": "file", - "description": "Flye log file", - "pattern": "*.log" - } - }, - { - "json": { - "type": "file", - "description": "Flye parameters", - "pattern": "*.json" - } + ], + "identifier": "biotools:Flye" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.", + "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" + } + } + ], + [ + { + "mode": { + "type": "string", + "description": "Flye mode depending on the input data (source and error rate)", + "pattern": "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "Assembled FASTA file", + "pattern": "*.fasta.gz" + } + } + ] + }, + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gfa.gz": { + "type": "file", + "description": "Repeat graph in gfa format", + "pattern": "*.gfa.gz" + } + } + ] + }, + { + "gv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gv.gz": { + "type": "file", + "description": "Repeat graph in gv format", + "pattern": "*.gv.gz" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Extra information and statistics about resulting contigs", + "pattern": "*.txt" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Flye log file", + "pattern": "*.log" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Flye parameters", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42765,45 +53997,56 @@ "doi": "10.1093/bioinformatics/btad153", "licence": [ "GPL v3-or-later" - ] + ], + "identifier": "biotools:foldcomp" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "pdb": { - "type": "file", - "description": "Protein structure(s) in PDB or CIF format to compress (also works with folder input)", - "pattern": "*.{pdb,cif}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pdb": { + "type": "file", + "description": "Protein structure(s) in PDB or CIF format to compress (also works with folder input)", + "pattern": "*.{pdb,cif}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fcz": { - "type": "file", - "description": "Either single compressed protein structure (if input was file) or folder with all compressed protein structures (if input was directory)\n", - "pattern": "{*_fcz,*.fcz}" - } + "fcz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*fcz": { + "type": "file", + "description": "Either single compressed protein structure (if input was file) or folder with all compressed protein structures (if input was directory)\n", + "pattern": "{*_fcz,*.fcz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42836,45 +54079,56 @@ "doi": "10.1093/bioinformatics/btad153", "licence": [ "GPL v3-or-later" - ] + ], + "identifier": "biotools:foldcomp" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fcz": { - "type": "file", - "description": "Foldcomp compressed protein structure(s) (also works with folder input)", - "pattern": "*{*,*.fcz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fcz": { + "type": "file", + "description": "Foldcomp compressed protein structure(s) (also works with folder input)", + "pattern": "*{*,*.fcz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "pdb": { - "type": "file", - "description": "Either single protein structure (if input was file) or folder with all decompressed protein structures (if input was directory)\n", - "pattern": "{*_pdb,*.pdb,*.cif}" - } + "pdb": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "{*pdb,*.cif}": { + "type": "file", + "description": "Either single protein structure (if input was file) or folder with all decompressed protein structures (if input was directory)\n", + "pattern": "{*_pdb,*.pdb,*.cif}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42905,58 +54159,81 @@ "doi": "10.1101/2024.08.01.606130", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "pdbs": { - "type": "file", - "description": "Input protein structures in PDB format.", - "pattern": "*.{pdb,mmcif}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "msa_3di": { - "type": "file", - "description": "Fasta file containing the multiple sequence alignment with 3Di alphabet", - "pattern": "*.{fa}" - } - }, - { - "msa_aa": { - "type": "file", - "description": "Fasta file containing the multiple sequence alignment with Amino Acid alphabet", - "pattern": "*.{fa}" - } + ], + "identifier": "biotools:foldmason" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pdbs": { + "type": "file", + "description": "Input protein structures in PDB format.", + "pattern": "*.{pdb,mmcif}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "msa_3di": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_3di.fa${compress ? '.gz' : ''}": { + "type": "file", + "description": "Fasta file containing the multiple sequence alignment with 3Di alphabet", + "pattern": "*.{fa}" + } + } + ] + }, + { + "msa_aa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_aa.fa${compress ? '.gz' : ''}": { + "type": "file", + "description": "Fasta file containing the multiple sequence alignment with Amino Acid alphabet", + "pattern": "*.{fa}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -42995,45 +54272,56 @@ "doi": "10.1038/s41587-023-01773-0", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:foldseek" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "pdb": { + "type": "file", + "description": "Protein structure(s) in PDB, mmCIF or mmJSON format (also works with folder input)", + "pattern": "*.{pdb,mmcif,mmjson}" + } } - }, - { - "pdb": { - "type": "file", - "description": "Protein structure(s) in PDB, mmCIF or mmJSON format (also works with folder input)", - "pattern": "*.{pdb,mmcif,mmjson}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing pdb database files", - "pattern": "*" - } + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${meta.id}": { + "type": "directory", + "description": "Directory containing pdb database files", + "pattern": "*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43063,58 +54351,71 @@ "doi": "10.1038/s41587-023-01773-0", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "pdb": { - "type": "file", - "description": "Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input)", - "pattern": "*.{pdb,mmcif,mmjson}" - } - }, - { - "meta_db": { - "type": "map", - "description": "Groovy Map containing sample information for the foldseek db\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "foldseek database from protein structures", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "aln": { - "type": "file", - "description": "Structural comparisons file output\nQuery, Target, Identity, Alignment length, Mismatches, Gap openings,\nQuery start, Query end, Target start, Target end, E-value, Bit score\n", - "pattern": "*.{m8}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:foldseek" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "pdb": { + "type": "file", + "description": "Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input)", + "pattern": "*.{pdb,mmcif,mmjson}" + } + } + ], + [ + { + "meta_db": { + "type": "map", + "description": "Groovy Map containing sample information for the foldseek db\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db": { + "type": "directory", + "description": "foldseek database from protein structures", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${meta.id}.m8": { + "type": "file", + "description": "Structural comparisons file output\nQuery, Target, Identity, Alignment length, Mismatches, Gap openings,\nQuery start, Query end, Target start, Target end, E-value, Bit score\n", + "pattern": "*.{m8}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43144,38 +54445,49 @@ "tool_dev_url": "https://github.com/stjude-rust-labs/fq", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Random generated FASTQ files.", - "pattern": "*_R[12].fastq.gz" - } + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Random generated FASTQ files.", + "pattern": "*_R[12].fastq.gz" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43207,39 +54519,57 @@ "tool_dev_url": "https://github.com/stjude-rust-labs/fq", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file list", - "pattern": "*.fastq{,.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file list", + "pattern": "*.fastq{,.gz}" + } } - } + ] ], "output": [ { - "lint": { - "type": "file", - "description": "Lint output", - "pattern": "*.fq_lint.txt" - } + "lint": [ + { + "meta": { + "type": "file", + "description": "Lint output", + "pattern": "*.fq_lint.txt" + } + }, + { + "*.fq_lint.txt": { + "type": "file", + "description": "Lint output", + "pattern": "*.fq_lint.txt" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43271,45 +54601,56 @@ "tool_dev_url": "https://github.com/stjude-rust-labs/fq", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fq,fastq}{,.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file", + "pattern": "*.{fq,fastq}{,.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Randomly sampled FASTQ files.", + "pattern": "*_R[12].fastq.gz" + } + } + ] }, { - "fastq": { - "type": "file", - "description": "Randomly sampled FASTQ files.", - "pattern": "*_R[12].fastq.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43350,65 +54691,96 @@ "documentation": "https://github.com/fulcrumgenomics/fqtk", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sample_sheet": { - "type": "file", - "description": "Tsv file, with two columns sample_id and barcode", - "pattern": "*.{tsv}" - } - }, - { - "fastq_readstructure_pairs": { - "type": "map", - "description": "List of lists i.e. [[, , ],...]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sample_fastq": { - "type": "file", - "description": "Demultiplexed per-sample FASTQ files", - "pattern": "output/*R*.fastq.gz" - } - }, - { - "metrics": { - "type": "file", - "description": "Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best\n", - "pattern": "output/demux-metrics.txt" - } - }, - { - "most_frequent_unmatched": { - "type": "file", - "description": "File containing unmatched fastq records\n", - "pattern": "output/unmatched*.fq.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sample_sheet": { + "type": "file", + "description": "Tsv file, with two columns sample_id and barcode", + "pattern": "*.{tsv}" + } + }, + { + "fastq_readstructure_pairs": { + "type": "map", + "description": "List of lists i.e. [[, , ],...]" + } + } + ] + ], + "output": [ + { + "sample_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/*.fq.gz": { + "type": "file", + "description": "Demultiplexed per-sample FASTQ files", + "pattern": "output/*R*.fastq.gz" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/demux-metrics.txt": { + "type": "file", + "description": "Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best\n", + "pattern": "output/demux-metrics.txt" + } + } + ] + }, + { + "most_frequent_unmatched": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/unmatched*.fq.gz": { + "type": "file", + "description": "File containing unmatched fastq records\n", + "pattern": "output/unmatched*.fq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43453,138 +54825,159 @@ "doi": "10.48550/arXiv.1207.3907", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_1": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_1_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "input_2": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_2_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "target_bed": { - "type": "file", - "description": "Optional - Limit analysis to targets listed in this BED-format FILE.", - "pattern": "*.bed" - } - }, - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file", - "pattern": ".{fa,fa.gz,fasta,fasta.gz}" - } - }, - { - "ref_idx_meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "reference fasta file index", - "pattern": "*.{fa,fasta}.fai" - } - }, - { - "samples_meta": { - "type": "map", - "description": "Groovy Map containing meta information for the samples file.\ne.g. [ id:'test_samples' ]\n" - } - }, - { - "samples": { - "type": "file", - "description": "Optional - Limit analysis to samples listed (one per line) in the FILE.", - "pattern": "*.txt" - } - }, - { - "populations_meta": { - "type": "map", - "description": "Groovy Map containing meta information for the populations file.\ne.g. [ id:'test_populations' ]\n" - } - }, - { - "populations": { - "type": "file", - "description": "Optional - Each line of FILE should list a sample and a population which it is part of.", - "pattern": "*.txt" - } - }, - { - "cnv_meta": { - "type": "map", - "description": "Groovy Map containing meta information for the cnv file.\ne.g. [ id:'test_cnv' ]\n" - } - }, - { - "cnv": { - "type": "file", - "description": "A copy number map BED file, which has either a sample-level ploidy:\nsample_name copy_number\nor a region-specific format:\nseq_name start end sample_name copy_number\n", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } + ], + "identifier": "biotools:freebayes" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_1": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_1_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai}" + } + }, + { + "input_2": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_2_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai}" + } + }, + { + "target_bed": { + "type": "file", + "description": "Optional - Limit analysis to targets listed in this BED-format FILE.", + "pattern": "*.bed" + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file", + "pattern": ".{fa,fa.gz,fasta,fasta.gz}" + } + } + ], + [ + { + "ref_idx_meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "reference fasta file index", + "pattern": "*.{fa,fasta}.fai" + } + } + ], + [ + { + "samples_meta": { + "type": "map", + "description": "Groovy Map containing meta information for the samples file.\ne.g. [ id:'test_samples' ]\n" + } + }, + { + "samples": { + "type": "file", + "description": "Optional - Limit analysis to samples listed (one per line) in the FILE.", + "pattern": "*.txt" + } + } + ], + [ + { + "populations_meta": { + "type": "map", + "description": "Groovy Map containing meta information for the populations file.\ne.g. [ id:'test_populations' ]\n" + } + }, + { + "populations": { + "type": "file", + "description": "Optional - Each line of FILE should list a sample and a population which it is part of.", + "pattern": "*.txt" + } + } + ], + [ + { + "cnv_meta": { + "type": "map", + "description": "Groovy Map containing meta information for the cnv file.\ne.g. [ id:'test_cnv' ]\n" + } + }, + { + "cnv": { + "type": "file", + "description": "A copy number map BED file, which has either a sample-level ploidy:\nsample_name copy_number\nor a region-specific format:\nseq_name start end sample_name copy_number\n", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43637,79 +55030,106 @@ "doi": "10.1038/s41586-022-05049-6", "licence": [ "BSD-2-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variants": { - "type": "file", - "description": "File containing identified variants in a gff-like format", - "pattern": "*.variants.tsv" - } - }, - { - "depths": { - "type": "file", - "description": "File containing depth of the variants", - "pattern": "*.depth.tsv" - } - }, - { - "repeats": { - "type": "integer", - "description": "Number of bootstrap repeats to perform" - } - }, - { - "barcodes": { - "type": "file", - "description": "File containing lineage defining barcodes", - "pattern": "*barcodes.csv" - } - }, - { - "lineages_meta": { - "type": "file", - "description": "File containing lineage metadata that correspond to barcodes", - "pattern": "*lineages.json" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "lineages": { - "type": "file", - "description": "a csv file that includes the lineages present and their corresponding abundances", - "pattern": "*lineages.csv" - } - }, - { - "summarized": { - "type": "file", - "description": "a csv file that includes the lineages present but summarized by constellation and their corresponding abundances", - "pattern": "*summarized.csv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "variants": { + "type": "file", + "description": "File containing identified variants in a gff-like format", + "pattern": "*.variants.tsv" + } + }, + { + "depths": { + "type": "file", + "description": "File containing depth of the variants", + "pattern": "*.depth.tsv" + } + } + ], + [ + { + "repeats": { + "type": "integer", + "description": "Number of bootstrap repeats to perform" + } + } + ], + [ + { + "barcodes": { + "type": "file", + "description": "File containing lineage defining barcodes", + "pattern": "*barcodes.csv" + } + } + ], + [ + { + "lineages_meta": { + "type": "file", + "description": "File containing lineage metadata that correspond to barcodes", + "pattern": "*lineages.json" + } + } + ] + ], + "output": [ + { + "lineages": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*lineages.csv": { + "type": "file", + "description": "a csv file that includes the lineages present and their corresponding abundances", + "pattern": "*lineages.csv" + } + } + ] + }, + { + "summarized": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*summarized.csv": { + "type": "file", + "description": "a csv file that includes the lineages present but summarized by constellation and their corresponding abundances", + "pattern": "*summarized.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43743,66 +55163,81 @@ "doi": "10.1038/s41586-022-05049-6", "licence": [ "BSD-2-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variants": { - "type": "file", - "description": "File containing identified variants in a gff-like format", - "pattern": "*.variants.tsv" - } - }, - { - "depths": { - "type": "file", - "description": "File containing depth of the variants", - "pattern": "*.depth.tsv" - } - }, - { - "barcodes": { - "type": "file", - "description": "File containing lineage defining barcodes", - "pattern": "*barcodes.csv" - } - }, - { - "lineages_meta": { - "type": "file", - "description": "File containing lineage metadata that correspond to barcodes", - "pattern": "*lineages.json" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "demix": { - "type": "file", - "description": "a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation", - "pattern": "*.demix.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "variants": { + "type": "file", + "description": "File containing identified variants in a gff-like format", + "pattern": "*.variants.tsv" + } + }, + { + "depths": { + "type": "file", + "description": "File containing depth of the variants", + "pattern": "*.depth.tsv" + } + } + ], + [ + { + "barcodes": { + "type": "file", + "description": "File containing lineage defining barcodes", + "pattern": "*barcodes.csv" + } + } + ], + [ + { + "lineages_meta": { + "type": "file", + "description": "File containing lineage metadata that correspond to barcodes", + "pattern": "*lineages.json" + } + } + ] + ], + "output": [ + { + "demix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation", + "pattern": "*.demix.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43835,46 +55270,65 @@ "doi": "10.1038/s41586-022-05049-6", "licence": [ "BSD-2-Clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "db_name": { - "type": "string", - "description": "The name of the database directory" + [ + { + "db_name": { + "type": "string", + "description": "The name of the database directory" + } } - } + ] ], "output": [ { - "barcodes": { - "type": "file", - "description": "File containing lineage defining barcodes", - "pattern": "*barcodes.csv" - } + "barcodes": [ + { + "${db_name}/usher_barcodes.csv": { + "type": "file", + "description": "File containing lineage defining barcodes", + "pattern": "*barcodes.csv" + } + } + ] }, { - "lineages_topology": { - "type": "file", - "description": "File containing the lineage topology", - "pattern": "*lineages.yml" - } + "lineages_topology": [ + { + "${db_name}/lineages.yml": { + "type": "file", + "description": "File containing the lineage topology", + "pattern": "*lineages.yml" + } + } + ] }, { - "lineages_meta": { - "type": "file", - "description": "File containing lineage metadata that correspond to barcodes", - "pattern": "*lineages.json" - } + "lineages_meta": [ + { + "${db_name}/curated_lineages.json": { + "type": "file", + "description": "File containing lineage metadata that correspond to barcodes", + "pattern": "*lineages.json" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43907,59 +55361,72 @@ "doi": "10.1038/s41586-022-05049-6", "licence": [ "BSD-2-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference sequence used for mapping and generating the BAM file", - "pattern": "*.fa" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variants": { - "type": "file", - "description": "File containing identified variants in a gff-like format", - "pattern": "*.variants.tsv" - } - }, - { - "depths": { - "type": "file", - "description": "File containing depth of the variants", - "pattern": "*.depth.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference sequence used for mapping and generating the BAM file", + "pattern": "*.fa" + } + } + ] + ], + "output": [ + { + "variants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.variants.tsv": { + "type": "file", + "description": "File containing identified variants in a gff-like format", + "pattern": "*.variants.tsv" + } + }, + { + "*.depth.tsv": { + "type": "file", + "description": "File containing identified variants in a gff-like format", + "pattern": "*.variants.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -43993,66 +55460,87 @@ "doi": "10.1111/NODOI", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bins": { - "type": "file", - "description": "A list of fasta-formatted genomes for dereplication", - "pattern": "*.{fa,fna,fa.gz, etc}" - } - }, - { - "qc_table": { - "type": "file", - "description": "(optional) Either a (CheckM)[https://nf-co.re/modules/checkm_lineagewf] summary TSV containing\ninformation on the completeness and contamination of the input genomes (13 columns),\nor a 3-column csv with the header `genome,completeness,contamination`.\nIn both cases the first column should contain the names of the input genome files,\nminus the last file extension\n(i.e. if the genome is gzipped, the genome name should retain the .fasta extension).\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "qc_format": { - "type": "string", - "description": "Defines the type if input table in `qc_table`, if specified.", - "pattern": "checkm|genome_info" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file in the format `representative_genome` \\t `member_genome`", - "pattern": "*.tsv" - } - }, - { - "dereplicated_bins": { - "type": "file", - "description": "The representative genomes following dereplication by galah.", - "pattern": "*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bins": { + "type": "file", + "description": "A list of fasta-formatted genomes for dereplication", + "pattern": "*.{fa,fna,fa.gz, etc}" + } + }, + { + "qc_table": { + "type": "file", + "description": "(optional) Either a (CheckM)[https://nf-co.re/modules/checkm_lineagewf] summary TSV containing\ninformation on the completeness and contamination of the input genomes (13 columns),\nor a 3-column csv with the header `genome,completeness,contamination`.\nIn both cases the first column should contain the names of the input genome files,\nminus the last file extension\n(i.e. if the genome is gzipped, the genome name should retain the .fasta extension).\n", + "pattern": "*.{csv,tsv}" + } + }, + { + "qc_format": { + "type": "string", + "description": "Defines the type if input table in `qc_table`, if specified.", + "pattern": "checkm|genome_info" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file in the format `representative_genome` \\t `member_genome`", + "pattern": "*.tsv" + } + } + ] + }, + { + "dereplicated_bins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}-dereplicated/*": { + "type": "file", + "description": "The representative genomes following dereplication by galah.", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44086,73 +55574,116 @@ "doi": "10.1093/bioinformatics/btab607", "licence": [ "Apache License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "db": { - "type": "file", - "description": "Database in FASTA format", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gamma": { - "type": "file", - "description": "GAMMA file with annotated gene matches", - "pattern": "*.{gamma}" - } - }, - { - "psl": { - "type": "file", - "description": "PSL file with all gene matches found", - "pattern": "*.{psl}" - } - }, - { - "gff": { - "type": "file", - "description": "GFF file", - "pattern": "*.{gff}" - } - }, - { - "fasta": { - "type": "file", - "description": "multifasta file of the gene matches", - "pattern": "*.{fasta}" - } + ], + "identifier": "biotools:gamma" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Database in FASTA format", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "gamma": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gamma": { + "type": "file", + "description": "GAMMA file with annotated gene matches", + "pattern": "*.{gamma}" + } + } + ] + }, + { + "psl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.psl": { + "type": "file", + "description": "PSL file with all gene matches found", + "pattern": "*.{psl}" + } + } + ] + }, + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "GFF file", + "pattern": "*.{gff}" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "multifasta file of the gene matches", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44191,80 +55722,104 @@ "doi": "10.1093/nar/gkz501", "licence": [ "GPL v3-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "aligment_files": { - "type": "file", - "description": "One or more sorted BAM/CRAM file(s)", - "pattern": "*.{bam,cram}" - } - }, - { - "alignment_indices": { - "type": "file", - "description": "The index/indices of the BAM/CRAM file(s)", - "pattern": "*.{bai,crai}" - } - }, - { - "ref_regions": { - "type": "file", - "description": "A reference set of regions to genotype in a BED-like format. The file should have following columns:\n1. The name of the chromosome on which the STR is located\n2. The start position of the STR on its chromosome\n3. The end position of the STR on its chromosome\n4. The motif length\n5. The repeat motif\n", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The resulting VCF file containing the genotypes", - "pattern": "*.vcf" - } - }, - { - "samplestats": { - "type": "file", - "description": "A tab-delimited file containing statistics for each sample", - "pattern": "*.tab" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment_files": { + "type": "file", + "description": "Alignment files" + } + }, + { + "alignment_indices": { + "type": "file", + "description": "The index/indices of the BAM/CRAM file(s)", + "pattern": "*.{bai,crai}" + } + }, + { + "ref_regions": { + "type": "file", + "description": "A reference set of regions to genotype in a BED-like format. The file should have following columns:\n1. The name of the chromosome on which the STR is located\n2. The start position of the STR on its chromosome\n3. The end position of the STR on its chromosome\n4. The motif length\n5. The repeat motif\n", + "pattern": "*.bed" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "The resulting VCF file containing the genotypes", + "pattern": "*.vcf" + } + } + ] + }, + { + "samplestats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.samplestats.tab": { + "type": "file", + "description": "A tab-delimited file containing statistics for each sample", + "pattern": "*.tab" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44300,65 +55855,90 @@ "doi": "10.1093/bioinformatics/btaa458", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "List of input FASTA files, or a directory containing input FASTA files.\nNote you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`.\n", - "pattern": "*" - } - }, - { - "taxonomy_files": { - "type": "file", - "description": "Pre-downloaded taxonomy files of input sequences. See ganon docs for formats" - } - }, - { - "genome_size_files": { - "type": "file", - "description": "Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats", - "pattern": "{species_genome_size.txt.gz,*_metadata.tar.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "db": { - "type": "file", - "description": "ganon database files", - "pattern": "*.{ibf,tax}" - } - }, - { - "info": { - "type": "file", - "description": "Copy of target info generated. Can be used for updating database.", - "pattern": "*info.tsv" - } + ], + "identifier": "biotools:ganon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "List of input FASTA files, or a directory containing input FASTA files.\nNote you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`.\n", + "pattern": "*" + } + } + ], + [ + { + "taxonomy_files": { + "type": "file", + "description": "Pre-downloaded taxonomy files of input sequences. See ganon docs for formats" + } + } + ], + [ + { + "genome_size_files": { + "type": "file", + "description": "Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats", + "pattern": "{species_genome_size.txt.gz,*_metadata.tar.gz}" + } + } + ] + ], + "output": [ + { + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{hibf,ibf,tax}": { + "type": "file", + "description": "ganon database files", + "pattern": "*.{ibf,tax}" + } + } + ] + }, + { + "info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.info.tsv": { + "type": "file", + "description": "Copy of target info generated. Can be used for updating database.", + "pattern": "*info.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44395,91 +55975,154 @@ "doi": "10.1093/bioinformatics/btaa458", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:ganon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastqs": { + "type": "file", + "description": "Single or paired FASTQ files, optionally gzipped", + "pattern": "*.{fq,fq.gz,fastq,fastq.gz}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Ganon database files from build or build-custom", + "pattern": "*.{ibf,tax}" + } + } + ] + ], + "output": [ + { + "tre": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tre": { + "type": "file", + "description": "Full ganon report file", + "pattern": "*.tre" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rep": { + "type": "file", + "description": "Plain ganon report file with only targets with match", + "pattern": "*.rep" + } + } + ] + }, + { + "one": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.one": { + "type": "file", + "description": "Information about a single (best) match of a given read after EM or LCA algorithms", + "pattern": "*.one" + } + } + ] + }, + { + "all": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.all": { + "type": "file", + "description": "Information of all matches to a given read", + "pattern": "*.all" + } + } + ] + }, + { + "unc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unc": { + "type": "file", + "description": "List of all reads without a hit", + "pattern": "*.unc" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Text file containing console output from ganon classify", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastqs": { - "type": "file", - "description": "Single or paired FASTQ files, optionally gzipped", - "pattern": "*.{fq,fq.gz,fastq,fastq.gz}" - } - }, - { - "db": { - "type": "file", - "description": "Ganon database files from build or build-custom", - "pattern": "*.{ibf,tax}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tre": { - "type": "file", - "description": "Full ganon report file", - "pattern": "*.tre" - } - }, - { - "report": { - "type": "file", - "description": "Plain ganon report file with only targets with match", - "pattern": "*.rep" - } - }, - { - "one": { - "type": "file", - "description": "Information about a single (best) match of a given read after EM or LCA algorithms", - "pattern": "*.one" - } - }, - { - "all": { - "type": "file", - "description": "Information of all matches to a given read", - "pattern": "*.all" - } - }, - { - "unc": { - "type": "file", - "description": "List of all reads without a hit", - "pattern": "*.unc" - } - }, - { - "log": { - "type": "file", - "description": "Text file containing console output from ganon classify", - "pattern": "*.log" - } - } - ], - "authors": [ - "@jfy133" + "authors": [ + "@jfy133" ], "maintainers": [ "@jfy133" @@ -44518,52 +56161,65 @@ "doi": "10.1093/bioinformatics/btaa458", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "rep": { - "type": "file", - "description": "Input 'repo' files from ganon classify", - "pattern": "*.rep" - } - }, - { - "db": { - "type": "file", - "description": "Ganon database files from build or build-custom", - "pattern": "*.{ibf,tax}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tre": { - "type": "file", - "description": "Output ganon report containing taxonomic profile information. Formatting of contents depends on --output-format.", - "pattern": "*.tre" - } + ], + "identifier": "biotools:ganon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rep": { + "type": "file", + "description": "Input 'repo' files from ganon classify", + "pattern": "*.rep" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Ganon database files from build or build-custom", + "pattern": "*.{ibf,tax}" + } + } + ] + ], + "output": [ + { + "tre": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tre": { + "type": "file", + "description": "Output ganon report containing taxonomic profile information. Formatting of contents depends on --output-format.", + "pattern": "*.tre" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44607,45 +56263,56 @@ "doi": "10.1093/bioinformatics/btaa458", "licence": [ "MIT" - ] + ], + "identifier": "biotools:ganon" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tre": { - "type": "file", - "description": "A list of 'tre' files from ganon report", - "pattern": "*.tre" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tre": { + "type": "file", + "description": "A list of 'tre' files from ganon report", + "pattern": "*.tre" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Output ganon table containing taxonomic profile information of multiple samples. Formatting of contents depends on --output-format.", + "pattern": "*.txt" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Output ganon table containing taxonomic profile information of multiple samples. Formatting of contents depends on --output-format.", - "pattern": "*.txt" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44685,65 +56352,146 @@ "doi": "10.1093/bioinformatics/btaa070", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "jplace": { - "type": "file", - "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", - "pattern": "*.{jplace,jplace.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "examineassign": { - "type": "directory", - "description": "Execution directory" - } - }, - { - "profile": { - "type": "file", - "description": "profile tsv file", - "pattern": "*profile.tsv" - } - }, - { - "labelled_tree": { - "type": "file", - "description": "labelled tree in newick format", - "pattern": "*labelled_tree.newick" - } - }, - { - "per_query": { - "type": "file", - "description": "per query taxonomy assignments in tsv format", - "pattern": "*per_query.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:GAPPA" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "jplace": { + "type": "file", + "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", + "pattern": "*.{jplace,jplace.gz}" + } + }, + { + "taxonomy": { + "type": "file", + "description": "taxonomy file" + } + } + ] + ], + "output": [ + { + "examineassign": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "./.": { + "type": "directory", + "description": "Execution directory" + } + } + ] + }, + { + "profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*profile.tsv": { + "type": "file", + "description": "profile tsv file", + "pattern": "*profile.tsv" + } + } + ] + }, + { + "labelled_tree": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*labelled_tree.newick": { + "type": "file", + "description": "labelled tree in newick format", + "pattern": "*labelled_tree.newick" + } + } + ] + }, + { + "per_query": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*per_query.tsv": { + "type": "file", + "description": "per query taxonomy assignments in tsv format", + "pattern": "*per_query.tsv" + } + } + ] + }, + { + "krona": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*krona.profile": { + "type": "file", + "description": "krona profile file", + "pattern": "*krona.profile" + } + } + ] + }, + { + "sativa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*sativa.tsv": { + "type": "file", + "description": "sativa output file", + "pattern": "*sativa.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44786,45 +56534,56 @@ "doi": "10.1093/bioinformatics/btaa070", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:GAPPA" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "jplace": { + "type": "file", + "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", + "pattern": "*.{jplace,jplace.gz}" + } } - }, - { - "jplace": { - "type": "file", - "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", - "pattern": "*.{jplace,jplace.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "newick": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.newick": { + "type": "file", + "description": "phylogenetic tree file in newick format", + "pattern": "*.newick" + } + } + ] }, { - "newick": { - "type": "file", - "description": "phylogenetic tree file in newick format", - "pattern": "*.newick" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44868,80 +56627,141 @@ "doi": "10.1093/bioinformatics/btaa070", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "jplace": { - "type": "file", - "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", - "pattern": "*.{jplace,jplace.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "newick": { - "type": "file", - "description": "phylogenetic tree file in newick format", - "pattern": "*.newick" - } - }, - { - "nexus": { - "type": "file", - "description": "coloured phylogenetic tree file in nexus format", - "pattern": "*.nexus" - } - }, - { - "phyloxml": { - "type": "file", - "description": "coloured phylogenetic tree file in phyloxml format", - "pattern": "*.phyloxml" - } - }, - { - "svg": { - "type": "file", - "description": "coloured phylogenetic tree file in svg format", - "pattern": "*.svg" - } - }, - { - "colours": { - "type": "file", - "description": "colours used in plot", - "pattern": "*.colours.txt" - } - }, - { - "log": { - "type": "file", - "description": "log file from the run", - "pattern": "*.log" - } + ], + "identifier": "biotools:GAPPA" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "jplace": { + "type": "file", + "description": "jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not", + "pattern": "*.{jplace,jplace.gz}" + } + } + ] + ], + "output": [ + { + "newick": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.newick": { + "type": "file", + "description": "phylogenetic tree file in newick format", + "pattern": "*.newick" + } + } + ] + }, + { + "nexus": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.nexus": { + "type": "file", + "description": "coloured phylogenetic tree file in nexus format", + "pattern": "*.nexus" + } + } + ] + }, + { + "phyloxml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.phyloxml": { + "type": "file", + "description": "coloured phylogenetic tree file in phyloxml format", + "pattern": "*.phyloxml" + } + } + ] + }, + { + "svg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "coloured phylogenetic tree file in svg format", + "pattern": "*.svg" + } + } + ] + }, + { + "colours": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.colours.txt": { + "type": "file", + "description": "colours used in plot", + "pattern": "*.colours.txt" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file from the run", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -44985,85 +56805,120 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "An optional BAM index file", - "pattern": "*.{bai}" - } - }, - { - "cram": { - "type": "file", - "description": "Output CRAM file", - "pattern": "*.{cram}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_index": { + "type": "file", + "description": "Reference genome index file", + "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "An optional BAM index file", + "pattern": "*.{bai}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -45105,136 +56960,168 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "One or more interval files to annotate", - "pattern": "*.{interval_list,list,bed}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "The sequence dictionary reference FASTA file", - "pattern": "*.dict" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "mappable_regions": { - "type": "file", - "description": "Optional - Umap single-read mappability track\nThe track should correspond to the appropriate read length and overlapping intervals must be merged\n", - "pattern": "*.bed(.gz)?" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "mappable_regions_tbi": { - "type": "file", - "description": "Optional - The index of the gzipped umap single-read mappability track", - "pattern": "*.bed.gz.tbi" - } - }, - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "segmental_duplication_regions": { - "type": "file", - "description": "Optional - Segmental-duplication track", - "pattern": "*.bed(.gz)?" - } - }, - { - "meta8": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "segmental_duplication_regions_tbi": { - "type": "file", - "description": "Optional - The index of the gzipped segmental-duplication track", - "pattern": "*.bed.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "annotated_intervals": { - "type": "file", - "description": "The output TSV file with a SAM-style header containing the annotated intervals", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "One or more interval files to annotate", + "pattern": "*.{interval_list,list,bed}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "The sequence dictionary reference FASTA file", + "pattern": "*.dict" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "mappable_regions": { + "type": "file", + "description": "Optional - Umap single-read mappability track\nThe track should correspond to the appropriate read length and overlapping intervals must be merged\n", + "pattern": "*.bed(.gz)?" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "mappable_regions_tbi": { + "type": "file", + "description": "Optional - The index of the gzipped umap single-read mappability track", + "pattern": "*.bed.gz.tbi" + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "segmental_duplication_regions": { + "type": "file", + "description": "Optional - Segmental-duplication track", + "pattern": "*.bed(.gz)?" + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "segmental_duplication_regions_tbi": { + "type": "file", + "description": "Optional - The index of the gzipped segmental-duplication track", + "pattern": "*.bed.gz.tbi" + } + } + ] + ], + "output": [ + { + "annotated_intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The output TSV file with a SAM-style header containing the annotated intervals", + "pattern": "*.tsv" + } + }, + { + "s": { + "type": "file", + "description": "The output TSV file with a SAM-style header containing the annotated intervals", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -45274,92 +57161,119 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "bqsr_table": { - "type": "file", - "description": "Recalibration table from gatk4_baserecalibrator" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Recalibrated BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Recalibrated CRAM file", - "pattern": "*.{cram}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + }, + { + "bqsr_table": { + "type": "file", + "description": "Recalibration table from gatk4_baserecalibrator" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Recalibrated BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Recalibrated CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -46978,95 +58892,130 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.", - "pattern": "*.vcf" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "tabix index for the input vcf file.", - "pattern": "*.vcf.tbi" - } - }, - { - "recal": { - "type": "file", - "description": "Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.", - "pattern": "*.recal" - } - }, - { - "recal_index": { - "type": "file", - "description": "Index file for the recalibration file.", - "pattern": ".recal.idx" - } - }, - { - "tranches": { - "type": "file", - "description": "Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.", - "pattern": ".tranches" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "compressed vcf file containing the recalibrated variants.", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of recalibrated vcf file.", - "pattern": "*vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.", + "pattern": "*.vcf" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "tabix index for the input vcf file.", + "pattern": "*.vcf.tbi" + } + }, + { + "recal": { + "type": "file", + "description": "Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": "*.recal" + } + }, + { + "recal_index": { + "type": "file", + "description": "Index file for the recalibration file.", + "pattern": ".recal.idx" + } + }, + { + "tranches": { + "type": "file", + "description": "Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": ".tranches" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "compressed vcf file containing the recalibrated variants.", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "compressed vcf file containing the recalibrated variants.", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "file", + "description": "Index of recalibrated vcf file.", + "pattern": "*vcf.gz.tbi" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of recalibrated vcf file.", + "pattern": "*vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -47105,111 +59054,123 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index": { - "type": "file", - "description": "index file for input file", - "pattern": "*.{bai,crai}" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "index file for VCF file", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "fasta index file", - "pattern": "*.{fai}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "dict": { - "type": "file", - "description": "dictionary file", - "pattern": "*.{dict}" - } - }, - { - "intervals": { - "type": "file", - "description": "interval file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "output file", - "pattern": "*.{csv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "index file for BAM file", + "pattern": "*.{bai}" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "index file for VCF file", + "pattern": "*.{vcf.gz.tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "fasta index file", + "pattern": "*.{fai}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "dict": { + "type": "file", + "description": "dictionary file", + "pattern": "*.{dict}" + } + } + ], + [ + { + "intervals": { + "type": "file", + "description": "interval file" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -47243,93 +59204,114 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "known_sites": { - "type": "file", - "description": "VCF files with known sites for indels / snps (optional)", - "pattern": "*.vcf.gz" - } - }, - { - "known_sites_tbi": { - "type": "file", - "description": "Tabix index of the known_sites (optional)", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "table": { - "type": "file", - "description": "Recalibration table from BaseRecalibrator", - "pattern": "*.{table}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "known_sites": { + "type": "file", + "description": "VCF files with known sites for indels / snps (optional)", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "known_sites_tbi": { + "type": "file", + "description": "Tabix index of the known_sites (optional)", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "Recalibration table from BaseRecalibrator", + "pattern": "*.{table}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -48951,52 +60933,79 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input bed file", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "interval_list": { - "type": "file", - "description": "gatk interval list file", - "pattern": "*.interval_list" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input bed file", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "interval_list": [ + { + "meta": { + "type": "file", + "description": "gatk interval list file", + "pattern": "*.interval_list" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "gatk interval list file", + "pattern": "*.interval_list" + } + }, + { + "_list": { + "type": "file", + "description": "gatk interval list file", + "pattern": "*.interval_list" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49054,53 +61063,82 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "pileup": { - "type": "file", - "description": "File containing the pileups summary table of a tumor sample to be used to calculate contamination.", - "pattern": "*.pileups.table" - } - }, - { - "matched": { - "type": "file", - "description": "File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input.", - "pattern": "*.pileups.table" - } - } - ], - "output": [ - { - "contamination": { - "type": "file", - "description": "File containing the contamination table.", - "pattern": "*.contamination.table" - } - }, - { - "segmentation": { - "type": "file", - "description": "output table containing segmentation of tumor minor allele fractions (optional)", - "pattern": "*.segmentation.table" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "pileup": { + "type": "file", + "description": "File containing the pileups summary table of a tumor sample to be used to calculate contamination.", + "pattern": "*.pileups.table" + } + }, + { + "matched": { + "type": "file", + "description": "File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input.", + "pattern": "*.pileups.table" + } + } + ] + ], + "output": [ + { + "contamination": [ + { + "meta": { + "type": "file", + "description": "File containing the contamination table.", + "pattern": "*.contamination.table" + } + }, + { + "*.contamination.table": { + "type": "file", + "description": "File containing the contamination table.", + "pattern": "*.contamination.table" + } + } + ] + }, + { + "segmentation": [ + { + "meta": { + "type": "file", + "description": "output table containing segmentation of tumor minor allele fractions (optional)", + "pattern": "*.segmentation.table" + } + }, + { + "*.segmentation.table": { + "type": "file", + "description": "output table containing segmentation of tumor minor allele fractions (optional)", + "pattern": "*.segmentation.table" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49147,87 +61185,99 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bam_index": { - "type": "file", - "description": "index of the BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "intervals": { - "type": "file", - "description": "BED file or interval list containing regions (optional)", - "pattern": "*.{bed,interval_list}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "The sequence dictionary of the reference FASTA file", - "pattern": "*.dict" - } - }, - { - "strtablefile": { - "type": "file", - "description": "The StrTableFile zip folder of the reference FASTA file", - "pattern": "*.zip" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "dragstr_model": { - "type": "file", - "description": "The DragSTR model", - "pattern": "*.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bam_index": { + "type": "file", + "description": "index of the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "The sequence dictionary of the reference FASTA file", + "pattern": "*.dict" + } + } + ], + [ + { + "strtablefile": { + "type": "file", + "description": "The StrTableFile zip folder of the reference FASTA file", + "pattern": "*.zip" + } + } + ] + ], + "output": [ + { + "dragstr_model": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "The DragSTR model", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49259,107 +61309,138 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "aligned_input": { - "type": "file", - "description": "BAM/CRAM file from alignment (optional)", - "pattern": "*.{bam,cram}" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "architecture": { - "type": "file", - "description": "Neural Net architecture configuration json file (optional)", - "pattern": "*.json" - } - }, - { - "weights": { - "type": "file", - "description": "Keras model HD5 file with neural net weights. (optional)", - "pattern": "*.hd5" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.vcf" - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "aligned_input": { + "type": "file", + "description": "BAM/CRAM file from alignment (optional)", + "pattern": "*.{bam,cram}" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "architecture": { + "type": "file", + "description": "Neural Net architecture configuration json file (optional)", + "pattern": "*.json" + } + } + ], + [ + { + "weights": { + "type": "file", + "description": "Keras model HD5 file with neural net weights. (optional)", + "pattern": "*.hd5" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cnn.vcf.gz": { + "type": "file", + "description": "Annotated VCF file", + "pattern": "*.vcf" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cnn.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49399,105 +61480,132 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "intervals": { - "type": "file", - "description": "A file containing the specified intervals", - "pattern": "*.{bed,intervals}" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional - Reference FASTA", - "pattern": "*.{fasta,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "Optional - Index of the reference FASTA file", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "Optional - Sequence dictionary of the reference FASTA file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hdf5": { - "type": "file", - "description": "The read counts in hdf5 format", - "pattern": "*.hdf5" - } - }, - { - "tsv": { - "type": "file", - "description": "The read counts in TSV format", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "intervals": { + "type": "file", + "description": "A file containing the specified intervals", + "pattern": "*.{bed,intervals}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Optional - Reference FASTA", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Optional - Index of the reference FASTA file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Optional - Sequence dictionary of the reference FASTA file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "hdf5": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hdf5": { + "type": "file", + "description": "The read counts in hdf5 format", + "pattern": "*.hdf5" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The read counts in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49540,122 +61648,189 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index of the BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "site_depth_vcf": { - "type": "file", - "description": "Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output", - "pattern": "*.vcf.gz" - } - }, - { - "site_depth_vcf_index": { - "type": "file", - "description": "Optional - index of the VCF file, needed for the site depths output", - "pattern": "*.tbi" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional - reference FASTA file needed when the input is a CRAM file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Optional - index of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "split_read_evidence": { - "type": "file", - "description": "Output file for split read evidence", - "pattern": "*.sr.txt.gz" - } - }, - { - "split_read_evidence_index": { - "type": "file", - "description": "Index of the output file for split read evidence", - "pattern": "*.sr.txt.gz.tbi" - } - }, - { - "paired_end_evidence": { - "type": "file", - "description": "Output file for paired end evidence", - "pattern": "*.pe.txt.gz" - } - }, - { - "paired_end_evidence_index": { - "type": "file", - "description": "Index of the output file for paired end evidence", - "pattern": "*.pe.txt.gz.tbi" - } - }, - { - "site_depths": { - "type": "file", - "description": "Output file for site depths", - "pattern": "*.sd.txt.gz" - } - }, - { - "site_depths_index": { - "type": "file", - "description": "Index of the output file for site depths", - "pattern": "*.sd.txt.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "site_depth_vcf": { + "type": "file", + "description": "Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output", + "pattern": "*.vcf.gz" + } + }, + { + "site_depth_vcf_tbi": { + "type": "file", + "description": "tbi index of the input VCF of SNPs marking loci for site depths", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Optional - reference FASTA file needed when the input is a CRAM file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Optional - index of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "split_read_evidence": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sr.txt.gz": { + "type": "file", + "description": "Output file for split read evidence", + "pattern": "*.sr.txt.gz" + } + } + ] + }, + { + "split_read_evidence_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sr.txt.gz.tbi": { + "type": "file", + "description": "Index of the output file for split read evidence", + "pattern": "*.sr.txt.gz.tbi" + } + } + ] + }, + { + "paired_end_evidence": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pe.txt.gz": { + "type": "file", + "description": "Output file for paired end evidence", + "pattern": "*.pe.txt.gz" + } + } + ] + }, + { + "paired_end_evidence_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pe.txt.gz.tbi": { + "type": "file", + "description": "Index of the output file for paired end evidence", + "pattern": "*.pe.txt.gz.tbi" + } + } + ] + }, + { + "site_depths": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sd.txt.gz": { + "type": "file", + "description": "Output file for site depths", + "pattern": "*.sd.txt.gz" + } + } + ] + }, + { + "site_depths_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sd.txt.gz.tbi": { + "type": "file", + "description": "Index of the output file for site depths", + "pattern": "*.sd.txt.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49690,67 +61865,91 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF files", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_idx": { - "type": "file", - "description": "VCF Index file", - "pattern": "*.vcf.gz.idx" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "FASTA dictionary file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "combined_gvcf": { - "type": "file", - "description": "Compressed Combined GVCF file", - "pattern": "*.combined.g.vcf.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF files", + "pattern": "*.vcf.gz" + } + }, + { + "vcf_idx": { + "type": "file", + "description": "VCF Index file", + "pattern": "*.vcf.gz.idx" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "FASTA dictionary file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "combined_gvcf": [ + { + "meta": { + "type": "file", + "description": "Compressed Combined GVCF file", + "pattern": "*.combined.g.vcf.gz" + } + }, + { + "*.combined.g.vcf.gz": { + "type": "file", + "description": "Compressed Combined GVCF file", + "pattern": "*.combined.g.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49788,47 +61987,62 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" + [ + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } } - }, - { - "fasta_fai": { - "type": "file", - "description": "index of the FASTA reference file", - "pattern": "*.fai" + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "index of the FASTA reference file", + "pattern": "*.fai" + } } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of the FASTA reference file", - "pattern": "*.dict" + ], + [ + { + "dict": { + "type": "file", + "description": "Sequence dictionary of the FASTA reference file", + "pattern": "*.dict" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "str_table": [ + { + "*.zip": { + "type": "file", + "description": "A zipped folder containing the STR table files", + "pattern": "*.zip" + } + } + ] }, { - "str_table": { - "type": "file", - "description": "A zipped folder containing the STR table files", - "pattern": "*.zip" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -49860,151 +62074,189 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "depth_evidence": { + "type": "file", + "description": "The depth evidence file", + "pattern": "*.rd.txt.gz" + } + }, + { + "depth_evidence_index": { + "type": "file", + "description": "The index of the depth evidence file", + "pattern": "*.rd.txt.gz.tbi" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference FASTA file needed when the input is a CRAM file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "Sequence dictionary of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "condensed_evidence": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rd.txt.gz": { + "type": "file", + "description": "The condensed depth evidence", + "pattern": "*.rd.txt.gz" + } + } + ] + }, + { + "condensed_evidence_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rd.txt.gz.tbi": { + "type": "file", + "description": "The condensed depth evidence", + "pattern": "*.rd.txt.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, + "authors": [ + "@nvnieuwk" + ], + "maintainers": [ + "@nvnieuwk" + ] + } + }, + { + "name": "gatk4_createreadcountpanelofnormals", + "path": "modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_createreadcountpanelofnormals", + "description": "Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel.", + "keywords": [ + "createreadcountpanelofnormals", + "gatk4", + "panelofnormals" + ], + "tools": [ { - "depth_evidence": { - "type": "file", - "description": "The depth evidence file", - "pattern": "*.rd.txt.gz" + "gatk4": { + "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", + "homepage": "https://gatk.broadinstitute.org/hc/en-us", + "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", + "doi": "10.1158/1538-7445.AM2017-3590", + "tool_dev_url": "https://github.com/broadinstitute/gatk", + "licence": [ + "Apache-2.0" + ], + "identifier": "" } - }, - { - "depth_evidence_index": { - "type": "file", - "description": "The index of the depth evidence file", - "pattern": "*.rd.txt.gz.tbi" + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "counts": { + "type": "file", + "description": "Read counts in hdf5 or tsv format.", + "pattern": "*.{hdf5,tsv}" + } } - }, + ] + ], + "output": [ { - "fasta": { - "type": "file", - "description": "Reference FASTA file needed when the input is a CRAM file", - "pattern": "*.{fasta,fa}" - } + "pon": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.hdf5": { + "type": "file", + "description": "Panel-of-normals file.", + "pattern": "*.{hdf5}" + } + } + ] }, { - "fasta_fai": { - "type": "file", - "description": "Index of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "condensed_evidence": { - "type": "file", - "description": "The condensed depth evidence", - "pattern": "*.rd.txt.gz" - } - }, - { - "condensed_evidence_index": { - "type": "file", - "description": "The condensed depth evidence", - "pattern": "*.rd.txt.gz.tbi" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gatk4_createreadcountpanelofnormals", - "path": "modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_createreadcountpanelofnormals", - "description": "Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel.", - "keywords": [ - "createreadcountpanelofnormals", - "gatk4", - "panelofnormals" - ], - "tools": [ - { - "gatk4": { - "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", - "homepage": "https://gatk.broadinstitute.org/hc/en-us", - "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590", - "tool_dev_url": "https://github.com/broadinstitute/gatk", - "licence": [ - "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "counts": { - "type": "file", - "description": "Read counts in hdf5 or tsv format.", - "pattern": "*.{hdf5,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pon": { - "type": "file", - "description": "Panel-of-normals file.", - "pattern": "*.{hdf5}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50043,39 +62295,57 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file", - "pattern": "*.{fasta,fa}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file", + "pattern": "*.{fasta,fa}" + } } - } + ] ], "output": [ { - "dict": { - "type": "file", - "description": "gatk dictionary file", - "pattern": "*.{dict}" - } + "dict": [ + { + "meta": { + "type": "file", + "description": "gatk dictionary file", + "pattern": "*.{dict}" + } + }, + { + "*.dict": { + "type": "file", + "description": "gatk dictionary file", + "pattern": "*.{dict}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50128,85 +62398,119 @@ "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", "homepage": "https://gatk.broadinstitute.org/hc/en-us", "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "genoomicsdb": { - "type": "directory", - "description": "genomicsDB workspace that contains the samples to create the somatic panel of normals with.", - "pattern": "*_genomicsDBworkspace" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "panel of normal as compressed vcf file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Tabix index of vcf file", - "pattern": "*vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "doi": "10.1158/1538-7445.AM2017-3590", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "genomicsdb": { + "type": "file", + "description": "GenomicsDB database" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "panel of normal as compressed vcf file", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "panel of normal as compressed vcf file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "file", + "description": "Tabix index of vcf file", + "pattern": "*vcf.gz.tbi" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Tabix index of vcf file", + "pattern": "*vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50245,65 +62549,88 @@ "tool_dev_url": "https://github.com/broadinstitute/gatk", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "counts": { - "type": "file", - "description": "Read counts in hdf5 or tsv format.", - "pattern": "*.{hdf5,tsv}" - } - }, - { - "pon": { - "type": "file", - "description": "Panel of normals file hdf5 or tsv format.", - "pattern": "*.{hdf5}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "standardized": { - "type": "file", - "description": "Standardized copy ratios file.", - "pattern": "*.{tsv}" - } - }, - { - "denoised": { - "type": "file", - "description": "Denoised copy ratios file", - "pattern": "*.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "counts": { + "type": "file", + "description": "Read counts in hdf5 or tsv format.", + "pattern": "*.{hdf5,tsv}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "pon": { + "type": "file", + "description": "Panel of normals file hdf5 or tsv format.", + "pattern": "*.{hdf5}" + } + } + ] + ], + "output": [ + { + "standardized": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_standardizedCR.tsv": { + "type": "file", + "description": "Standardized copy ratios file.", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "denoised": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_denoisedCR.tsv": { + "type": "file", + "description": "Denoised copy ratios file", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50342,85 +62669,110 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "counts": { - "type": "file", - "description": "One or more count TSV files created with gatk/collectreadcounts", - "pattern": "*.tsv" - } - }, - { - "bed": { - "type": "file", - "description": "Optional - A bed file containing the intervals to include in the process", - "pattern": "*.bed" - } - }, - { - "exclude_beds": { - "type": "file", - "description": "Optional - One or more bed files containing intervals to exclude from the process", - "pattern": "*.bed" - } - }, - { - "contig_ploidy_table": { - "type": "file", - "description": "The contig ploidy priors table", - "pattern": "*.tsv" - } - }, - { - "ploidy_model": { - "type": "directory", - "description": "Optional - A folder containing the ploidy model.\nWhen a model is supplied to tool will run in CASE mode.\npattern: '*-model/'\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "calls": { - "type": "directory", - "description": "A folder containing the calls from the input files", - "pattern": "*-calls/" - } - }, - { - "model": { - "type": "directory", - "description": "A folder containing the model from the input files.\nThis will only be created in COHORT mode (when no model is supplied to the process).\n", - "pattern": "*-model/" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "counts": { + "type": "file", + "description": "One or more count TSV files created with gatk/collectreadcounts", + "pattern": "*.tsv" + } + }, + { + "bed": { + "type": "file", + "description": "Optional - A bed file containing the intervals to include in the process", + "pattern": "*.bed" + } + }, + { + "exclude_beds": { + "type": "file", + "description": "Optional - One or more bed files containing intervals to exclude from the process", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "ploidy_model": { + "type": "directory", + "description": "Optional - A folder containing the ploidy model.\nWhen a model is supplied to tool will run in CASE mode.\npattern: '*-model/'\n" + } + } + ], + [ + { + "contig_ploidy_table": { + "type": "file", + "description": "The contig ploidy priors table", + "pattern": "*.tsv" + } + } + ] + ], + "output": [ + { + "calls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-calls": { + "type": "directory", + "description": "A folder containing the calls from the input files", + "pattern": "*-calls/" + } + } + ] + }, + { + "model": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-model": { + "type": "directory", + "description": "A folder containing the model from the input files.\nThis will only be created in COHORT mode (when no model is supplied to the process).\n", + "pattern": "*-model/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50464,66 +62816,83 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "metrics": { - "type": "file", - "description": "File containing metrics on the input files", - "pattern": "*.{metrics}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "File containing metrics on the input files", + "pattern": "*.{metrics}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50565,45 +62934,56 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", + "pattern": "*.fastq.gz" + } } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", - "pattern": "*.fastq.gz" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Converted BAM file", - "pattern": "*.bam" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Converted BAM file", + "pattern": "*.bam" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50635,71 +63015,93 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Processed interval list file (processed_intervals.interval_list)", - "pattern": "*.interval_list" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "read_counts": { - "type": "file", - "description": "Read counts input file", - "pattern": "*.{tsv, hdf5}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "annotated_intervals": { - "type": "file", - "description": "Annotated intervals TSV file (annotated_intervals.tsv).", - "pattern": "*.tsv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "interval_list": { - "type": "file", - "description": "Filtered interval list file", - "pattern": "*.interval_list" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Processed interval list file (processed_intervals.interval_list)", + "pattern": "*.interval_list" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "read_counts": { + "type": "file", + "description": "Read counts input file", + "pattern": "*.{tsv, hdf5}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "annotated_intervals": { + "type": "file", + "description": "Annotated intervals TSV file (annotated_intervals.tsv).", + "pattern": "*.tsv" + } + } + ] + ], + "output": [ + { + "interval_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "Filtered interval list file", + "pattern": "*.interval_list" + } + }, + { + "_list": { + "type": "file", + "description": "Filtered interval list file", + "pattern": "*.interval_list" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -50738,178 +63140,224 @@ "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", "homepage": "https://gatk.broadinstitute.org/hc/en-us", "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590" - } + "doi": "10.1158/1538-7445.AM2017-3590", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "compressed vcf file of mutect2calls", + "pattern": "*.vcf.gz" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Tabix index of vcf file", + "pattern": "*vcf.gz.tbi" + } + }, + { + "stats": { + "type": "file", + "description": "Stats file that pairs with output vcf file", + "pattern": "*vcf.gz.stats" + } + }, + { + "orientationbias": { + "type": "file", + "description": "files containing artifact priors for input vcf. Optional input.", + "pattern": "*.artifact-prior.tar.gz" + } + }, + { + "segmentation": { + "type": "file", + "description": "tables containing segmentation information for input vcf. Optional input.", + "pattern": "*.segmentation.table" + } + }, + { + "table": { + "type": "file", + "description": "table(s) containing contamination data for input vcf. Optional input, takes priority over estimate.", + "pattern": "*.contamination.table" + } + }, + { + "estimate": { + "type": "float", + "description": "estimation of contamination value as a double. Optional input, will only be used if table is not specified." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "file containing filtered mutect2 calls.", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "file containing filtered mutect2 calls.", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "file", + "description": "tbi file that pairs with vcf.", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "tbi file that pairs with vcf.", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "file", + "description": "file containing statistics of the filtermutectcalls run.", + "pattern": "*.filteringStats.tsv" + } + }, + { + "*.filteringStats.tsv": { + "type": "file", + "description": "file containing statistics of the filtermutectcalls run.", + "pattern": "*.filteringStats.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "compressed vcf file of mutect2calls", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Tabix index of vcf file", - "pattern": "*vcf.gz.tbi" - } - }, - { - "stats": { - "type": "file", - "description": "Stats file that pairs with output vcf file", - "pattern": "*vcf.gz.stats" - } - }, - { - "orientationbias": { - "type": "file", - "description": "files containing artifact priors for input vcf. Optional input.", - "pattern": "*.artifact-prior.tar.gz" - } - }, - { - "segmentation": { - "type": "file", - "description": "tables containing segmentation information for input vcf. Optional input.", - "pattern": "*.segmentation.table" - } - }, - { - "table": { - "type": "file", - "description": "table(s) containing contamination data for input vcf. Optional input, takes priority over estimate.", - "pattern": "*.contamination.table" - } - }, - { - "estimate": { - "type": "float", - "description": "estimation of contamination value as a double. Optional input, will only be used if table is not specified." - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "file containing filtered mutect2 calls.", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "tbi file that pairs with vcf.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "stats": { - "type": "file", - "description": "file containing statistics of the filtermutectcalls run.", - "pattern": "*.filteringStats.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@GCJMackenzie", - "@maxulysse", - "@ramprasadn" - ], - "maintainers": [ - "@GCJMackenzie", - "@maxulysse", - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "2.2.0" - }, - { - "name": "rnadnavar", - "version": "dev" - }, - { - "name": "sarek", - "version": "3.4.4" - }, - { - "name": "variantcatalogue", - "version": "dev" - } - ] - }, - { - "name": "gatk4_filtervarianttranches", - "path": "modules/nf-core/gatk4/filtervarianttranches/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_filtervarianttranches", - "description": "Apply tranche filtering", - "keywords": [ - "filtervarianttranches", - "gatk4", - "tranche filtering" - ], - "tools": [ + "authors": [ + "@GCJMackenzie", + "@maxulysse", + "@ramprasadn" + ], + "maintainers": [ + "@GCJMackenzie", + "@maxulysse", + "@ramprasadn" + ] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "2.2.0" + }, + { + "name": "rnadnavar", + "version": "dev" + }, + { + "name": "sarek", + "version": "3.4.4" + }, + { + "name": "variantcatalogue", + "version": "dev" + } + ] + }, + { + "name": "gatk4_filtervarianttranches", + "path": "modules/nf-core/gatk4/filtervarianttranches/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_filtervarianttranches", + "description": "Apply tranche filtering", + "keywords": [ + "filtervarianttranches", + "gatk4", + "tranche filtering" + ], + "tools": [ { "gatk4": { "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", @@ -50918,94 +63366,131 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "a VCF file containing variants, must have info key:CNN_2D", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "tbi file matching with -vcf", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "resources": { - "type": "list", - "description": "resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", - "pattern": "*.vcf.gz" - } - }, - { - "resources_index": { - "type": "list", - "description": "Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", - "pattern": "*.vcf.gz" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": ".dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "a VCF file containing variants, must have info key:CNN_2D", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "tbi file matching with -vcf", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "intervals": { + "type": "file", + "description": "Intervals" + } + } + ], + [ + { + "resources": { + "type": "list", + "description": "resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "resources_index": { + "type": "list", + "description": "Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": ".dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -51045,45 +63530,56 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "table": { - "type": "file", - "description": "File(s) containing BQSR table(s)", - "pattern": "*.table" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "table": { + "type": "file", + "description": "File(s) containing BQSR table(s)", + "pattern": "*.table" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "table": { - "type": "file", - "description": "File containing joined BQSR table", - "pattern": "*.table" - } + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "File containing joined BQSR table", + "pattern": "*.table" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -51126,45 +63622,64 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pileup": { - "type": "file", - "description": "Pileup files from gatk4/getpileupsummaries", - "pattern": "*.pileups.table" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "table": { - "type": "file", - "description": "pileup summaries table file", - "pattern": "*.pileups.table" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pileup": { + "type": "file", + "description": "Pileup files from gatk4/getpileupsummaries", + "pattern": "*.pileups.table" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "dictionary" + } + } + ] + ], + "output": [ + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pileups.table": { + "type": "file", + "description": "pileup summaries table file", + "pattern": "*.pileups.table" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -51207,102 +63722,155 @@ "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", "homepage": "https://gatk.broadinstitute.org/hc/en-us", "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "list", - "description": "either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used.", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "list", - "description": "list of tbi files that match with the input vcf files", - "pattern": "*.vcf.gz_tbi" - } - }, - { - "wspace": { - "type": "file", - "description": "path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode.", - "pattern": "/path/to/existing/gendb" - } - }, - { - "interval_file": { - "type": "file", - "description": "file containing the intervals to be used when creating the genomicsdb", - "pattern": "*.interval_list" - } - }, - { - "interval_value": { - "type": "string", - "description": "if an intervals file has not been spcified, the value enetered here will be used as an interval via the \"-L\" argument", - "pattern": "example: chr1:1000-10000" - } - }, - { - "run_intlist": { - "type": "boolean", - "description": "Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.", - "pattern": "true/false" - } - }, - { - "run_updatewspace": { - "type": "boolean", - "description": "Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.", - "pattern": "true/false" - } - }, - { - "input_map": { - "type": "boolean", - "description": "Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb.", - "pattern": "*.sample_map" - } - } - ], - "output": [ - { - "genomicsdb": { - "type": "directory", - "description": "Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db", - "pattern": "*/$prefix" - } - }, - { - "updatedb": { - "type": "directory", - "description": "Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace.", - "pattern": "same/path/as/wspace" - } - }, - { - "intervallist": { - "type": "file", - "description": "File containing the intervals used to generate the genomicsdb, only created by get intervals mode.", - "pattern": "*.interval_list" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "doi": "10.1158/1538-7445.AM2017-3590", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "list", + "description": "either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used.", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "list", + "description": "list of tbi files that match with the input vcf files", + "pattern": "*.vcf.gz_tbi" + } + }, + { + "interval_file": { + "type": "file", + "description": "file containing the intervals to be used when creating the genomicsdb", + "pattern": "*.interval_list" + } + }, + { + "interval_value": { + "type": "string", + "description": "if an intervals file has not been spcified, the value enetered here will be used as an interval via the \"-L\" argument", + "pattern": "example: chr1:1000-10000" + } + }, + { + "wspace": { + "type": "file", + "description": "path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode.", + "pattern": "/path/to/existing/gendb" + } + } + ], + [ + { + "run_intlist": { + "type": "boolean", + "description": "Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.", + "pattern": "true/false" + } + } + ], + [ + { + "run_updatewspace": { + "type": "boolean", + "description": "Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.", + "pattern": "true/false" + } + } + ], + [ + { + "input_map": { + "type": "boolean", + "description": "Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb.", + "pattern": "*.sample_map" + } + } + ] + ], + "output": [ + { + "genomicsdb": [ + { + "meta": { + "type": "directory", + "description": "Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db", + "pattern": "*/$prefix" + } + }, + { + "$prefix": { + "type": "directory", + "description": "Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db", + "pattern": "*/$prefix" + } + } + ] + }, + { + "updatedb": [ + { + "meta": { + "type": "directory", + "description": "Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace.", + "pattern": "same/path/as/wspace" + } + }, + { + "$updated_db": { + "type": "directory", + "description": "Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace.", + "pattern": "same/path/as/wspace" + } + } + ] + }, + { + "intervallist": [ + { + "meta": { + "type": "file", + "description": "File containing the intervals used to generate the genomicsdb, only created by get intervals mode.", + "pattern": "*.interval_list" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "File containing the intervals used to generate the genomicsdb, only created by get intervals mode.", + "pattern": "*.interval_list" + } + }, + { + "list": { + "type": "file", + "description": "File containing the intervals used to generate the genomicsdb, only created by get intervals mode.", + "pattern": "*.interval_list" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -51346,136 +63914,167 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "gVCF(.gz) file or a GenomicsDB\n", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "gvcf_index": { - "type": "file", - "description": "index of gvcf file, or empty when providing GenomicsDB\n", - "pattern": "*.{idx,tbi}" - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file with the genomic regions included in the library (optional)" - } - }, - { - "intervals_index": { - "type": "file", - "description": "Interval index file (optional)" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai information\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fasta index file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing dict information\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Reference fasta sequence dict file", - "pattern": "*.dict" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test' ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "dbSNP VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing dbsnp tbi information\ne.g. [ id:'test' ]\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "dbSNP VCF index file", - "pattern": "*.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Genotyped VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Tbi index for VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "gVCF(.gz) file or a GenomicsDB\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "gvcf_index": { + "type": "file", + "description": "index of gvcf file, or empty when providing GenomicsDB\n", + "pattern": "*.{idx,tbi}" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file with the genomic regions included in the library (optional)" + } + }, + { + "intervals_index": { + "type": "file", + "description": "Interval index file (optional)" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fasta index file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing dict information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Reference fasta sequence dict file", + "pattern": "*.dict" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "dbSNP VCF file", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing dbsnp tbi information\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "dbSNP VCF index file", + "pattern": "*.tbi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Genotyped VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Tbi index for VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -51515,85 +64114,116 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tsv": { + "type": "file", + "description": "One or more count TSV files created with gatk/collectreadcounts", + "pattern": "*.tsv" + } + }, + { + "intervals": { + "type": "file", + "description": "Optional - A bed file containing the intervals to include in the process", + "pattern": "*.bed" + } + }, + { + "ploidy": { + "type": "directory", + "description": "Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode", + "pattern": "*-calls" + } + }, + { + "model": { + "type": "directory", + "description": "Optional - directory containing the model produced by germlinecnvcaller cohort mode", + "pattern": "*-cnv-model/*-model" + } + } + ] + ], + "output": [ + { + "cohortcalls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cnv-model/*-calls": { + "type": "directory", + "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", + "pattern": "*-cnv-model/*-calls" + } + } + ] + }, + { + "cohortmodel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cnv-model/*-model": { + "type": "directory", + "description": "Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode", + "pattern": "*-cnv-model/*-model" + } + } + ] + }, + { + "casecalls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cnv-calls/*-calls": { + "type": "directory", + "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", + "pattern": "*-cnv-calls/*-calls" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "One or more count TSV files created with gatk/collectreadcounts", - "pattern": "*.tsv" - } - }, - { - "intervals": { - "type": "file", - "description": "Optional - A bed file containing the intervals to include in the process", - "pattern": "*.bed" - } - }, - { - "model": { - "type": "directory", - "description": "Optional - directory containing the model produced by germlinecnvcaller cohort mode", - "pattern": "*-cnv-model/*-model" - } - }, - { - "ploidy": { - "type": "directory", - "description": "Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode", - "pattern": "*-calls" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cohortcalls": { - "type": "directory", - "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", - "pattern": "*-cnv-model/*-calls" - } - }, - { - "cohortmodel": { - "type": "directory", - "description": "Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode", - "pattern": "*-cnv-model/*-model" - } - }, - { - "casecalls": { - "type": "directory", - "description": "Tar gzipped directory containing calls produced by germlinecnvcaller case mode", - "pattern": "*-cnv-calls/*-calls" - } - } - ], - "authors": [ - "@ryanjameskennedy", - "@ViktorHy" + "authors": [ + "@ryanjameskennedy", + "@ViktorHy" ], "maintainers": [ "@ryanjameskennedy", @@ -51633,106 +64263,133 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file to be summarised.", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM file index.", - "pattern": "*.{bai,crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.", - "pattern": "*.interval_list" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "variants": { - "type": "file", - "description": "Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.", - "pattern": "*.vcf.gz" - } - }, - { - "variants_tbi": { - "type": "file", - "description": "Index file for the germline resource.", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "pileup": { - "type": "file", - "description": "File containing the pileup summary table.", - "pattern": "*.pileups.table" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file to be summarised.", + "pattern": "*.{bam,cram}" + } + }, + { + "index": { + "type": "file", + "description": "Index file for the input BAM/CRAM file.", + "pattern": "*.{bam.bai,cram.crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.", + "pattern": "*.interval_list" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "variants": { + "type": "file", + "description": "Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "variants_tbi": { + "type": "file", + "description": "Index file for the germline resource.", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.pileups.table": { + "type": "file", + "description": "Table containing read counts for each site.", + "pattern": "*.pileups.table" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -51774,142 +64431,183 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "dragstr_model": { - "type": "file", - "description": "Text file containing the DragSTR model of the used BAM/CRAM file (optional)", - "pattern": "*.txt" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "VCF index of dbsnp (optional)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "bam": { - "type": "file", - "description": "Assembled haplotypes and locally realigned reads", - "pattern": "*.realigned.bam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + }, + { + "dragstr_model": { + "type": "file", + "description": "Text file containing the DragSTR model of the used BAM/CRAM file (optional)", + "pattern": "*.txt" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file containing known sites (optional)" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing dbsnp information\ne.g. [ id:'test_dbsnp' ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "VCF index of dbsnp (optional)" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.realigned.bam": { + "type": "file", + "description": "Assembled haplotypes and locally realigned reads", + "pattern": "*.realigned.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -51955,45 +64653,56 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "feature_file": { + "type": "file", + "description": "VCF/BED file", + "pattern": "*.{vcf,vcf.gz,bed,bed.gz}" + } } - }, - { - "feature_file": { - "type": "file", - "description": "VCF/BED file", - "pattern": "*.{vcf,vcf.gz,bed,bed.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Index for VCF/BED file", - "pattern": "*.{tbi,idx}" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{tbi,idx}": { + "type": "file", + "description": "Index for VCF/BED file", + "pattern": "*.{tbi,idx}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -52041,45 +64750,55 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "interval": { - "type": "file", - "description": "Interval list", - "pattern": "*.{interval,interval_list}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "IntervalList file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -52122,45 +64841,62 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "interval_list": { - "type": "file", - "description": "Interval list file", - "pattern": "*.interval_list" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "interval_list": { - "type": "file", - "description": "Interval list files", - "pattern": "*.interval_list" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file" + } + } + ] + ], + "output": [ + { + "interval_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_split/*/*.interval_list": { + "type": "file", + "description": "Interval list files", + "pattern": "*.interval_list" + } + }, + { + "_list": { + "type": "file", + "description": "Interval list files", + "pattern": "*.interval_list" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -52207,39 +64943,57 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "f1r2": { + "type": "list", + "description": "list of f1r2 files to be used as input.", + "pattern": "*.f1r2.tar.gz" + } } - }, - { - "f1r2": { - "type": "list", - "description": "list of f1r2 files to be used as input.", - "pattern": "*.f1r2.tar.gz" - } - } + ] ], "output": [ { - "artifactprior": { - "type": "file", - "description": "file containing artifact-priors to be used by filtermutectcalls", - "pattern": "*.tar.gz" - } + "artifactprior": [ + { + "meta": { + "type": "file", + "description": "file containing artifact-priors to be used by filtermutectcalls", + "pattern": "*.tar.gz" + } + }, + { + "*.tar.gz": { + "type": "file", + "description": "file containing artifact-priors to be used by filtermutectcalls", + "pattern": "*.tar.gz" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -52283,84 +65037,111 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The vcf file to be normalized\ne.g. 'file1.vcf.gz'\n" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the vcf file to be normalized\ne.g. 'file1.vcf.gz.tbi'\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF normalized output file", - "pattern": "*.{vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "Tbi index for VCF file", - "pattern": "*.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The vcf file to be normalized\ne.g. 'file1.vcf.gz'\n" + } + }, + { + "tbi": { + "type": "file", + "description": "Index of the vcf file to be normalized\ne.g. 'file1.vcf.gz.tbi'\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF normalized output file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Tbi index for VCF file", + "pattern": "*.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -52400,87 +65181,142 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file", - "pattern": "*.{fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Fasta index file", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Marked duplicates BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Marked duplicates CRAM file", - "pattern": "*.{cram}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bam.bai}" - } - }, - { - "crai": { - "type": "file", - "description": "CRAM index file", - "pattern": "*.{cram.crai}" - } - }, - { - "metrics": { - "type": "file", - "description": "Duplicate metrics file generated by GATK", - "pattern": "*.{metrics.txt}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Fasta file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Fasta index file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*cram": { + "type": "file", + "description": "Marked duplicates CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*bam": { + "type": "file", + "description": "Marked duplicates BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "CRAM index file", + "pattern": "*.{cram.crai}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bam.bai}" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "Duplicate metrics file generated by GATK", + "pattern": "*.{metrics.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54097,70 +66933,92 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "aligned": { - "type": "file", - "description": "The aligned bam file", - "pattern": "*.{bam}" - } - }, - { - "unaligned": { - "type": "file", - "description": "The unmaped bam file", - "pattern": "*.{bam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "The merged bam file", - "pattern": "*.bam" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "aligned": { + "type": "file", + "description": "The aligned bam file", + "pattern": "*.{bam}" + } + }, + { + "unmapped": { + "type": "file", + "description": "The unmapped bam file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "file", + "description": "The merged bam file", + "pattern": "*.bam" + } + }, + { + "*.bam": { + "type": "file", + "description": "The merged bam file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54202,45 +67060,56 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "stats": { - "type": "file", - "description": "Stats file", - "pattern": "*.{stats}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "stats": { + "type": "file", + "description": "Stats file", + "pattern": "*.{stats}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.stats": { + "type": "file", + "description": "Stats file", + "pattern": "*.vcf.gz.stats" + } + } + ] }, { - "stats": { - "type": "file", - "description": "Stats file", - "pattern": "*.vcf.gz.stats" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54286,59 +67155,90 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "list", - "description": "Two or more VCF files", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } - }, - { - "dict": { - "type": "file", - "description": "Optional Sequence Dictionary as input", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "merged vcf file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "index files for the merged vcf files", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "list", + "description": "Two or more VCF files", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "dict": { + "type": "file", + "description": "Optional Sequence Dictionary as input", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "merged vcf file", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "merged vcf file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "file", + "description": "index files for the merged vcf files", + "pattern": "*.tbi" + } + }, + { + "*.tbi": { + "type": "file", + "description": "index files for the merged vcf files", + "pattern": "*.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54395,141 +67295,206 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "input": { - "type": "list", - "description": "list of BAM files, also able to take CRAM as an input", - "pattern": "*.{bam/cram}" - } - }, - { - "input_index": { - "type": "list", - "description": "list of BAM file indexes, also able to take CRAM indexes as an input", - "pattern": "*.{bam.bai/cram.crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Specify region the tools is run on.", - "pattern": ".{bed,interval_list}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "germline_resource": { - "type": "file", - "description": "Population vcf of germline sequencing, containing allele fractions.", - "pattern": "*.vcf.gz" - } - }, - { - "germline_resource_tbi": { - "type": "file", - "description": "Index file for the germline resource.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "panel_of_normals": { - "type": "file", - "description": "vcf file to be used as a panel of normals.", - "pattern": "*.vcf.gz" - } - }, - { - "panel_of_normals_tbi": { - "type": "file", - "description": "Index for the panel of normals.", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "compressed vcf file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of vcf file", - "pattern": "*vcf.gz.tbi" - } - }, - { - "stats": { - "type": "file", - "description": "Stats file that pairs with output vcf file", - "pattern": "*vcf.gz.stats" - } - }, - { - "f1r2": { - "type": "file", - "description": "file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)", - "pattern": "*.f1r2.tar.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "input": { + "type": "list", + "description": "list of BAM files, also able to take CRAM as an input", + "pattern": "*.{bam/cram}" + } + }, + { + "input_index": { + "type": "list", + "description": "list of BAM file indexes, also able to take CRAM indexes as an input", + "pattern": "*.{bam.bai/cram.crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "Specify region the tools is run on.", + "pattern": ".{bed,interval_list}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "germline_resource": { + "type": "file", + "description": "Population vcf of germline sequencing, containing allele fractions.", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "germline_resource_tbi": { + "type": "file", + "description": "Index file for the germline resource.", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "panel_of_normals": { + "type": "file", + "description": "vcf file to be used as a panel of normals.", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "panel_of_normals_tbi": { + "type": "file", + "description": "Index for the panel of normals.", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "compressed vcf file", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "compressed vcf file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "file", + "description": "Index of vcf file", + "pattern": "*vcf.gz.tbi" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of vcf file", + "pattern": "*vcf.gz.tbi" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "file", + "description": "Stats file that pairs with output vcf file", + "pattern": "*vcf.gz.stats" + } + }, + { + "*.stats": { + "type": "file", + "description": "Stats file that pairs with output vcf file", + "pattern": "*vcf.gz.stats" + } + } + ] + }, + { + "f1r2": [ + { + "meta": { + "type": "file", + "description": "file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)", + "pattern": "*.f1r2.tar.gz" + } + }, + { + "*.f1r2.tar.gz": { + "type": "file", + "description": "file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)", + "pattern": "*.f1r2.tar.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54585,73 +67550,111 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ploidy": { - "type": "directory", - "description": "Optional - A folder containing the ploidy model.\nWhen a model is supplied to tool will run in CASE mode.\n", - "pattern": "*-calls/" - } - }, - { - "calls": { - "type": "directory", - "description": "A folder containing the calls from the input files", - "pattern": "*-cnv-calls/*-calls" - } - }, - { - "model": { - "type": "directory", - "description": "A folder containing the model from the input files.\nThis will only be created in COHORT mode (when no model is supplied to the process).\n", - "pattern": "*-cnv-model/*-model" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "denoised": { - "type": "file", - "description": "Denoised copy ratio file", - "pattern": "*.vcf.gz" - } - }, - { - "segments": { - "type": "file", - "description": "Segments VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "intervals": { - "type": "file", - "description": "Intervals VCF file", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "calls": { + "type": "directory", + "description": "A folder containing the calls from the input files", + "pattern": "*-cnv-calls/*-calls" + } + }, + { + "model": { + "type": "directory", + "description": "A folder containing the model from the input files.\nThis will only be created in COHORT mode (when no model is supplied to the process).\n", + "pattern": "*-cnv-model/*-model" + } + }, + { + "ploidy": { + "type": "directory", + "description": "Optional - A folder containing the ploidy model.\nWhen a model is supplied to tool will run in CASE mode.\n", + "pattern": "*-calls/" + } + } + ] + ], + "output": [ + { + "intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genotyped_intervals.vcf.gz": { + "type": "file", + "description": "Intervals VCF file", + "pattern": "*.vcf.gz" + } + }, + { + "s": { + "type": "file", + "description": "Intervals VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "segments": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genotyped_segments.vcf.gz": { + "type": "file", + "description": "Segments VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "denoised": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_denoised.vcf.gz": { + "type": "file", + "description": "Denoised copy ratio file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54690,97 +67693,123 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional)", - "pattern": "*.{bed,interval_list}" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "exclude_intervals": { - "type": "file", - "description": "Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional)", - "pattern": "*.{bed,interval_list}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "interval_list": { - "type": "file", - "description": "Processed interval list file", - "pattern": "*.{bed,interval_list}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional)", + "pattern": "*.{bed,interval_list}" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "exclude_intervals": { + "type": "file", + "description": "Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional)", + "pattern": "*.{bed,interval_list}" + } + } + ] + ], + "output": [ + { + "interval_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "Processed interval list file", + "pattern": "*.{bed,interval_list}" + } + }, + { + "_list": { + "type": "file", + "description": "Processed interval list file", + "pattern": "*.{bed,interval_list}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54824,105 +67853,142 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "reference fasta index file", - "pattern": "*.{fai}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "reference fasta dictionary file", - "pattern": "*.{dict}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Sorted CRAM file", - "pattern": "*.{cram}" - } - }, - { - "sam": { - "type": "file", - "description": "Sorted SAM file", - "pattern": "*.{sam}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "index": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "reference fasta index file", + "pattern": "*.{fai}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "reference fasta dictionary file", + "pattern": "*.{dict}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "Sorted CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sam": { + "type": "file", + "description": "Sorted SAM file", + "pattern": "*.{sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -54964,110 +68030,139 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "evidence_files": { + "type": "file", + "description": "The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence.", + "pattern": "*.{pe,sr,baf,rd}.txt(.gz)" + } + }, + { + "evidence_indices": { + "type": "file", + "description": "The indices of the evidence files created by CollectSVEvidence", + "pattern": "*.{pe,sr,baf,rd}.txt(.gz).tbi" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "An optional BED file", + "pattern": "*.bed" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "An optional reference FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "An optional reference FASTA file index", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "The mandatory sequence dictionary file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "printed_evidence": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "The output file containing the discordant read pairs or the soft clipped reads", + "pattern": "*.{pe,sr,baf,rd}.txt.gz" + } + } + ] + }, + { + "printed_evidence_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz.tbi": { + "type": "file", + "description": "The index file of the output compressed text file containing the discordant read pairs or the soft clipped reads", + "pattern": "*.{pe,sr,baf,rd}.txt.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "evidence_files": { - "type": "file", - "description": "The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence.", - "pattern": "*.{pe,sr,baf,rd}.txt(.gz)" - } - }, - { - "evidence_indices": { - "type": "file", - "description": "The indices of the evidence files created by CollectSVEvidence", - "pattern": "*.{pe,sr,baf,rd}.txt(.gz).tbi" - } - }, - { - "bed": { - "type": "file", - "description": "An optional BED file", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "An optional reference FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "An optional reference FASTA file index", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "The mandatory sequence dictionary file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "printed_evidence": { - "type": "file", - "description": "The output file containing the discordant read pairs or the soft clipped reads", - "pattern": "*.{pe,sr,baf,rd}.txt.gz" - } - }, - { - "printed_evidence": { - "type": "file", - "description": "The index of the output file containing the discordant read pairs or the soft clipped reads", - "pattern": "*.{pe,sr,baf,rd}.txt.gz.tbi" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - } - }, - { - "name": "gatk4_reblockgvcf", - "path": "modules/nf-core/gatk4/reblockgvcf/meta.yml", - "type": "module", - "meta": { - "name": "gatk4_reblockgvcf", - "description": "Condenses homRef blocks in a single-sample GVCF", - "keywords": [ - "gatk4", - "gvcf", - "reblockgvcf" - ], - "tools": [ + "authors": [ + "@nvnieuwk" + ], + "maintainers": [ + "@nvnieuwk" + ] + } + }, + { + "name": "gatk4_reblockgvcf", + "path": "modules/nf-core/gatk4/reblockgvcf/meta.yml", + "type": "module", + "meta": { + "name": "gatk4_reblockgvcf", + "description": "Condenses homRef blocks in a single-sample GVCF", + "keywords": [ + "gatk4", + "gvcf", + "reblockgvcf" + ], + "tools": [ { "gatk4": { "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", @@ -55076,98 +68171,119 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gvcf": { - "type": "file", - "description": "GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode", - "pattern": "*.{vcf,gvcf}.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the GVCF file", - "pattern": "*.tbi" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "VCF index of dbsnp (optional)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gvcf": { - "type": "file", - "description": "Filtered GVCF", - "pattern": "*rb.g.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the filtered GVCF", - "pattern": "*rb.g.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gvcf": { + "type": "file", + "description": "GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode", + "pattern": "*.{vcf,gvcf}.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "Index of the GVCF file", + "pattern": "*.tbi" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "dbsnp": { + "type": "file", + "description": "VCF file containing known sites (optional)" + } + } + ], + [ + { + "dbsnp_tbi": { + "type": "file", + "description": "VCF index of dbsnp (optional)" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rb.g.vcf.gz": { + "type": "file", + "description": "The reblocked GVCF file", + "pattern": "*.rb.g.vcf.gz" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of the reblocked GVCF file", + "pattern": "*.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55199,39 +68315,57 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bam": { - "type": "file", - "description": "The input bam/sam file", - "pattern": "*.{bam,sam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bam": { + "type": "file", + "description": "The input bam/sam file", + "pattern": "*.{bam,sam}" + } } - } + ] ], "output": [ { - "bam": { - "type": "file", - "description": "The reverted bam/sam file", - "pattern": "*.reverted.bam" - } + "bam": [ + { + "meta": { + "type": "file", + "description": "The reverted bam/sam file", + "pattern": "*.reverted.bam" + } + }, + { + "*.bam": { + "type": "file", + "description": "The reverted bam/sam file", + "pattern": "*.reverted.bam" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55269,39 +68403,57 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input SAM/BAM file", - "pattern": "*.{bam,sam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input SAM/BAM file", + "pattern": "*.{bam,sam}" + } } - } + ] ], "output": [ { - "fastq": { - "type": "file", - "description": "converted fastq file", - "pattern": "*.fastq" - } + "fastq": [ + { + "meta": { + "type": "file", + "description": "converted fastq file", + "pattern": "*.fastq" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "converted fastq file", + "pattern": "*.fastq" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55344,66 +68496,87 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "list", - "description": "VCF(.gz) file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "vcf_idx": { - "type": "list", - "description": "VCF file index", - "pattern": "*.{idx,tbi}" - } - }, - { - "intervals": { - "type": "file", - "description": "One or more genomic intervals over which to operate", - "pattern": ".intervals" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.selectvariants.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "list", - "description": "VCF file index", - "pattern": "*.{idx,tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "list", + "description": "VCF(.gz) file", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "vcf_idx": { + "type": "list", + "description": "VCF file index", + "pattern": "*.{idx,tbi}" + } + }, + { + "intervals": { + "type": "file", + "description": "One or more genomic intervals over which to operate", + "pattern": ".intervals" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.selectvariants.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55446,99 +68619,185 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "index for fasta file", - "pattern": "*.{fai}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "sequence dictionary file", - "pattern": "*.{dict}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "dict": { - "type": "file", - "description": "sequence dictionary file", - "pattern": "*.{dict}" - } - }, - { - "intervals": { - "type": "file", - "description": "Intervals file for the fasta file", - "pattern": "*.{intervals}" - } - }, - { - "shift_back_chain": { - "type": "file", - "description": "The shiftback chain file to use when lifting over", - "pattern": "*.{back_chain}" - } - }, - { - "shift_fa": { - "type": "file", - "description": "Shifted fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "shift_intervals": { - "type": "file", - "description": "Intervals file for the shifted fasta file", - "pattern": "*.{shifted.intervals}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "index for fasta file", + "pattern": "*.{fai}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "sequence dictionary file", + "pattern": "*.{dict}" + } + } + ] + ], + "output": [ + { + "shift_fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_shift.fasta": { + "type": "file", + "description": "Shifted fasta file", + "pattern": "*.{fa,fasta}" + } + } + ] + }, + { + "shift_fai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_shift.fasta.fai": { + "type": "file", + "description": "Index file for the shifted fasta file", + "pattern": "*.{fai}" + } + } + ] + }, + { + "shift_back_chain": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_shift.back_chain": { + "type": "file", + "description": "The shiftback chain file to use when lifting over", + "pattern": "*.{back_chain}" + } + } + ] + }, + { + "dict": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_shift.dict": { + "type": "file", + "description": "sequence dictionary file", + "pattern": "*.{dict}" + } + } + ] + }, + { + "intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.intervals": { + "type": "file", + "description": "Intervals file for the fasta file", + "pattern": "*.{intervals}" + } + }, + { + "s": { + "type": "file", + "description": "Intervals file for the fasta file", + "pattern": "*.{intervals}" + } + } + ] + }, + { + "shift_intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.shifted.intervals": { + "type": "file", + "description": "Intervals file for the shifted fasta file", + "pattern": "*.{shifted.intervals}" + } + }, + { + "s": { + "type": "file", + "description": "Intervals file for the shifted fasta file", + "pattern": "*.{shifted.intervals}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55577,94 +68836,123 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "site_depths": { - "type": "file", - "description": "Files containing site depths", - "pattern": "*.sd.txt.gz" - } - }, - { - "site_depths_indices": { - "type": "file", - "description": "The indices of the site depth files", - "pattern": "*.sd.txt.gz.tbi" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF of SNPs marking loci for site depths", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the input VCF of SNPs marking loci for site depths", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "The sequence dictionary of the reference FASTA file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "baf": { - "type": "file", - "description": "The created BAF file", - "pattern": "*.baf.txt.gz" - } - }, - { - "baf_tbi": { - "type": "file", - "description": "The index of the created BAF file", - "pattern": "*.baf.txt.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "site_depths": { + "type": "file", + "description": "Files containing site depths", + "pattern": "*.sd.txt.gz" + } + }, + { + "site_depths_indices": { + "type": "file", + "description": "The indices of the site depth files", + "pattern": "*.sd.txt.gz.tbi" + } + } + ], + [ + { + "vcf": { + "type": "file", + "description": "Input VCF of SNPs marking loci for site depths", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "Index of the input VCF of SNPs marking loci for site depths", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "The sequence dictionary of the reference FASTA file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "baf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.baf.txt.gz": { + "type": "file", + "description": "The created BAF file", + "pattern": "*.baf.txt.gz" + } + } + ] + }, + { + "baf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.baf.txt.gz.tbi": { + "type": "file", + "description": "The index of the created BAF file", + "pattern": "*.baf.txt.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55697,45 +68985,56 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cram": { - "type": "file", - "description": "The CRAM file to split", - "pattern": "*.cram" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cram": { + "type": "file", + "description": "The CRAM file to split", + "pattern": "*.cram" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "split_crams": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "A list of split CRAM files", + "pattern": "*.cram" + } + } + ] }, { - "split_crams": { - "type": "file", - "description": "A list of split CRAM files", - "pattern": "*.cram" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55769,84 +69068,100 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "interval": { - "type": "file", - "description": "Interval list or BED", - "pattern": "*.{interval,interval_list,bed}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference FASTA", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference FASTA index", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Reference sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "A list of scattered interval lists", - "pattern": "*.interval_list" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference FASTA", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference FASTA index", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Reference sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "split_intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "**.interval_list": { + "type": "file", + "description": "interval files", + "pattern": "*.interval_list" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -55886,91 +69201,115 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bam": { - "type": "list", - "description": "BAM/SAM/CRAM file containing reads", - "pattern": "*.{bam,sam,cram}" - } - }, - { - "bai": { - "type": "list", - "description": "BAI/SAI/CRAI index file (optional)", - "pattern": "*.{bai,sai,crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'reference' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'reference' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Output file with split reads (BAM/SAM/CRAM)", - "pattern": "*.{bam,sam,cram}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bam": { + "type": "list", + "description": "BAM/SAM/CRAM file containing reads", + "pattern": "*.{bam,sam,cram}" + } + }, + { + "bai": { + "type": "list", + "description": "BAI/SAI/CRAI index file (optional)", + "pattern": "*.{bai,sai,crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'reference' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "file", + "description": "Output file with split reads (BAM/SAM/CRAM)", + "pattern": "*.{bam,sam,cram}" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output file with split reads (BAM/SAM/CRAM)", + "pattern": "*.{bam,sam,cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -56015,87 +69354,114 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "A VCF file created with a structural variant caller", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "The index file of the VCF", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "bed": { - "type": "file", - "description": "Regions to limit the analysis to", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional - reference FASTA file needed when the input is a CRAM file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Optional - index of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "annotated_vcf": { - "type": "file", - "description": "The annotated structural variant VCF", - "pattern": "*.vcf.gz" - } - }, - { - "index": { - "type": "file", - "description": "The index of the VCF", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "A VCF file created with a structural variant caller", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "The index file of the VCF", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "bed": { + "type": "file", + "description": "Regions to limit the analysis to", + "pattern": "*.bed" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Optional - reference FASTA file needed when the input is a CRAM file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Optional - index of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "annotated_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The annotated structural variant VCF", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -56128,87 +69494,116 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "file", - "description": "One or more VCF files created with a structural variant caller", - "pattern": "*.vcf.gz" - } - }, - { - "indices": { - "type": "file", - "description": "Index files for the VCFs", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "ploidy_table": { - "type": "file", - "description": "The sample ploidy table", - "pattern": "*.tsv" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference FASTA file needed when the input is a CRAM file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.fai" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of the reference FASTA file needed when the input is a CRAM file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "clustered_vcf": { - "type": "file", - "description": "The VCF containing the clustered VCFs", - "pattern": "*.vcf.gz" - } - }, - { - "clustered_vcf_index": { - "type": "file", - "description": "The index of the VCF containing the clustered VCFs", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "One or more VCF files created with a structural variant caller", + "pattern": "*.vcf.gz" + } + }, + { + "indices": { + "type": "file", + "description": "Index files for the VCFs", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "ploidy_table": { + "type": "file", + "description": "The sample ploidy table", + "pattern": "*.tsv" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference FASTA file needed when the input is a CRAM file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "Sequence dictionary of the reference FASTA file needed when the input is a CRAM file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "clustered_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The VCF containing the clustered VCFs", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "clustered_vcf_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF containing the clustered VCFs", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -56241,92 +69636,127 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "list", - "description": "List of VCF(.gz) files", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "vcf_tbi": { - "type": "list", - "description": "List of VCF file indexes", - "pattern": "*.{idx,tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of reference genome", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of fastea file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "list", + "description": "List of VCF(.gz) files", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "list", + "description": "List of VCF file indexes", + "pattern": "*.{tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of fastea file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -56379,108 +69809,171 @@ "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n", "homepage": "https://gatk.broadinstitute.org/hc/en-us", "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s", - "doi": "10.1158/1538-7445.AM2017-3590" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "input vcf file containing the variants to be recalibrated", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "tbi file matching with -vcf", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "resource_vcf": { - "type": "file", - "description": "all resource vcf files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz" - } - }, - { - "resource_tbi": { - "type": "file", - "description": "all resource tbi files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "labels": { - "type": "string", - "description": "necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "recal": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal" - } - }, - { - "idx": { - "type": "file", - "description": "Index file for the recal output file", - "pattern": "*.idx" - } - }, - { - "tranches": { - "type": "file", - "description": "Output tranches file used by ApplyVQSR", - "pattern": "*.tranches" - } - }, - { - "plots": { - "type": "file", - "description": "Optional output rscript file to aid in visualization of the input data and learned model.", - "pattern": "*plots.R" - } - }, - { - "version": { - "type": "file", - "description": "File containing software versions", - "pattern": "*.versions.yml" - } + "doi": "10.1158/1538-7445.AM2017-3590", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "input vcf file containing the variants to be recalibrated", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "tbi file matching with -vcf", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "resource_vcf": { + "type": "file", + "description": "all resource vcf files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "resource_tbi": { + "type": "file", + "description": "all resource tbi files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "labels": { + "type": "string", + "description": "necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "recal": [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal" + } + }, + { + "*.recal": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal" + } + } + ] + }, + { + "idx": [ + { + "meta": { + "type": "file", + "description": "Index file for the recal output file", + "pattern": "*.idx" + } + }, + { + "*.idx": { + "type": "file", + "description": "Index file for the recal output file", + "pattern": "*.idx" + } + } + ] + }, + { + "tranches": [ + { + "meta": { + "type": "file", + "description": "Output tranches file used by ApplyVQSR", + "pattern": "*.tranches" + } + }, + { + "*.tranches": { + "type": "file", + "description": "Output tranches file used by ApplyVQSR", + "pattern": "*.tranches" + } + } + ] + }, + { + "plots": [ + { + "meta": { + "type": "file", + "description": "Optional output rscript file to aid in visualization of the input data and learned model.", + "pattern": "*plots.R" + } + }, + { + "*plots.R": { + "type": "file", + "description": "Optional output rscript file to aid in visualization of the input data and learned model.", + "pattern": "*plots.R" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -56525,106 +70018,130 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk.\ne.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file.", - "pattern": "*.{idx,tbi}" - } - }, - { - "arguments_file": { - "type": "file", - "description": "optional GATK arguments file", - "pattern": "*.{txt,list,args,arguments}" - } - }, - { - "include_intervals": { - "type": "file", - "description": "optional GATK region file", - "pattern": "*.{bed,bed.gz,interval,interval_list}" - } - }, - { - "exclude_intervals": { - "type": "file", - "description": "optional GATK exclude region file", - "pattern": "*.{bed,bed.gz,interval,interval_list}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of reference genome", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of fastea file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "table": { - "type": "file", - "description": "GATK output", - "pattern": "*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk.\ne.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file.", + "pattern": "*.{idx,tbi}" + } + }, + { + "arguments_file": { + "type": "file", + "description": "optional GATK arguments file", + "pattern": "*.{txt,list,args,arguments}" + } + }, + { + "include_intervals": { + "type": "file", + "description": "optional GATK region file", + "pattern": "*.{bed,bed.gz,interval,interval_list}" + } + }, + { + "exclude_intervals": { + "type": "file", + "description": "optional GATK exclude region file", + "pattern": "*.{bed,bed.gz,interval,interval_list}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of fastea file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "table": [ + { + "meta": { + "type": "file", + "description": "GATK output", + "pattern": "*.tsv" + } + }, + { + "*.tsv": { + "type": "file", + "description": "GATK output", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -56658,98 +70175,125 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + }, + { + "bqsr_table": { + "type": "file", + "description": "Recalibration table from gatk4_baserecalibrator" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Recalibrated BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Recalibrated CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "bqsr_table": { - "type": "file", - "description": "Recalibration table from gatk4_baserecalibrator" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Recalibrated BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Recalibrated CRAM file", - "pattern": "*.{cram}" - } - } - ], - "authors": [ - "@yocra3", - "@FriederikeHanssen", - "@maxulysse" + "authors": [ + "@yocra3", + "@FriederikeHanssen", + "@maxulysse" ], "maintainers": [ "@yocra3", @@ -56787,93 +70331,114 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "known_sites": { - "type": "file", - "description": "VCF files with known sites for indels / snps (optional)", - "pattern": "*.vcf.gz" - } - }, - { - "known_sites_tbi": { - "type": "file", - "description": "Tabix index of the known_sites (optional)", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "table": { - "type": "file", - "description": "Recalibration table from BaseRecalibrator", - "pattern": "*.{table}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "known_sites": { + "type": "file", + "description": "VCF files with known sites for indels / snps (optional)", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "known_sites_tbi": { + "type": "file", + "description": "Tabix index of the known_sites (optional)", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "Recalibration table from BaseRecalibrator", + "pattern": "*.{table}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -56917,73 +70482,117 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "Marked duplicates BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bam_index": { - "type": "file", - "description": "Optional BAM index file", - "pattern": "*.bai" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Marked duplicates BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ] + }, + { + "bam_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bai": { + "type": "file", + "description": "Optional BAM index file", + "pattern": "*.bai" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "Metrics file", + "pattern": "*.metrics" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57030,118 +70639,137 @@ "https://software.broadinstitute.org/gatk/download/licensing", "BSD", "https://www.broadinstitute.org/gatk/about/#licensing" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and indexed BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "intervals": { - "type": "file", - "description": "Intervals file created by gatk3 RealignerTargetCreator", - "pattern": "*.{intervals,list}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file used to generate BAM file", - "pattern": ".{fasta,fa,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference file used to generate BAM file", - "pattern": ".fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK dict file for reference", - "pattern": ".dict" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "known_vcf": { - "type": "file", - "description": "Optional input VCF file(s) with known indels", - "pattern": ".vcf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and indexed BAM file with local realignment around variants", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Output BAM Index file", - "pattern": "*.bai" - } + ], + "identifier": "biotools:gatk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted and indexed BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + }, + { + "intervals": { + "type": "file", + "description": "Intervals file created by gatk3 RealignerTargetCreator", + "pattern": "*.{intervals,list}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file used to generate BAM file", + "pattern": ".{fasta,fa,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference file used to generate BAM file", + "pattern": ".fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK dict file for reference", + "pattern": ".dict" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_vcf": { + "type": "file", + "description": "Optional input VCF file(s) with known indels", + "pattern": ".vcf" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted and indexed BAM file with local realignment around variants", + "pattern": "*.bam" + } + }, + { + "*.bai": { + "type": "file", + "description": "Sorted and indexed BAM file with local realignment around variants", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57177,104 +70805,130 @@ "https://software.broadinstitute.org/gatk/download/licensing", "BSD", "https://www.broadinstitute.org/gatk/about/#licensing" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and indexed BAM/CRAM/SAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file used to generate BAM file", - "pattern": ".{fasta,fa,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference file used to generate BAM file", - "pattern": ".fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK dict file for reference", - "pattern": ".dict" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "known_vcf": { - "type": "file", - "description": "Optional input VCF file(s) with known indels", - "pattern": ".vcf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "intervals": { - "type": "file", - "description": "File containg intervals that represent sites of extant and potential indels.", - "pattern": "*.intervals" - } + ], + "identifier": "biotools:gatk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted and indexed BAM/CRAM/SAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file used to generate BAM file", + "pattern": ".{fasta,fa,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference file used to generate BAM file", + "pattern": ".fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK dict file for reference", + "pattern": ".dict" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing file meta-information for known_vcf.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_vcf": { + "type": "file", + "description": "Optional input VCF file(s) with known indels", + "pattern": ".vcf" + } + } + ] + ], + "output": [ + { + "intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.intervals": { + "type": "file", + "description": "File containg intervals that represent sites of extant and potential indels.", + "pattern": "*.intervals" + } + }, + { + "s": { + "type": "file", + "description": "File containg intervals that represent sites of extant and potential indels.", + "pattern": "*.intervals" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57307,143 +70961,168 @@ "https://software.broadinstitute.org/gatk/download/licensing", "BSD", "https://www.broadinstitute.org/gatk/about/#licensing" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and indexed BAM/CRAM/SAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file used to generate BAM file", - "pattern": ".{fasta,fa,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference file used to generate BAM file", - "pattern": ".fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK dict file for reference", - "pattern": ".dict" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)", - "pattern": "*.intervals" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing file meta-information for the contamination file.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contamination": { - "type": "file", - "description": "Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove", - "pattern": "*" - } - }, - { - "meta7": { - "type": "map", - "description": "Groovy Map containing file meta-information for the dbsnps file.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)", - "pattern": "*" - } - }, - { - "meta8": { - "type": "map", - "description": "Groovy Map containing file meta-information for the VCF comparison file.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "comp": { - "type": "file", - "description": "Comparison VCF file (optional)", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file containing called variants", - "pattern": "*.vcf.gz" - } + ], + "identifier": "biotools:gatk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted and indexed BAM/CRAM/SAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file used to generate BAM file", + "pattern": ".{fasta,fa,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference file used to generate BAM file", + "pattern": ".fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK dict file for reference", + "pattern": ".dict" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)", + "pattern": "*.intervals" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing file meta-information for the contamination file.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contamination": { + "type": "file", + "description": "Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove", + "pattern": "*" + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing file meta-information for the dbsnps file.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file containing known sites (optional)", + "pattern": "*" + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing file meta-information for the VCF comparison file.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "comp": { + "type": "file", + "description": "Comparison VCF file (optional)", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file containing called variants", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57479,52 +71158,65 @@ "tool_dev_url": "https://www.gnu.org/prep/ftp.html", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file", - "pattern": "*" - } - }, - { - "program_file": { - "type": "file", - "description": "Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic.", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "The output file - specify the name of this file using `ext.prefix` and the extension using `ext.suffix`", - "pattern": "*" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file", + "pattern": "*" + } + } + ], + [ + { + "program_file": { + "type": "file", + "description": "Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic.", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${suffix}": { + "type": "file", + "description": "The output file - specify the name of this file using `ext.prefix` and the extension using `ext.suffix`", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57580,86 +71272,139 @@ "doi": "10.1101/2021.05.03.442509", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.)", - "pattern": "*" - } - }, - { - "hmm": { - "type": "file", - "description": "Alternative HMM file(s) to use in HMMER format", - "pattern": "*.hmm" - } - }, - { - "model_dir": { - "type": "directory", - "description": "Path to an alternative CRF (Conditional Random Fields) module to use" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "genes": { - "type": "file", - "description": "TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found.", - "pattern": "*.genes.tsv" - } - }, - { - "features": { - "type": "file", - "description": "TSV file containing identified domains", - "pattern": "*.features.tsv" - } - }, - { - "clusters": { - "type": "file", - "description": "TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found.", - "pattern": "*.clusters.tsv" - } - }, - { - "gbk": { - "type": "file", - "description": "Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found.", - "pattern": "*.gbk" - } - }, - { - "json": { - "type": "file", - "description": "AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found.", - "pattern": "*.gbk" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.)", + "pattern": "*" + } + }, + { + "hmm": { + "type": "file", + "description": "Alternative HMM file(s) to use in HMMER format", + "pattern": "*.hmm" + } + } + ], + [ + { + "model_dir": { + "type": "directory", + "description": "Path to an alternative CRF (Conditional Random Fields) module to use" + } + } + ] + ], + "output": [ + { + "genes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.genes.tsv": { + "type": "file", + "description": "TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found.", + "pattern": "*.genes.tsv" + } + } + ] + }, + { + "features": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.features.tsv": { + "type": "file", + "description": "TSV file containing identified domains", + "pattern": "*.features.tsv" + } + } + ] + }, + { + "clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clusters.tsv": { + "type": "file", + "description": "TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found.", + "pattern": "*.clusters.tsv" + } + } + ] + }, + { + "gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_cluster_*.gbk": { + "type": "file", + "description": "Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found.", + "pattern": "*.gbk" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found.", + "pattern": "*.gbk" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57696,65 +71441,88 @@ "homepage": "https://paoloribeca.science/gem", "licence": [ "Custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "map": { - "type": "file", - "description": "The mappability file created from the index", - "pattern": "*.mappability" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing index information\n" - } - }, - { - "index": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.gem" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bedgraph": { - "type": "file", - "description": "The resulting bedgraph file", - "pattern": "*.bg" - } - }, - { - "sizes": { - "type": "file", - "description": "The chromosome sizes", - "pattern": "*.sizes" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "map": { + "type": "file", + "description": "The mappability file created from the index", + "pattern": "*.mappability" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "index": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.gem" + } + } + ] + ], + "output": [ + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bg": { + "type": "file", + "description": "The resulting bedgraph file", + "pattern": "*.bg" + } + } + ] + }, + { + "sizes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sizes": { + "type": "file", + "description": "The chromosome sizes", + "pattern": "*.sizes" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57785,52 +71553,73 @@ "homepage": "https://paoloribeca.science/gem", "licence": [ "Custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference FASTA file to index", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gem": { - "type": "file", - "description": "The created index", - "pattern": "*.gem" - } - }, - { - "log": { - "type": "file", - "description": "The execution log", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A reference FASTA file to index", + "pattern": "*.{fasta,fa,fna}" + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gem": { + "type": "file", + "description": "The GEM index file", + "pattern": "*.gem" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "The execution log", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57861,51 +71650,64 @@ "homepage": "https://paoloribeca.science/gem", "licence": [ "Custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "The index created with gem-indexer from the reference FASTA", - "pattern": "*.gem" - } - }, - { - "read_length": { - "type": "integer", - "description": "The read length to define the mappability of" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "map": { - "type": "file", - "description": "The resulting mappability file", - "pattern": "*.mappability" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "The index created with gem-indexer from the reference FASTA", + "pattern": "*.gem" + } + } + ], + [ + { + "read_length": { + "type": "integer", + "description": "The read length to define the mappability of" + } + } + ] + ], + "output": [ + { + "map": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mappability": { + "type": "file", + "description": "The resulting mappability file", + "pattern": "*.mappability" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -57935,52 +71737,73 @@ "homepage": "https://github.com/miqalvarez/gem3/tree/gem3-indexer", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the fasta file\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference FASTA file to index", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gem": { - "type": "file", - "description": "The created index", - "pattern": "*.gem" - } - }, - { - "info": { - "type": "file", - "description": "The execution log", - "pattern": "*.info" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information about the fasta file\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A reference FASTA file to index", + "pattern": "*.{fasta,fa,fna}" + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gem": { + "type": "file", + "description": "The GEM index file", + "pattern": "*.gem" + } + } + ] + }, + { + "info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.info": { + "type": "file", + "description": "The execution log", + "pattern": "*.info" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58010,65 +71833,80 @@ "homepage": "https://github.com/smarco/gem3-mapper", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - }, - { - "gem": { - "type": "file", - "description": "GEM3 genome index files", - "pattern": "*.{gem}" - } - }, - { - "sort_bam": { - "type": "boolean", - "description": "use samtools sort (true) or samtools view (false)", - "pattern": "true or false" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference/index information\ne.g. [ id:'test' ]\n" + } + }, + { + "gem": { + "type": "file", + "description": "GEM3 genome index files", + "pattern": "*.{gem}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } + } + ], + [ + { + "sort_bam": { + "type": "boolean", + "description": "use samtools sort (true) or samtools view (false)", + "pattern": "true or false" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58096,87 +71934,158 @@ "tool_dev_url": "https://github.com/thegenemyers/GENESCOPE.FK", "licence": [ "https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastk_histex_histogram": { - "type": "file", - "description": "A histogram formatted for GeneScope using the -G parameter from Fastk Histex", - "pattern": "*.hist" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "linear_plot": { - "type": "file", - "description": "A GeneScope linear plot in PNG format", - "pattern": "*_linear_plot.png" - } - }, - { - "transformed_linear_plot": { - "type": "file", - "description": "A GeneScope transformed linear plot in PNG format", - "pattern": "*_transformed_linear_plot.png" - } - }, - { - "log_plot": { - "type": "file", - "description": "A GeneScope log plot in PNG format", - "pattern": "*_log_plot.png" - } - }, - { - "transformed_log_plot": { - "type": "file", - "description": "A GeneScope transformed log plot in PNG format", - "pattern": "*_transformed_log_plot.png" - } - }, - { - "model": { - "type": "file", - "description": "GeneScope model fit summary", - "pattern": "*_model.txt" - } - }, - { - "summary": { - "type": "file", - "description": "GeneScope histogram summary", - "pattern": "*_summary.txt" - } - }, - { - "kmer_cov": { - "type": "float", - "description": "Average kmer coverage value extracted from summary file", - "pattern": "[0-9.]+" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastk_histex_histogram": { + "type": "file", + "description": "A histogram formatted for GeneScope using the -G parameter from Fastk Histex", + "pattern": "*.hist" + } + } + ] + ], + "output": [ + { + "linear_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_linear_plot.png": { + "type": "file", + "description": "A GeneScope linear plot in PNG format", + "pattern": "*_linear_plot.png" + } + } + ] + }, + { + "log_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_log_plot.png": { + "type": "file", + "description": "A GeneScope log plot in PNG format", + "pattern": "*_log_plot.png" + } + } + ] + }, + { + "model": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_model.txt": { + "type": "file", + "description": "GeneScope model fit summary", + "pattern": "*_model.txt" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary.txt": { + "type": "file", + "description": "GeneScope histogram summary", + "pattern": "*_summary.txt" + } + } + ] + }, + { + "transformed_linear_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_transformed_linear_plot.png": { + "type": "file", + "description": "A GeneScope transformed linear plot in PNG format", + "pattern": "*_transformed_linear_plot.png" + } + } + ] + }, + { + "transformed_log_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_transformed_log_plot.png": { + "type": "file", + "description": "A GeneScope transformed log plot in PNG format", + "pattern": "*_transformed_log_plot.png" + } + } + ] + }, + { + "kmer_cov": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "KMERCOV": { + "type": "float", + "description": "Average kmer coverage value extracted from summary file", + "pattern": "[0-9.]+" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58215,44 +72124,55 @@ "doi": "10.1093/bioinformatics/btaa222", "licence": [ "BSD-3-Clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file to index", - "pattern": "*.{fasta,fa,fna}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file to index", + "pattern": "*.{fasta,fa,fna}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Genmap index directory" + } + } + ] }, { - "index": { - "type": "directory", - "description": "Genmap index directory" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58296,78 +72216,121 @@ "doi": "10.1093/bioinformatics/btaa222", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "index directory" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing regions information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "regions": { - "type": "file", - "description": "optional - a bed file with regions to define the mappability off", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "wig": { - "type": "file", - "description": "genmap wig mappability file", - "pattern": "*.wig" - } - }, - { - "bedgraph": { - "type": "file", - "description": "genmap bedgraph mappability file", - "pattern": "*.bedgraph" - } - }, - { - "txt": { - "type": "file", - "description": "genmap text mappability file", - "pattern": "*.txt" - } - }, - { - "csv": { - "type": "file", - "description": "genmap csv mappability file", - "pattern": "*.csv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "index directory" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing regions information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "optional - a bed file with regions to define the mappability off", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "genmap wig mappability file", + "pattern": "*.wig" + } + } + ] + }, + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedgraph": { + "type": "file", + "description": "genmap bedgraph mappability file", + "pattern": "*.bedgraph" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "genmap text mappability file", + "pattern": "*.txt" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "genmap csv mappability file", + "pattern": "*.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58401,45 +72364,56 @@ "tool_dev_url": "https://github.com/moonso", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_annotate.vcf": { + "type": "file", + "description": "Annotated VCF file", + "pattern": "*.{vcf}" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.{vcf}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58477,45 +72451,56 @@ "tool_dev_url": "https://github.com/moonso", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf}" + } } - }, - { - "input_vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ] #\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ] #\n" + } + }, + { + "*_compound.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.{vcf}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58553,63 +72538,77 @@ "tool_dev_url": "https://github.com/moonso", "licence": [ "MIT" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf}" + } + } + ], + [ + { + "fam": { + "type": "file", + "description": "file with family information" + } + } + ], + [ + { + "reduced_penetrance": { + "type": "file", + "description": "file with gene ids that have reduced penetrance", + "pattern": "*.{tsv}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_models.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.{vcf}" - } - }, - { - "reduced_penetrance": { - "type": "file", - "description": "file with gene ids that have reduced penetrance", - "pattern": "*.{tsv}" - } - }, - { - "family_file": { - "type": "file", - "description": "ped file", - "pattern": "*.{ped}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.{vcf}" - } - } - ], - "authors": [ - "@ramprasadn" + "authors": [ + "@ramprasadn" ], "maintainers": [ "@ramprasadn" @@ -58643,59 +72642,73 @@ "tool_dev_url": "https://github.com/moonso", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.{vcf}" - } - }, - { - "family_file": { - "type": "file", - "description": "ped file", - "pattern": "*.{ped}" - } - }, - { - "score_config": { - "type": "file", - "description": "rank model config file", - "pattern": "*.{ini}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.{vcf}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf}" + } + } + ], + [ + { + "fam": { + "type": "file", + "description": "file with family information" + } + } + ], + [ + { + "score_config": { + "type": "file", + "description": "rank model config file", + "pattern": "*.{ini}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_score.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58738,24 +72751,33 @@ "doi": "10.1101/2023.03.05.531206", "licence": [ "Lawrence Berkeley National Labs BSD variant license" - ] + ], + "identifier": "biotools:genomad" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "genomad_db": [ + { + "genomad_db/": { + "type": "directory", + "description": "Directory containing downloaded data with directory being named \"genomad_db\"", + "pattern": "genomad_db" + } + } + ] }, { - "genomad_db": { - "type": "directory", - "description": "Directory containing downloaded data with directory being named \"genomad_db\"", - "pattern": "genomad_db" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58802,135 +72824,268 @@ "doi": "10.1101/2023.03.05.531206", "licence": [ "Lawrence Berkeley National Labs BSD variant license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing contigs/scaffolds/chromosomes", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "genomad_db": { - "type": "directory", - "description": "Directory pointing to geNomad database" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "aggregated_classification": { - "type": "file", - "description": "Combined classification scores for each contig/scaffold/chromosome", - "pattern": "*_aggregated_classification.tsv" - } - }, - { - "taxonomy": { - "type": "file", - "description": "Detailed output of geNomad's marker gene taxonomy analysis", - "pattern": "*_taxonomy.tsv" - } - }, - { - "provirus": { - "type": "file", - "description": "Detailed output of each provirus identified by geNomad's find_proviruses module", - "pattern": "*_provirus.tsv" - } - }, - { - "compositions": { - "type": "file", - "description": "OPTIONAL - Predicted sample composition when `--enable-score-calibration` is used", - "pattern": "*_compositions.tsv" - } - }, - { - "calibrated_classification": { - "type": "file", - "description": "OPTIONAL - Classification scores that have been adjusted based on sample composition when `--enable-score-calibration` is used`", - "pattern": "*_calibrated_aggregated_classification.tsv" - } - }, - { - "plasmid_fasta": { - "type": "file", - "description": "FASTA file containing predicted plasmid sequences", - "pattern": "*_plasmid.fna" - } - }, - { - "plasmid_genes": { - "type": "file", - "description": "TSV file containing predicted plasmid genes and their annotations", - "pattern": "*_plasmid_genes.tsv" - } - }, - { - "plasmid_proteins": { - "type": "file", - "description": "FASTA file containing predicted plasmid protein sequences", - "pattern": "*_plasmid_proteins.faa" - } - }, - { - "plasmid_summary": { - "type": "file", - "description": "TSV file containing a summary of geNomad's plasmid predictions", - "pattern": "*_plasmid_summary.tsv" - } - }, - { - "virus_fasta": { - "type": "file", - "description": "FASTA file containing predicted virus sequences", - "pattern": "*_virus.fna" - } - }, - { - "virus_genes": { - "type": "file", - "description": "TSV file containing predicted virus genes and their annotations", - "pattern": "*_virus_genes.tsv" - } - }, - { - "virus_proteins": { - "type": "file", - "description": "FASTA file containing predicted virus protein sequences", - "pattern": "*_virus_proteins.faa" - } - }, - { - "virus_summary": { - "type": "file", - "description": "TSV file containing a summary of geNomad's virus predictions", - "pattern": "*_virus_summary.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:genomad" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing contigs/scaffolds/chromosomes", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "genomad_db": { + "type": "directory", + "description": "Directory pointing to geNomad database" + } + } + ] + ], + "output": [ + { + "aggregated_classification": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_aggregated_classification/*_aggregated_classification.tsv": { + "type": "file", + "description": "Combined classification scores for each contig/scaffold/chromosome", + "pattern": "*_aggregated_classification.tsv" + } + } + ] + }, + { + "taxonomy": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_annotate/*_taxonomy.tsv": { + "type": "file", + "description": "Detailed output of geNomad's marker gene taxonomy analysis", + "pattern": "*_taxonomy.tsv" + } + } + ] + }, + { + "provirus": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_find_proviruses/*_provirus.tsv": { + "type": "file", + "description": "Detailed output of each provirus identified by geNomad's find_proviruses module", + "pattern": "*_provirus.tsv" + } + } + ] + }, + { + "compositions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_score_calibration/*_compositions.tsv": { + "type": "file", + "description": "OPTIONAL - Predicted sample composition when `--enable-score-calibration` is used", + "pattern": "*_compositions.tsv" + } + } + ] + }, + { + "calibrated_classification": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_score_calibration/*_calibrated_aggregated_classification.tsv": { + "type": "file", + "description": "OPTIONAL - Classification scores that have been adjusted based on sample composition when `--enable-score-calibration` is used`", + "pattern": "*_calibrated_aggregated_classification.tsv" + } + } + ] + }, + { + "plasmid_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_plasmid.fna.gz": { + "type": "file", + "description": "FASTA file containing predicted plasmid sequences", + "pattern": "*_plasmid.fna" + } + } + ] + }, + { + "plasmid_genes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_plasmid_genes.tsv": { + "type": "file", + "description": "TSV file containing predicted plasmid genes and their annotations", + "pattern": "*_plasmid_genes.tsv" + } + } + ] + }, + { + "plasmid_proteins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_plasmid_proteins.faa.gz": { + "type": "file", + "description": "FASTA file containing predicted plasmid protein sequences", + "pattern": "*_plasmid_proteins.faa" + } + } + ] + }, + { + "plasmid_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_plasmid_summary.tsv": { + "type": "file", + "description": "TSV file containing a summary of geNomad's plasmid predictions", + "pattern": "*_plasmid_summary.tsv" + } + } + ] + }, + { + "virus_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_virus.fna.gz": { + "type": "file", + "description": "FASTA file containing predicted virus sequences", + "pattern": "*_virus.fna" + } + } + ] + }, + { + "virus_genes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_virus_genes.tsv": { + "type": "file", + "description": "TSV file containing predicted virus genes and their annotations", + "pattern": "*_virus_genes.tsv" + } + } + ] + }, + { + "virus_proteins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_virus_proteins.faa.gz": { + "type": "file", + "description": "FASTA file containing predicted virus protein sequences", + "pattern": "*_virus_proteins.faa" + } + } + ] + }, + { + "virus_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_summary/*_virus_summary.tsv": { + "type": "file", + "description": "TSV file containing a summary of geNomad's virus predictions", + "pattern": "*_virus_summary.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -58974,101 +73129,175 @@ "doi": "10.1038/s41467-020-14998-3", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "histogram": { - "type": "file", - "description": "A K-mer histogram file", - "pattern": "*.hist" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "linear_plot_png": { - "type": "file", - "description": "A genomescope2 linear plot in PNG format", - "pattern": "*_linear_plot.png" - } - }, - { - "linear_plot_png": { - "type": "file", - "description": "A genomescope2 linear plot in PNG format", - "pattern": "*_linear_plot.png" - } - }, - { - "transformed_linear_plot_png": { - "type": "file", - "description": "A genomescope2 transformed linear plot in PNG format", - "pattern": "*_transformed_linear_plot.png" - } - }, - { - "log_plot_png": { - "type": "file", - "description": "A genomescope2 log plot in PNG format", - "pattern": "*_log_plot.png" - } - }, - { - "transformed_log_plot_png": { - "type": "file", - "description": "A genomescope2 transformed log plot in PNG format", - "pattern": "*_transformed_log_plot.png" - } - }, - { - "model": { - "type": "file", - "description": "Genomescope2 model fit summary", - "pattern": "*_model.txt" - } - }, - { - "summary": { - "type": "file", - "description": "Genomescope2 histogram summary", - "pattern": "*_summary.txt" - } - }, - { - "lookup_table": { - "type": "file", - "description": "Fitted histogram lookup table", - "pattern": "*_lookup_table.txt" - } - }, - { - "fitted_histogram_png": { - "type": "file", - "description": "A genomescope2 fitted histogram plot in PNG format", - "pattern": "*_fitted_hist.png" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "histogram": { + "type": "file", + "description": "A K-mer histogram file", + "pattern": "*.hist" + } + } + ] + ], + "output": [ + { + "linear_plot_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_linear_plot.png": { + "type": "file", + "description": "A genomescope2 linear plot in PNG format", + "pattern": "*_linear_plot.png" + } + } + ] + }, + { + "transformed_linear_plot_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_transformed_linear_plot.png": { + "type": "file", + "description": "A genomescope2 transformed linear plot in PNG format", + "pattern": "*_transformed_linear_plot.png" + } + } + ] + }, + { + "log_plot_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_log_plot.png": { + "type": "file", + "description": "A genomescope2 log plot in PNG format", + "pattern": "*_log_plot.png" + } + } + ] + }, + { + "transformed_log_plot_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_transformed_log_plot.png": { + "type": "file", + "description": "A genomescope2 transformed log plot in PNG format", + "pattern": "*_transformed_log_plot.png" + } + } + ] + }, + { + "model": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_model.txt": { + "type": "file", + "description": "Genomescope2 model fit summary", + "pattern": "*_model.txt" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_summary.txt": { + "type": "file", + "description": "Genomescope2 histogram summary", + "pattern": "*_summary.txt" + } + } + ] + }, + { + "lookup_table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_lookup_table.txt": { + "type": "file", + "description": "Fitted histogram lookup table", + "pattern": "*_lookup_table.txt" + } + } + ] + }, + { + "fitted_histogram_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_fitted_hist.png": { + "type": "file", + "description": "A genomescope2 fitted histogram plot in PNG format", + "pattern": "*_fitted_hist.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59106,45 +73335,56 @@ "tool_dev_url": "https://github.com/katholt/genotyphi", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "json": { + "type": "file", + "description": "JSON formatted file of Mykrobe results", + "pattern": "*.json" + } } - }, - { - "json": { - "type": "file", - "description": "JSON formatted file of Mykrobe results", - "pattern": "*.json" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A tab-delimited file of predicted genotypes", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "A tab-delimited file of predicted genotypes", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59176,111 +73416,154 @@ "tool_dev_url": "https://github.com/jsh58/Genrich", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "treatment_bam": { - "type": "file", - "description": "Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates", - "pattern": "*.{bam,sam}" - } - }, - { - "control_bam": { - "type": "file", - "description": "Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples", - "pattern": "*.{bam,sam}" - } - }, - { - "blacklist_bed": { - "type": "file", - "description": "Bed file containing genomic intervals to exclude from the analysis", - "pattern": "*.{bed}" - } - }, - { - "save_pvalues": { - "type": "boolean", - "description": "Create bedgraph-ish file for p/q-values file" - } - }, - { - "save_pileup": { - "type": "boolean", - "description": "Create bedgraph-ish file for pileups and p-values" - } - }, - { - "save_bed": { - "type": "boolean", - "description": "Create BED file for reads/fragments/intervals" - } - }, - { - "save_duplicates": { - "type": "boolean", - "description": "Create PCR duplicates file (only works if -r option is set)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "peaks": { - "type": "file", - "description": "Output file is in ENCODE narrowPeak format", - "pattern": "*.{narrowPeak}" - } - }, - { - "bedgraph_pvalues": { - "type": "file", - "description": "bedGraph file containing p/q values", - "pattern": "*.{pvalues.bedGraph}" - } - }, - { - "bedgraph_pileup": { - "type": "file", - "description": "bedGraph file containing pileups and p-values", - "pattern": "*.{pileup.bedGraph}" - } - }, - { - "bed_intervals": { - "type": "file", - "description": "Bed file containing annotated intervals", - "pattern": "*.{intervals.bed}" - } - }, - { - "duplicates": { - "type": "file", - "description": "Text output file containing intervals corresponding to PCR duplicates", - "pattern": "*.{intervals.txt}" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.txt}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "treatment_bam": { + "type": "file", + "description": "Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates", + "pattern": "*.{bam,sam}" + } + }, + { + "control_bam": { + "type": "file", + "description": "Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "blacklist_bed": { + "type": "file", + "description": "Bed file containing genomic intervals to exclude from the analysis", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "peak": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.narrowPeak": { + "type": "file", + "description": "Narrow peak file containing genomic intervals of significant enrichment", + "pattern": "*.{narrowPeak}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "bedgraph_pvalues": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvalues.bedGraph": { + "type": "file", + "description": "bedGraph file containing p/q values", + "pattern": "*.{pvalues.bedGraph}" + } + }, + { + "ues": { + "type": "file", + "description": "bedGraph file containing p/q values", + "pattern": "*.{pvalues.bedGraph}" + } + } + ] + }, + { + "bedgraph_pileup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pileup.bedGraph": { + "type": "file", + "description": "bedGraph file containing pileups and p-values", + "pattern": "*.{pileup.bedGraph}" + } + } + ] + }, + { + "bed_intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.intervals.bed": { + "type": "file", + "description": "Bed file containing annotated intervals", + "pattern": "*.{intervals.bed}" + } + }, + { + "s": { + "type": "file", + "description": "Bed file containing annotated intervals", + "pattern": "*.{intervals.bed}" + } + } + ] + }, + { + "duplicates": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.duplicates.txt": { + "type": "file", + "description": "Text output file containing intervals corresponding to PCR duplicates", + "pattern": "*.{intervals.txt}" + } + } + ] } ], "authors": [ @@ -59316,38 +73599,50 @@ "licence": [ "BSD-2-clause" ], - "args_id": "$args" + "args_id": "$args", + "identifier": "" } } ], "input": [ - { - "geo_accession": { - "type": "string", - "description": "GEO accession ID" + [ + { + "geo_accession": { + "type": "string", + "description": "GEO accession ID" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "geo_accession": { - "type": "string", - "description": "String with the GEO accession" - } + "samples": [ + { + "${geo_accession}": { + "type": "file", + "description": "List of sample files fetched", + "pattern": "${geo_accession}/*.CEL.gz" + } + }, + { + "${geo_accession}/*.CEL.gz": { + "type": "file", + "description": "List of sample files fetched", + "pattern": "${geo_accession}/*.CEL.gz" + } + } + ] }, { - "samples": { - "type": "file", - "description": "List of sample files fetched", - "pattern": "${geo_accession}/*.CEL.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59380,52 +73675,92 @@ "doi": "10.1093/bioinformatics/btm254", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata about the GEO dataset, minimally 'id'.\n" - } - }, - { - "querygse": { - "type": "string", - "description": "GSE identifier to pass to getGEO()\n" - } - } - ], - "output": [ - { - "rds": { - "type": "file", - "description": "R object containing GEO data", - "pattern": "*.rds" - } - }, - { - "expression": { - "type": "file", - "description": "TSV-format expression matrix", - "pattern": "*matrix.tsv" - } - }, - { - "annotation": { - "type": "file", - "description": "TSV-format annotation file", - "pattern": "*annotation.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:geoquery" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata about the GEO dataset, minimally 'id'.\n" + } + }, + { + "querygse": { + "type": "string", + "description": "GSE identifier to pass to getGEO()\n" + } + } + ] + ], + "output": [ + { + "rds": [ + { + "meta": { + "type": "file", + "description": "R object containing GEO data", + "pattern": "*.rds" + } + }, + { + "*.rds": { + "type": "file", + "description": "R object containing GEO data", + "pattern": "*.rds" + } + } + ] + }, + { + "expression": [ + { + "meta": { + "type": "file", + "description": "TSV-format expression matrix", + "pattern": "*matrix.tsv" + } + }, + { + "*matrix.tsv": { + "type": "file", + "description": "TSV-format expression matrix", + "pattern": "*matrix.tsv" + } + } + ] + }, + { + "annotation": [ + { + "meta": { + "type": "file", + "description": "TSV-format annotation file", + "pattern": "*annotation.tsv" + } + }, + { + "*annotation.tsv": { + "type": "file", + "description": "TSV-format annotation file", + "pattern": "*annotation.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59468,37 +73803,48 @@ "doi": "10.1186/s13059-020-02154-5", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:getorganelle" } } ], "input": [ - { - "organelle_type": { - "type": "string", - "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" + [ + { + "organelle_type": { + "type": "string", + "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "organelle_type": { - "type": "string", - "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" - } + "db": [ + { + "organelle_type": { + "type": "string", + "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" + } + }, + { + "getorganelle": { + "type": "directory", + "description": "Downloaded database for GetOrganelle" + } + } + ] }, { - "db": { - "type": "directory", - "description": "Downloaded database for GetOrganelle" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59529,63 +73875,80 @@ "doi": "10.1186/s13059-020-02154-5", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Input fastq files", - "pattern": "*.{fastq.gz}" - } - }, - { - "organelle_type": { - "type": "string", - "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" - } - }, - { - "db": { - "type": "directory", - "description": "GetOrganelle database" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Complete or partial organelle sequences", - "pattern": "*.fasta.gz" - } - }, - { - "etc": { - "type": "file", - "description": "Other output files" - } + ], + "identifier": "biotools:getorganelle" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Input fastq files", + "pattern": "*.{fastq.gz}" + } + } + ], + [ + { + "organelle_type": { + "type": "string", + "description": "Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)\n" + } + }, + { + "db": { + "type": "directory", + "description": "GetOrganelle database" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "results/${prefix}.${organelle_type}.fasta.gz": { + "type": "file", + "description": "Complete or partial organelle sequences", + "pattern": "*.fasta.gz" + } + } + ] + }, + { + "etc": [ + { + "results/*": { + "type": "file", + "description": "Other output files" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59614,52 +73977,73 @@ "documentation": "https://github.com/marschall-lab/GFAffix", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Variation graph in GFA format", - "pattern": "*.{gfa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Non-redundant variation graph in GFA 1.0 format", - "pattern": "*.{gfa}" - } - }, - { - "affixes": { - "type": "file", - "description": "Shared affixes in tab-separated values (TSV) text format", - "pattern": "*.{txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Variation graph in GFA format", + "pattern": "*.{gfa}" + } + } + ] + ], + "output": [ + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gfa": { + "type": "file", + "description": "Non-redundant variation graph in GFA 1.0 format", + "pattern": "*.{gfa}" + } + } + ] + }, + { + "affixes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Shared affixes in tab-separated values (TSV) text format", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59701,126 +74085,161 @@ "doi": "10.1093/bioinformatics/btac460", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:gfastats" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "Draft assembly file", + "pattern": "*.{fasta,fastq,gfa}(.gz)?" + } + } + ], + [ + { + "out_fmt": { + "type": "string", + "description": "Output format (fasta, fastq, gfa)" + } + } + ], + [ + { + "genome_size": { + "type": "integer", + "description": "estimated genome size (bp) for NG* statistics (optional)." + } + } + ], + [ + { + "target": { + "type": "string", + "description": "target specific sequence by header, optionally with coordinates (optional)." + } + } + ], + [ + { + "agpfile": { + "type": "file", + "description": "converts input agp to path and replaces existing paths." + } + } + ], + [ + { + "include_bed": { + "type": "file", + "description": "generates output on a subset list of headers or coordinates in 0-based bed format." + } + } + ], + [ + { + "exclude_bed": { + "type": "file", + "description": "opposite of --include-bed. They can be combined (no coordinates)." + } + } + ], + [ + { + "instructions": { + "type": "file", + "description": "set of instructions provided as an ordered list." + } + } + ] + ], + "output": [ + { + "assembly_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.assembly_summary": { + "type": "file", + "description": "Assembly summary statistics file", + "pattern": "*.assembly_summary" + } + } + ] + }, + { + "assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${out_fmt}.gz": { + "type": "file", + "description": "The assembly as modified by gfastats", + "pattern": "*.{fasta,fastq,gfa}.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "Draft assembly file", - "pattern": "*.{fasta,fastq,gfa}(.gz)?" - } - }, - { - "out_fmt": { - "type": "string", - "description": "Output format (fasta, fastq, gfa)" - } - }, - { - "genome_size": { - "type": "integer", - "description": "estimated genome size (bp) for NG* statistics (optional)." - } - }, - { - "target": { - "type": "string", - "description": "target specific sequence by header, optionally with coordinates (optional)." - } - }, - { - "agpfile": { - "type": "file", - "description": "converts input agp to path and replaces existing paths." - } - }, - { - "include_bed": { - "type": "file", - "description": "generates output on a subset list of headers or coordinates in 0-based bed format." - } - }, - { - "exclude_bed": { - "type": "file", - "description": "opposite of --include-bed. They can be combined (no coordinates)." - } - }, - { - "instructions": { - "type": "file", - "description": "set of instructions provided as an ordered list." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "assembly_summary": { - "type": "file", - "description": "Assembly summary statistics file", - "pattern": "*.assembly_summary" - } - }, - { - "assembly": { - "type": "file", - "description": "The assembly as modified by gfastats", - "pattern": "*.{fasta,fastq,gfa}.gz" - } - } - ], - "authors": [ - "@mahesh-panchal" - ], - "maintainers": [ - "@mahesh-panchal" - ] - }, - "pipelines": [ - { - "name": "pairgenomealign", - "version": "1.0.0" - } - ] - }, - { - "name": "gfatools_gfa2fa", - "path": "modules/nf-core/gfatools/gfa2fa/meta.yml", - "type": "module", - "meta": { - "name": "gfatools_gfa2fa", - "description": "Converts GFA or rGFA files to FASTA", - "keywords": [ - "gfa", - "rgfa", - "fasta", - "assembly", - "genome graph", - "genomics" - ], - "tools": [ + "authors": [ + "@mahesh-panchal" + ], + "maintainers": [ + "@mahesh-panchal" + ] + }, + "pipelines": [ + { + "name": "pairgenomealign", + "version": "1.0.0" + } + ] + }, + { + "name": "gfatools_gfa2fa", + "path": "modules/nf-core/gfatools/gfa2fa/meta.yml", + "type": "module", + "meta": { + "name": "gfatools_gfa2fa", + "description": "Converts GFA or rGFA files to FASTA", + "keywords": [ + "gfa", + "rgfa", + "fasta", + "assembly", + "genome graph", + "genomics" + ], + "tools": [ { "gfatools": { "description": "Tools for manipulating sequence graphs in the GFA and rGFA formats", @@ -59830,45 +74249,56 @@ "doi": "no DOI available", "licence": [ "Unknown" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "gfa": { - "type": "file", - "description": "GFA or rGFA file", - "pattern": "*.gfa" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "gfa": { + "type": "file", + "description": "GFA or rGFA file", + "pattern": "*.gfa" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "FASTA file", + "pattern": "*.fasta" + } + } + ] }, { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.fasta" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59904,45 +74334,56 @@ "doi": "no DOI available", "licence": [ "Unknown" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "gfa": { - "type": "file", - "description": "GFA or rGFA file", - "pattern": "*.gfa" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "gfa": { + "type": "file", + "description": "GFA or rGFA file", + "pattern": "*.gfa" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "Summary statistics of the GFA file", + "pattern": "*.stats" + } + } + ] }, { - "stats": { - "type": "file", - "description": "Summary statistics of the GFA file", - "pattern": "*.stats" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -59976,108 +74417,195 @@ "doi": "10.12688/f1000research.23297.1", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gtfs": { - "type": "file", - "description": "GTF/GFF files\ne.g. [ 'file_1.gtf', 'file_2.gtf' ]\n", - "pattern": "*.{gtf,gff}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference fasta file (optional)", - "pattern": "*.{fasta,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "Index for fasta file", - "pattern": "*.fai" - } - }, - { - "reference_gtf": { - "type": "file", - "description": "Reference annotation in gtf/gff format (optional)", - "pattern": "*.{gtf,gff}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "annotated_gtf": { - "type": "file", - "description": "Annotated gtf file when reference gtf is provided (optional)\n", - "pattern": "*.annotated.gtf" - } - }, - { - "combined_gtf": { - "type": "file", - "description": "Combined gtf file when multiple input files are\nprovided (optional)\n", - "pattern": "*.annotated.gtf" - } - }, - { - "tmap": { - "type": "file", - "description": "File listing the most closely matching reference transcript\nfor each query transcript (optional)\n", - "pattern": "*.tmap" - } - }, - { - "refmap": { - "type": "file", - "description": "File listing the reference transcripts with overlapping\nquery transcripts (optional)\n", - "pattern": "*.refmap" - } - }, - { - "loci": { - "type": "file", - "description": "File with loci", - "pattern": "*.loci" - } - }, - { - "stats": { - "type": "file", - "description": "File with stats for input transcripts as compared to\nreference alternatively stats for the combined gtf\n", - "pattern": "*.stats" - } - }, - { - "tracking": { - "type": "file", - "description": "This file matches transcripts up between samples\n", - "pattern": "*.tracking" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:gffcompare" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtfs": { + "type": "file", + "description": "GTF/GFF files\ne.g. [ 'file_1.gtf', 'file_2.gtf' ]\n", + "pattern": "*.{gtf,gff}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference fasta file (optional)", + "pattern": "*.{fasta,fa}" + } + }, + { + "fai": { + "type": "file", + "description": "Index for fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference_gtf": { + "type": "file", + "description": "Reference annotation in gtf/gff format (optional)", + "pattern": "*.{gtf,gff}" + } + } + ] + ], + "output": [ + { + "annotated_gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.annotated.gtf": { + "type": "file", + "description": "Annotated gtf file when reference gtf is provided (optional)\n", + "pattern": "*.annotated.gtf" + } + } + ] + }, + { + "combined_gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.combined.gtf": { + "type": "file", + "description": "Combined gtf file when multiple input files are\nprovided (optional)\n", + "pattern": "*.annotated.gtf" + } + } + ] + }, + { + "tmap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tmap": { + "type": "file", + "description": "File listing the most closely matching reference transcript\nfor each query transcript (optional)\n", + "pattern": "*.tmap" + } + } + ] + }, + { + "refmap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.refmap": { + "type": "file", + "description": "File listing the reference transcripts with overlapping\nquery transcripts (optional)\n", + "pattern": "*.refmap" + } + } + ] + }, + { + "loci": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.loci": { + "type": "file", + "description": "File with loci", + "pattern": "*.loci" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "File with stats for input transcripts as compared to\nreference alternatively stats for the combined gtf\n", + "pattern": "*.stats" + } + } + ] + }, + { + "tracking": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tracking": { + "type": "file", + "description": "This file matches transcripts up between samples\n", + "pattern": "*.tracking" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60111,66 +74639,99 @@ "doi": "10.12688/f1000research.23297.1", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "A reference file in either the GFF3, GFF2 or GTF format.", - "pattern": "*.{gff, gtf}" - } - }, - { - "fasta": { - "type": "file", - "description": "A multi-fasta file with the genomic sequences", - "pattern": "*.{fasta,fa,faa,fas,fsa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file resulting from the conversion of the GFF input file if '-T' argument is present", - "pattern": "*.{gtf}" - } - }, - { - "gffread_gff": { - "type": "file", - "description": "GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent", - "pattern": "*.gff3" - } - }, - { - "gffread_fasta": { - "type": "file", - "description": "Fasta file produced when either of '-w', '-x', '-y' parameters is present", - "pattern": "*.fasta" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:gffread" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "A reference file in either the GFF3, GFF2 or GTF format.", + "pattern": "*.{gff, gtf}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "A multi-fasta file with the genomic sequences", + "pattern": "*.{fasta,fa,faa,fas,fsa}" + } + } + ] + ], + "output": [ + { + "gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gtf": { + "type": "file", + "description": "GTF file resulting from the conversion of the GFF input file if '-T' argument is present", + "pattern": "*.{gtf}" + } + } + ] + }, + { + "gffread_gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent", + "pattern": "*.gff3" + } + } + ] + }, + { + "gffread_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing meta data\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Fasta file produced when either of '-w', '-x', '-y' parameters is present", + "pattern": "*.fasta" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60248,51 +74809,71 @@ "doi": "10.1093/bioinformatics/btac836", "licence": [ "BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "files": { - "type": "file", - "description": "Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "File containing output of gget command (-o for most gget tools).", - "pattern": "*.{json,csv}" - } - }, - { - "file": { - "type": "file", - "description": "Path to any file downloaded by gget", - "pattern": "*" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "files": { + "type": "file", + "description": "Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle.\n" + } + } + ] + ], + "output": [ + { + "files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*[!versions.yml][!${prefix}.${extension}]*": { + "type": "file", + "description": "File containing output of gget command." + } + } + ] + }, + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${extension}": { + "type": "file", + "description": "File containing output of gget command (-o for most gget tools).", + "pattern": "*.{json,csv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60326,7 +74907,8 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] + ], + "identifier": "biotools:glimpse2" } } ], @@ -60334,73 +74916,87 @@ "AVX2" ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "region": { - "type": "string", - "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genomic map information\ne.g. [ map:'GRCh38' ]\n" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap" - } - }, - { - "model": { - "type": "string", - "description": "Algorithm model to use:\n\"recursive\": Recursive algorithm\n\"sequential\": Sequential algorithm (Recommended)\n\"uniform-number-variants\": Experimental. Uniform the number of variants in the sequential algorithm\n", - "pattern": "{recursive,sequential,uniform-number-variants}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "chunk_chr": { - "type": "file", - "description": "Tab delimited output txt file containing buffer and imputation regions.", - "pattern": "*.{txt}" - } + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "region": { + "type": "string", + "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genomic map information\ne.g. [ map:'GRCh38' ]\n" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap" + } + } + ], + [ + { + "model": { + "type": "string", + "description": "Algorithm model to use:\n\"recursive\": Recursive algorithm\n\"sequential\": Sequential algorithm (Recommended)\n\"uniform-number-variants\": Experimental. Uniform the number of variants in the sequential algorithm\n", + "pattern": "{recursive,sequential,uniform-number-variants}" + } + } + ] + ], + "output": [ + { + "chunk_chr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab delimited output txt file containing buffer and imputation regions.", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60440,147 +75036,238 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). Can also be a list of such regions.", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "freq": { - "type": "file", - "description": "File containing allele frequencies at each site.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "truth": { - "type": "file", - "description": "Validation dataset called at the same positions as the imputed file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "estimate": { - "type": "file", - "description": "Imputed dataset file obtain after phasing.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "samples": { - "type": "file", - "description": "List of samples to process, one sample ID per line.", - "pattern": "*.{txt,tsv}" - } - }, - { - "groups": { - "type": "file", - "description": "Alternative to frequency bins, group bins are user defined, provided in a file.", - "pattern": "*.{txt,tsv}" - } - }, - { - "bins": { - "type": "string", - "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n", - "pattern": "0 0.01 0.05 ... 0.5" - } - }, - { - "ac_bins": { - "type": "string", - "description": "User-defined allele count bins used for rsquared computations.", - "pattern": "1 2 5 10 20 ... 100000" - } - }, - { - "allele_counts": { - "type": "string", - "description": "Default allele count bins used for rsquared computations.\nAN field must be defined in the frequency file.\n" - } - }, - { - "min_val_gl": { - "type": "float", - "description": "Minimum genotype likelihood probability P(G|R) in validation data.\nSet to zero to have no filter of if using –gt-validation\n" - } - }, - { - "min_val_dp": { - "type": "integer", - "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error.\nSet to zero to have no filter of if using –gt-validation\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } - }, - { - "errors_cal": { - "type": "file", - "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.cal.txt.gz" - } - }, - { - "errors_grp": { - "type": "file", - "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.grp.txt.gz" - } - }, - { - "errors_spl": { - "type": "file", - "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.spl.txt.gz" - } - }, - { - "rsquare_grp": { - "type": "file", - "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.grp.txt.gz" - } - }, - { - "rsquare_spl": { - "type": "file", - "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.spl.txt.gz" - } - }, - { - "rsquare_per_site": { - "type": "file", - "description": "Variant r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "_r2_sites.txt.gz" - } + ], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "estimate": { + "type": "file", + "description": "Imputed dataset file obtain after phasing.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "estimate_index": { + "type": "file", + "description": "Index file for the imputed dataset file." + } + }, + { + "truth": { + "type": "file", + "description": "Validation dataset called at the same positions as the imputed file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "truth_index": { + "type": "file", + "description": "Index file for the truth file." + } + }, + { + "freq": { + "type": "file", + "description": "File containing allele frequencies at each site.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "freq_index": { + "type": "file", + "description": "Index file for the allele frequencies file." + } + }, + { + "samples": { + "type": "file", + "description": "List of samples to process, one sample ID per line.", + "pattern": "*.{txt,tsv}" + } + }, + { + "region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). Can also be a list of such regions.", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "groups": { + "type": "file", + "description": "Alternative to frequency bins, group bins are user defined, provided in a file.", + "pattern": "*.{txt,tsv}" + } + }, + { + "bins": { + "type": "string", + "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n", + "pattern": "0 0.01 0.05 ... 0.5" + } + }, + { + "ac_bins": { + "type": "string", + "description": "User-defined allele count bins used for rsquared computations.", + "pattern": "1 2 5 10 20 ... 100000" + } + }, + { + "allele_counts": { + "type": "string", + "description": "Default allele count bins used for rsquared computations.\nAN field must be defined in the frequency file.\n" + } + } + ], + [ + { + "min_val_gl": { + "type": "float", + "description": "Minimum genotype likelihood probability P(G|R) in validation data.\nSet to zero to have no filter of if using –gt-validation\n" + } + } + ], + [ + { + "min_val_dp": { + "type": "integer", + "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error.\nSet to zero to have no filter of if using –gt-validation\n" + } + } + ] + ], + "output": [ + { + "errors_cal": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.cal.txt.gz": { + "type": "file", + "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.cal.txt.gz" + } + } + ] + }, + { + "errors_grp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.grp.txt.gz": { + "type": "file", + "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.grp.txt.gz" + } + } + ] + }, + { + "errors_spl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.spl.txt.gz": { + "type": "file", + "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.spl.txt.gz" + } + } + ] + }, + { + "rsquare_grp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.grp.txt.gz": { + "type": "file", + "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.grp.txt.gz" + } + } + ] + }, + { + "rsquare_spl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.spl.txt.gz": { + "type": "file", + "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.spl.txt.gz" + } + } + ] + }, + { + "rsquare_per_site": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_r2_sites.txt.gz": { + "type": "file", + "description": "Variant r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "_r2_sites.txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60620,52 +75307,63 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_list": { - "type": "file", - "description": "VCF/BCF file containing genotype probabilities (GP field).", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{csi,tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "merged_variants": { - "type": "file", - "description": "Output ligated (phased) file in VCF/BCF format.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } + ], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_list": { + "type": "file", + "description": "VCF/BCF file containing genotype probabilities (GP field).", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{csi,tbi}" + } + } + ] + ], + "output": [ + { + "merged_variants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output ligated (phased) file in VCF/BCF format.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60705,121 +75403,144 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.\nWhen using BAM/CRAM the name of the file is used as samples name.\n", - "pattern": "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input BAM/CRAM/VCF/BCF file.", - "pattern": "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "samples_file": { - "type": "file", - "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", - "pattern": "*.{txt,tsv}" - } - }, - { - "input_region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "output_region": { - "type": "string", - "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genomic map information\ne.g. `[ map:'GRCh38' ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}" - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.\nOptional if reference panel is in bin format.\n", - "pattern": "*.gmap" - } - }, - { - "fasta_reference": { - "type": "file", - "description": "Faidx-indexed reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", - "pattern": "*.fasta" - } - }, - { - "fasta_reference_index": { - "type": "file", - "description": "Faidx index of the reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "phased_variants": { - "type": "file", - "description": "Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "stats_coverage": { - "type": "file", - "description": "Optional coverage statistic file created when BAM/CRAM files are used as inputs.", - "pattern": "*.txt.gz" - } + ], + "identifier": "biotools:glimpse2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.\nWhen using BAM/CRAM the name of the file is used as samples name.\n", + "pattern": "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input BAM/CRAM/VCF/BCF file.", + "pattern": "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "samples_file": { + "type": "file", + "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", + "pattern": "*.{txt,tsv}" + } + }, + { + "input_region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "output_region": { + "type": "string", + "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).\nOptional if reference panel is in bin format.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}" + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.\nOptional if reference panel is in bin format.\n", + "pattern": "*.gmap" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genomic map information\ne.g. `[ map:'GRCh38' ]`\n" + } + }, + { + "fasta_reference": { + "type": "file", + "description": "Faidx-indexed reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", + "pattern": "*.fasta" + } + }, + { + "fasta_reference_index": { + "type": "file", + "description": "Faidx index of the reference sequence file in the appropriate genome build.\nNecessary for CRAM files.\n", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "phased_variants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.{vcf,vcf.gz,bcf,bgen}": { + "type": "file", + "description": "Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "stats_coverage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Optional coverage statistic file created when BAM/CRAM files are used as inputs.", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60859,7 +75580,8 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] + ], + "identifier": "biotools:glimpse2" } } ], @@ -60867,74 +75589,86 @@ "AVX2" ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}" - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "input_region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "output_region": { - "type": "string", - "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genomic map information\ne.g. `[ map:'GRCh38' ]`\n" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bin_ref": { - "type": "file", - "description": "binary reference panel", - "pattern": "*.bin" - } + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}" + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "input_region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "output_region": { + "type": "string", + "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genomic map information\ne.g. `[ map:'GRCh38' ]`\n" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap" + } + } + ] + ], + "output": [ + { + "bin_ref": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bin": { + "type": "file", + "description": "binary reference panel", + "pattern": "*.bin" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -60973,51 +75707,68 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "region": { - "type": "string", - "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Tab delimited output txt file containing buffer and imputation regions.", - "pattern": "*.{txt}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index file for the input VCF/BCF file." + } + }, + { + "region": { + "type": "string", + "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n" + } + } + ] + ], + "output": [ + { + "chunk_chr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab delimited output txt file containing buffer and imputation regions.", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61057,112 +75808,187 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "freq": { - "type": "file", - "description": "File containing allele frequencies at each site.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "truth": { - "type": "file", - "description": "Validation dataset called at the same positions as the imputed file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "estimate": { - "type": "file", - "description": "Imputed data.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "min_prob": { - "type": "float", - "description": "Minimum posterior probability P(G|R) in validation data" - } - }, - { - "min_dp": { - "type": "integer", - "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and --minDP > 0, the program exits with an error.\n" - } - }, - { - "bins": { - "type": "string", - "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "errors_cal": { - "type": "file", - "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.cal.txt.gz" - } - }, - { - "errors_grp": { - "type": "file", - "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.grp.txt.gz" - } - }, - { - "errors_spl": { - "type": "file", - "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.errors.spl.txt.gz" - } - }, - { - "rsquared_grp": { - "type": "file", - "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.grp.txt.gz" - } - }, - { - "rsquared_spl": { - "type": "file", - "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", - "pattern": "*.rsquare.spl.txt.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "estimate": { + "type": "file", + "description": "Imputed data.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "estimate_index": { + "type": "file", + "description": "Index file for the imputed data." + } + }, + { + "freq": { + "type": "file", + "description": "File containing allele frequencies at each site.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "freq_index": { + "type": "file", + "description": "Index file for the allele frequencies file." + } + }, + { + "truth": { + "type": "file", + "description": "Validation dataset called at the same positions as the imputed file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "truth_index": { + "type": "file", + "description": "Index file for the truth file." + } + }, + { + "region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], + [ + { + "min_prob": { + "type": "float", + "description": "Minimum posterior probability P(G|R) in validation data" + } + } + ], + [ + { + "min_dp": { + "type": "integer", + "description": "Minimum coverage in validation data.\nIf FORMAT/DP is missing and --minDP > 0, the program exits with an error.\n" + } + } + ], + [ + { + "bins": { + "type": "string", + "description": "Allele frequency bins used for rsquared computations.\nBy default they should as MAF bins [0-0.5], while\nthey should take the full range [0-1] if --use-ref-alt is used.\n" + } + } + ] + ], + "output": [ + { + "errors_cal": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.cal.txt.gz": { + "type": "file", + "description": "Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.cal.txt.gz" + } + } + ] + }, + { + "errors_grp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.grp.txt.gz": { + "type": "file", + "description": "Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.grp.txt.gz" + } + } + ] + }, + { + "errors_spl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.error.spl.txt.gz": { + "type": "file", + "description": "Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.errors.spl.txt.gz" + } + } + ] + }, + { + "rsquare_grp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.grp.txt.gz": { + "type": "file", + "description": "Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.grp.txt.gz" + } + } + ] + }, + { + "rsquare_spl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rsquare.spl.txt.gz": { + "type": "file", + "description": "Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.", + "pattern": "*.rsquare.spl.txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61196,52 +76022,63 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_list": { - "type": "file", - "description": "VCF/BCF file containing genotype probabilities (GP field).", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "merged_variants": { - "type": "file", - "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_list": { + "type": "file", + "description": "VCF/BCF file containing genotype probabilities (GP field).", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + } + ] + ], + "output": [ + { + "merged_variants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61281,94 +76118,105 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz,bcf.gz}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "samples_file": { - "type": "file", - "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", - "pattern": "*.{txt,tsv}" - } - }, - { - "input_region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "output_region": { - "type": "string", - "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}" - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "phased_variants": { - "type": "file", - "description": "Output VCF/BCF file containing genotype probabilities (GP field),\nimputed dosages (DS field), best guess genotypes (GT field),\nsampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz,bcf.gz}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "samples_file": { + "type": "file", + "description": "File with sample names and ploidy information.\nOne sample per line with a mandatory second column indicating ploidy (1 or 2).\nSample names that are not present are assumed to have ploidy 2 (diploids).\nGLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.\n", + "pattern": "*.{txt,tsv}" + } + }, + { + "input_region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "output_region": { + "type": "string", + "description": "Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}" + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap" + } + } + ] + ], + "output": [ + { + "phased_variants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file containing genotype probabilities (GP field),\nimputed dosages (DS field), best guess genotypes (GT field),\nsampled haplotypes in the last (max 16) main iterations (HS field) and info-score.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61407,45 +76255,56 @@ "doi": "10.1038/s41588-020-00756-0", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "VCF/BCF file generated using GLIMPSE ligate", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } } - }, - { - "input": { - "type": "file", - "description": "VCF/BCF file generated using GLIMPSE ligate", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "haplo_sampled": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file containing phased genotypes.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] }, { - "haplo_sampled": { - "type": "file", - "description": "Output VCF/BCF file containing phased genotypes.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61477,39 +76336,57 @@ "doi": "10.1101/343970", "licence": [ "Apache-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "gvcfs": { - "type": "list", - "description": "Input genomic vcf files", - "pattern": "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "gvcfs": { + "type": "list", + "description": "Input genomic vcf files", + "pattern": "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bcf": [ + { + "meta": { + "type": "file", + "description": "merged BCF file", + "pattern": "*.bcf" + } + }, + { + "*.bcf": { + "type": "file", + "description": "merged BCF file", + "pattern": "*.bcf" + } + } + ] }, { - "bcf": { - "type": "file", - "description": "merged BCF file", - "pattern": "*.bcf" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61552,109 +76429,178 @@ "doi": "10.1186/s13059-020-02084-2", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "hto_matrix": { - "type": "file", - "description": "path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters" - } - }, - { - "hto_names": { - "type": "string", - "description": "Comma separated list of HTO names, without whitespace\n" - } - }, - { - "type_report": { - "type": "boolean", - "description": "If true, full classification report is generated, otherwise the simplified classification report.\n" - } - }, - { - "summary_report": { - "type": "boolean", - "description": "If true, summary report is generated.\n" - } - }, - { - "skip": { - "type": "file", - "description": "Load a full classification report and skip the mtx folder as input. Require a path argument.\n" - } - }, - { - "examine": { - "type": "file", - "description": "Provide the cell list. Requires a file argument. Only executes if -u is set.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "barcodes": { - "type": "file", - "description": "barcodes tsv file with removed cell-hashing-identifiable multiplets\n", - "pattern": "barcodes.tsv.gz" - } - }, - { - "matrix": { - "type": "file", - "description": "matrix mtx.tsv file with removed cell-hashing-identifiable multiplets\n", - "pattern": "matrix.mtx.gz" - } - }, - { - "features": { - "type": "file", - "description": "features tsv file with removed cell-hashing-identifiable multiplets\n", - "pattern": "features.tsv.gz" - } - }, - { - "classification_report": { - "type": "file", - "description": "full or simplified classification report\n", - "pattern": "GMM_*.csv" - } - }, - { - "config_report": { - "type": "file", - "description": "Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report.\n", - "pattern": "GMM_*.csv" - } - }, - { - "summary_report": { - "type": "file", - "description": "summary report, optional output\n", - "pattern": "test/summary_report_*.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "hto_matrix": { + "type": "file", + "description": "path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters" + } + }, + { + "hto_names": { + "type": "string", + "description": "Comma separated list of HTO names, without whitespace\n" + } + } + ], + [ + { + "type_report": { + "type": "boolean", + "description": "If true, full classification report is generated, otherwise the simplified classification report.\n" + } + } + ], + [ + { + "summary_report": { + "type": "boolean", + "description": "If true, summary report is generated.\n" + } + } + ], + [ + { + "skip": { + "type": "file", + "description": "Load a full classification report and skip the mtx folder as input. Require a path argument.\n" + } + } + ], + [ + { + "examine": { + "type": "file", + "description": "Provide the cell list. Requires a file argument. Only executes if -u is set.\n" + } + } + ] + ], + "output": [ + { + "barcodes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "barcodes.tsv.gz\" ": { + "type": "file", + "description": "barcodes tsv file with removed cell-hashing-identifiable multiplets\n", + "pattern": "barcodes.tsv.gz" + } + } + ] + }, + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "matrix.mtx.gz\" ": { + "type": "file", + "description": "matrix mtx.tsv file with removed cell-hashing-identifiable multiplets\n", + "pattern": "matrix.mtx.gz" + } + } + ] + }, + { + "features": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "features.tsv.gz\" ": { + "type": "file", + "description": "features tsv file with removed cell-hashing-identifiable multiplets\n", + "pattern": "features.tsv.gz" + } + } + ] + }, + { + "classification_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "GMM_*.csv\" ": { + "type": "file", + "description": "full or simplified classification report\n", + "pattern": "GMM_*.csv" + } + } + ] + }, + { + "config_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "GMM_*.config\" ": { + "type": "file", + "description": "Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report.\n", + "pattern": "GMM_*.csv" + } + } + ] + }, + { + "summary_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "summary_report_*.txt": { + "type": "file", + "description": "summary report, optional output\n", + "pattern": "test/summary_report_*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61691,45 +76637,49 @@ "documentation": "https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html", "licence": [ "GPL" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Draft assembly file", - "pattern": "*.{txt,bed,interval,genome,bins}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Draft assembly file", + "pattern": "*.{txt,bed,interval,genome,bins}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sorted": { - "type": "file", - "description": "The sorted txt file generated by sort", - "pattern": "*.{txt,bed,interval,genome,bins}" - } + "sorted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61777,43 +76727,54 @@ "doi": "10.5281/zenodo.581670", "licence": [ "GPL" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Text file, possibly gzip file" + } } + ] + ], + "output": [ + { + "split": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + " \"*split*\" ": { + "type": "file", + "description": "Split files", + "pattern": "*split*" + } + } + ] }, { - "input": { - "type": "file", - "description": "Text file, possibly gzip file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "split": { - "type": "file", - "description": "Split files", - "pattern": "*split*" - } - }, - { - "versions": { - "type": "file", - "description": "The split files" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "The split files" + } + } + ] } ], "authors": [ @@ -61845,51 +76806,62 @@ "tool_dev_url": "https://genomehubs.github.io/goat-cli/goat_cli/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "taxon": { - "type": "string", - "description": "The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank.\n" - } - }, - { - "taxa_file": { - "type": "file", - "description": "A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line\nshould contain a single entry.File size is limited to 500 entries.\n", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "taxonsearch": { - "type": "file", - "description": "TSV file containing search results.", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:goat" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "taxon": { + "type": "string", + "description": "The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank.\n" + } + }, + { + "taxa_file": { + "type": "file", + "description": "A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line\nshould contain a single entry.File size is limited to 500 entries.\n", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "taxonsearch": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file containing search results.", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -61924,58 +76896,179 @@ "doi": "10.1093/gigascience/gix090", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" - } - }, - { - "bams": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM files", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "indexes": { - "type": "file", - "description": "BAI/CRAI files", - "pattern": "*.{bai,crai}" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output": { - "type": "file", - "description": "Files generated by indexcov" - } - }, - { - "bams": { - "type": "file", - "description": "Sorted ans indexed BAM or CRAM index (.crai) files", - "pattern": "*.{bam,crai}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" + } + }, + { + "bams": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM files", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "indexes": { + "type": "file", + "description": "BAI/CRAI files", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*": { + "type": "file", + "description": "Files generated by indexcov" + } + } + ] + }, + { + "ped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*ped": { + "type": "file", + "description": "ped files", + "pattern": "*ped" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*bed.gz": { + "type": "file", + "description": "bed files", + "pattern": "*bed.gz" + } + } + ] + }, + { + "bed_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*bed.gz.tbi": { + "type": "file", + "description": "bed index files", + "pattern": "*bed.gz.tbi" + } + } + ] + }, + { + "roc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*roc": { + "type": "file", + "description": "roc files", + "pattern": "*roc" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*html": { + "type": "file", + "description": "html files", + "pattern": "*html" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*png": { + "type": "file", + "description": "png files", + "pattern": "*png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62010,58 +77103,79 @@ "doi": "10.1093/gigascience/gix090", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bai": { - "type": "file", - "description": "BAI/CRAI file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fasta index file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Bed file containing split regions", - "pattern": "*.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bai": { + "type": "file", + "description": "BAI/CRAI file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fasta index file", + "pattern": "*.fai" + } + } + ], + [ + { + "split": { + "type": "boolean", + "description": "Split the regions" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file containing split regions", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62096,126 +77210,193 @@ "doi": "10.1093/nar/gkad347", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "de_file": { - "type": "file", - "pattern": "*.{csv,tsv}", - "description": "CSV or TSV-format tabular file with differential analysis outputs\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "The contrast variable that is being investigated in DE analysis, e.g. \"treatment\".\n" - } - }, - { - "reference": { - "type": "string", - "description": "The contrast level of the reference samples, e.g. \"control\"\n" - } - }, - { - "target": { - "type": "string", - "description": "The contrast level of the target samples, e.g. \"treated\"\n" - } - }, - { - "background_file": { - "type": "file", - "pattern": "*.{csv,tsv,txt}", - "description": "Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs.\n" - } - }, - { - "gmt_file": { - "type": "file", - "pattern": "*.gmt", - "description": "Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "all_enrich": { - "type": "file", - "description": "TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found\n", - "pattern": "*gprofiler2.*all_enriched_pathways.tsv" - } - }, - { - "rds": { - "type": "file", - "description": "RDS file; R object containing the results of the gost query\n", - "pattern": "*gprofiler2.*gost_results.rds" - } - }, - { - "plot_png": { - "type": "file", - "description": "PNG file; Manhattan plot of all enriched pathways\n", - "pattern": "*gprofiler2.*gostplot.png" - } - }, - { - "plot_html": { - "type": "file", - "description": "HTML file; interactive Manhattan plot of all enriched pathways\n", - "pattern": "*gprofiler2.*gostplot.html" - } - }, - { - "sub_enrich": { - "type": "file", - "description": "TSV file; table listing enriched pathways that were found from one particular source\n", - "pattern": "*gprofiler2.*sub_enriched_pathways.tsv" - } - }, - { - "sub_plot": { - "type": "file", - "description": "PNG file; bar plot showing the fraction of genes that were found enriched in each pathway\n", - "pattern": "*gprofiler2.*sub_enriched_pathways.png" - } - }, - { - "filtered_gmt": { - "type": "file", - "description": "GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources\n", - "pattern": "*ENSG_filtered.gmt" - } - }, - { - "session_info": { - "type": "file", - "description": "Log file containing information about the R session that was run for this module\n", - "pattern": "*R_sessionInfo.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "de_file": { + "type": "file", + "pattern": "*.{csv,tsv}", + "description": "CSV or TSV-format tabular file with differential analysis outputs\n" + } + } + ], + [ + { + "gmt_file": { + "type": "file", + "pattern": "*.gmt", + "description": "Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases\n" + } + } + ], + [ + { + "background_file": { + "type": "file", + "pattern": "*.{csv,tsv,txt}", + "description": "Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs.\n" + } + } + ] + ], + "output": [ + { + "all_enrich": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.all_enriched_pathways.tsv": { + "type": "file", + "description": "TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found\n", + "pattern": "*gprofiler2.*all_enriched_pathways.tsv" + } + } + ] + }, + { + "rds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.gost_results.rds": { + "type": "file", + "description": "RDS file; R object containing the results of the gost query\n", + "pattern": "*gprofiler2.*gost_results.rds" + } + } + ] + }, + { + "plot_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.gostplot.png": { + "type": "file", + "description": "PNG file; Manhattan plot of all enriched pathways\n", + "pattern": "*gprofiler2.*gostplot.png" + } + } + ] + }, + { + "plot_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.gostplot.html": { + "type": "file", + "description": "HTML file; interactive Manhattan plot of all enriched pathways\n", + "pattern": "*gprofiler2.*gostplot.html" + } + } + ] + }, + { + "sub_enrich": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.*.sub_enriched_pathways.tsv": { + "type": "file", + "description": "TSV file; table listing enriched pathways that were found from one particular source\n", + "pattern": "*gprofiler2.*sub_enriched_pathways.tsv" + } + } + ] + }, + { + "sub_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*.gprofiler2.*.sub_enriched_pathways.png": { + "type": "file", + "description": "PNG file; bar plot showing the fraction of genes that were found enriched in each pathway\n", + "pattern": "*gprofiler2.*sub_enriched_pathways.png" + } + } + ] + }, + { + "filtered_gmt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*ENSG_filtered.gmt": { + "type": "file", + "description": "GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources\n", + "pattern": "*ENSG_filtered.gmt" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*R_sessionInfo.log": { + "type": "file", + "description": "Log file containing information about the R session that was run for this module\n", + "pattern": "*R_sessionInfo.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62246,32 +77427,49 @@ "grabix": { "description": "a wee tool for random access into BGZF files.", "homepage": "https://github.com/arq5x/grabix", - "documentation": "https://github.com/arq5x/grabix" + "documentation": "https://github.com/arq5x/grabix", + "identifier": "" } } ], "input": [ - { - "input": { - "type": "file", - "pattern": "*.gz", - "description": "file to check compression" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "pattern": "*.gz", + "description": "file to check compression" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "compress_bgzip": [ + { + "meta": { + "type": "string", + "description": "environmental variable with value \"yes\" or \"no\"" + } + } + ] }, { - "compress_bgzip": { - "type": "string", - "description": "environmental variable with value \"yes\" or \"no\"" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62304,56 +77502,71 @@ "documentation": "https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input FASTQ files\nand paired-end data, respectively.\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format.\n" - } - }, - { - "index": { - "type": "file", - "description": "FASTA index in gmidx.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sam": { - "type": "file", - "description": "Alignment in SAM format", - "pattern": "*.sam" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:Graphmap2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "file containing reads to be aligned." + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format.\n" + } + } + ], + [ + { + "index": { + "type": "file", + "description": "FASTA index in gmidx.\n" + } + } + ] + ], + "output": [ + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "Alignment in SAM format", + "pattern": "*.sam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62386,32 +77599,43 @@ "documentation": "https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads", "licence": [ "MIT" - ] + ], + "identifier": "biotools:Graphmap2" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format.\n" + [ + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format.\n" + } } - } + ] ], "output": [ { - "gmidx": { - "type": "file", - "description": "Graphmap2 fasta index in gmidx format", - "pattern": "*.gmidx" - } + "index": [ + { + "*.gmidx": { + "type": "file", + "description": "Index file in gmidx format", + "pattern": "*.gmidx" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62448,80 +77672,119 @@ "doi": "10.1038/ng.3964", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file. This is automatically found base on BAM input file name", - "pattern": "*.{bai}" - } - }, - { - "ref": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fa, fasta, fas}" - } - }, - { - "ref_fai": { - "type": "file", - "description": "Reference index file. This is automatically found based on referece input file name.", - "pattern": "*.{.fai}" - } - }, - { - "region_file": { - "type": "file", - "description": "File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or `--region` (in ext.args) must be specified.", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with genotyped variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index file", - "pattern": "*.{vcf.gz.tbi}" - } + ], + "identifier": "biotools:Graphtyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file. This is automatically found base on BAM input file name", + "pattern": "*.{bai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fa, fasta, fas}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "ref_fai": { + "type": "file", + "description": "Reference index file. This is automatically found based on referece input file name.", + "pattern": "*.{.fai}" + } + } + ], + [ + { + "region_file": { + "type": "file", + "description": "File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or `--region` (in ext.args) must be specified.", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "results/*/*.vcf.gz": { + "type": "file", + "description": "VCF file with genotyped variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "results/*/*.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62561,52 +77824,73 @@ "doi": "10.1038/ng.3964", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF files", - "pattern": "*.{vcf,vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Concatenated VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "Concatenated VCF file index", - "pattern": "*.{tbi}" - } + ], + "identifier": "biotools:Graphtyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF files", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Concatenated VCF file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Concatenated VCF file index", + "pattern": "*.{tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62646,65 +77930,100 @@ "doi": "10.1186/s13059-021-02423-x", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "inputs": { - "type": "file", - "description": "One or more input BAM/CRAM file(s)", - "pattern": "*.{bam,cram}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta", - "pattern": "*.{fa,fna,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference fasta", - "pattern": "*.fai" - } - }, - { - "bwa_index": { - "type": "directory", - "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The called VCF file created by Gridss' call step", - "pattern": "*.vcf.gz" - } + ], + "identifier": "biotools:gridss" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "inputs": { + "type": "file", + "description": "One or more input BAM/CRAM file(s)", + "pattern": "*.{bam,cram}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta", + "pattern": "*.{fa,fna,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference fasta", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\n" + } + }, + { + "bwa_index": { + "type": "directory", + "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The called VCF file created by Gridss' call step", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -62738,212 +78057,262 @@ "doi": "10.1186/s13059-021-02423-x", "licence": [ "GPL v3" - ] - } + ], + "identifier": "biotools:gridss" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "GRIDSS generated vcf file", + "pattern": "*.vcf" + } + }, + { + "bedpe": { + "type": "file", + "description": "GRIDSS generated bedpe file", + "pattern": "*.bedpe" + } + }, + { + "bed": { + "type": "file", + "description": "GRIDSS generated bed file", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta", + "pattern": "*.{fa,fna,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fai information\ne.g. [ id:'test']\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the reference fasta", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing bwa generated index information\ne.g. [ id:'test']\n" + } + }, + { + "bwa_index": { + "type": "directory", + "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step" + } + } + ] + ], + "output": [ + { + "bedpe": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bedpe": { + "type": "file", + "description": "GRIDSS generated breakpoint pon bedpe file", + "pattern": "*.bedpe" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "GRIDSS generated breakpoint pon bed file", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, + "authors": [ + "@kubranarci" + ] + } + }, + { + "name": "gridss_gridsssomaticfilter", + "path": "modules/nf-core/gridss/gridsssomaticfilter/meta.yml", + "type": "module", + "meta": { + "name": "gridss_gridsssomaticfilter", + "description": "GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.", + "keywords": [ + "gridss", + "structural variants", + "somatic variants", + "vcf" + ], + "tools": [ { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fai information\ne.g. [ id:'test']\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing bwa generated index information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "GRIDSS generated vcf file", - "pattern": "*.vcf" - } - }, - { - "bedpe": { - "type": "file", - "description": "GRIDSS generated bedpe file", - "pattern": "*.bedpe" - } - }, - { - "bed": { - "type": "file", - "description": "GRIDSS generated bed file", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta", - "pattern": "*.{fa,fna,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference fasta", - "pattern": "*.fai" - } - }, - { - "bwa_index": { - "type": "directory", - "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bedpe": { - "type": "file", - "description": "GRIDSS generated breakpoint pon bedpe file", - "pattern": "*.bedpe" - } - }, - { - "bed": { - "type": "file", - "description": "GRIDSS generated breakpoint pon bed file", - "pattern": "*.bed" - } - } - ], - "authors": [ - "@kubranarci" - ] - } - }, - { - "name": "gridss_gridsssomaticfilter", - "path": "modules/nf-core/gridss/gridsssomaticfilter/meta.yml", - "type": "module", - "meta": { - "name": "gridss_gridsssomaticfilter", - "description": "GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.", - "keywords": [ - "gridss", - "structural variants", - "somatic variants", - "vcf" - ], - "tools": [ - { - "gridss": { - "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite", - "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation", - "tool_dev_url": "https://github.com/PapenfussLab/gridss", - "doi": "10.1186/s13059-021-02423-x", - "licence": [ - "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information for PONDIR\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file, must be generated with GRIDSS", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "pondir": { - "type": "directory", - "description": "Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "high_conf_sv": { - "type": "file", - "description": "VCF file including high confidence somatic SVs", - "pattern": "*.vcf.bgz" - } - }, - { - "all_sv": { - "type": "file", - "description": "VCF file including all somatic SVs", - "pattern": "*.vcf.bgz" - } - } - ], - "authors": [ - "@kubranarci" - ] - } - }, - { - "name": "gsea_gsea", - "path": "modules/nf-core/gsea/gsea/meta.yml", - "type": "module", - "meta": { - "name": "gsea_gsea", - "description": "run the Broad Gene Set Enrichment tool in GSEA mode", - "keywords": [ - "gene set analysis", - "enrichment", - "gsea", - "gene set" - ], - "tools": [ + "gridss": { + "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite", + "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation", + "tool_dev_url": "https://github.com/PapenfussLab/gridss", + "doi": "10.1186/s13059-021-02423-x", + "licence": [ + "GPL v3" + ], + "identifier": "biotools:gridss" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF file, must be generated with GRIDSS", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information for PONDIR\ne.g. [ id:'test']\n" + } + }, + { + "pondir": { + "type": "directory", + "description": "Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON." + } + } + ] + ], + "output": [ + { + "high_conf_sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.high_confidence_somatic.vcf.bgz": { + "type": "file", + "description": "VCF file including high confidence somatic SVs", + "pattern": "*.vcf.bgz" + } + } + ] + }, + { + "all_sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.all_somatic.vcf.bgz": { + "type": "file", + "description": "VCF file including all somatic SVs", + "pattern": "*.vcf.bgz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@kubranarci" + ] + } + }, + { + "name": "gsea_gsea", + "path": "modules/nf-core/gsea/gsea/meta.yml", + "type": "module", + "meta": { + "name": "gsea_gsea", + "description": "run the Broad Gene Set Enrichment tool in GSEA mode", + "keywords": [ + "gene set analysis", + "enrichment", + "gsea", + "gene set" + ], + "tools": [ { "gsea": { "description": "Gene Set Enrichment Analysis (GSEA)", @@ -62952,218 +78321,440 @@ "doi": "10.1073/pnas.0506580102", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ].\n" - } - }, - { - "gct": { - "type": "file", - "description": "GCT file with expression values", - "pattern": "*.{gct}" - } - }, - { - "cls": { - "type": "file", - "description": "CL file with the classes of the samples in the GCT file", - "pattern": "*.{gct}" - } - }, - { - "gene_sets": { - "type": "file", - "description": "GMX or GMT file with gene sets", - "pattern": "*.{gmx,gmt}" - } - }, - { - "reference": { - "type": "string", - "description": "String indicating which of the classes in the cls file should be used\nas the reference level of the comparison.\n" - } - }, - { - "target": { - "type": "string", - "description": "String indicating which of the classes in the cls file should be used\nas the target level of the comparison.\n" - } - }, - { - "chip": { - "type": "file", - "description": "optional Broad-style chip file mapping identifiers in gct to\nthose in gene_sets\n", - "pattern": "*.{chip}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" - } - }, - { - "rpt": { - "type": "file", - "description": "File containing parameter settings used", - "pattern": "*.rpt" - } - }, - { - "index_html": { - "type": "file", - "description": "Top level report HTML file", - "pattern": "index.html" - } - }, - { - "heat_map_corr_plot": { - "type": "file", - "description": "HTML file combining heatmap and rank correlation plot", - "pattern": "heat_map_corr_plot.html" - } - }, - { - "report_tsvs_ref": { - "type": "file", - "description": "Main TSV results report file for the reference group.", - "pattern": "gsea_report_for_reference*.tsv" - } - }, - { - "report_htmls_ref": { - "type": "file", - "description": "Main HTML results report file for the reference group. sample groups", - "pattern": "gsea_report_for_reference*.html" - } - }, - { - "report_tsvs_target": { - "type": "file", - "description": "Main TSV results report file for the target group.", - "pattern": "gsea_report_for_target*.tsv" - } - }, - { - "report_htmls_target": { - "type": "file", - "description": "Main HTML results report file for the target group.", - "pattern": "gsea_report_for_target*.html" - } - }, - { - "ranked_gene_list": { - "type": "file", - "description": "TSV file with ranked gene list and scores", - "pattern": "ranked_gene_list*.tsv" - } - }, - { - "gene_set_sizes": { - "type": "file", - "description": "TSV file with gene set sizes", - "pattern": "gene_set_sizes.tsv" - } - }, - { - "butterfly_plot": { - "type": "file", - "description": "Butterfly plot with gene rank plotted against score", - "pattern": "butterfly_plot.png" - } - }, - { - "histogram": { - "type": "file", - "description": "Plot showing number of gene sets by enrichment score", - "pattern": "global_es_histogram.png" - } - }, - { - "heatmap": { - "type": "file", - "description": "Heat Map of the top 50 features for each phenotype in test", - "pattern": "heat_map_1.png" - } - }, - { - "pvalues_vs_nes_plot": { - "type": "file", - "description": "Plot showing FDR q-value by normalised enrichment score", - "pattern": "pvalues_vs_nes_plot" - } - }, - { - "ranked_list_corr": { - "type": "file", - "description": "Ranked Gene List Correlation Profile", - "pattern": "ranked_list_corr_2.png" - } - }, - { - "gene_set_tsv": { - "type": "list", - "description": "Where -make_sets is not set to false, TSV files, one file for each gene set, with detail on enrichment for each gene", - "pattern": "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" - } - }, - { - "gene_set_html": { - "type": "list", - "description": "Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene", - "pattern": "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" - } - }, - { - "gene_set_heatmap": { - "type": "list", - "description": "Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene", - "pattern": "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" - } - }, - { - "snapshot": { - "type": "list", - "description": "HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot", - "pattern": "*_snapshot*.html" - } - }, - { - "gene_set_enplot": { - "type": "list", - "description": "Where -make_sets is not set to false, PNG-format enrichment (barcode) plots, one file for each gene set, showing how genes contribute to enrichment.", - "pattern": "enplot*.png" - } - }, - { - "gene_set_dist": { - "type": "list", - "description": "Where -make_sets is not set to false, PNG-format enrichment score distributions plots, one file for each gene set.", - "pattern": "gset_rnd_es_dist*.png" - } - }, - { - "archive": { - "type": "file", - "description": "Where -zip_report is set, a zip archive containing all outputs", - "pattern": "*.zip" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:gsea" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ].\n" + } + }, + { + "gct": { + "type": "file", + "description": "GCT file with expression values", + "pattern": "*.{gct}" + } + }, + { + "cls": { + "type": "file", + "description": "CL file with the classes of the samples in the GCT file", + "pattern": "*.{gct}" + } + }, + { + "gene_sets": { + "type": "file", + "description": "GMX or GMT file with gene sets", + "pattern": "*.{gmx,gmt}" + } + } + ], + [ + { + "reference": { + "type": "string", + "description": "String indicating which of the classes in the cls file should be used\nas the reference level of the comparison.\n" + } + }, + { + "target": { + "type": "string", + "description": "String indicating which of the classes in the cls file should be used\nas the target level of the comparison.\n" + } + } + ], + [ + { + "chip": { + "type": "file", + "description": "optional Broad-style chip file mapping identifiers in gct to\nthose in gene_sets\n", + "pattern": "*.{chip}" + } + } + ] + ], + "output": [ + { + "rpt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*.rpt": { + "type": "file", + "description": "File containing parameter settings used", + "pattern": "*.rpt" + } + } + ] + }, + { + "index_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*index.html": { + "type": "file", + "description": "Top level report HTML file", + "pattern": "index.html" + } + } + ] + }, + { + "heat_map_corr_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*heat_map_corr_plot.html": { + "type": "file", + "description": "HTML file combining heatmap and rank correlation plot", + "pattern": "heat_map_corr_plot.html" + } + } + ] + }, + { + "report_tsvs_ref": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*gsea_report_for_${reference}.tsv": { + "type": "file", + "description": "Main TSV results report file for the reference group.", + "pattern": "gsea_report_for_reference*.tsv" + } + } + ] + }, + { + "report_htmls_ref": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*gsea_report_for_${reference}.html": { + "type": "file", + "description": "Main HTML results report file for the reference group. sample groups", + "pattern": "gsea_report_for_reference*.html" + } + } + ] + }, + { + "report_tsvs_target": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*gsea_report_for_${target}.tsv": { + "type": "file", + "description": "Main TSV results report file for the target group.", + "pattern": "gsea_report_for_target*.tsv" + } + } + ] + }, + { + "report_htmls_target": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*gsea_report_for_${target}.html": { + "type": "file", + "description": "Main HTML results report file for the target group.", + "pattern": "gsea_report_for_target*.html" + } + } + ] + }, + { + "ranked_gene_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*ranked_gene_list*.tsv": { + "type": "file", + "description": "TSV file with ranked gene list and scores", + "pattern": "ranked_gene_list*.tsv" + } + } + ] + }, + { + "gene_set_sizes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*gene_set_sizes.tsv": { + "type": "file", + "description": "TSV file with gene set sizes", + "pattern": "gene_set_sizes.tsv" + } + } + ] + }, + { + "histogram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*global_es_histogram.png": { + "type": "file", + "description": "Plot showing number of gene sets by enrichment score", + "pattern": "global_es_histogram.png" + } + } + ] + }, + { + "heatmap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*heat_map_1.png": { + "type": "file", + "description": "Heat Map of the top 50 features for each phenotype in test", + "pattern": "heat_map_1.png" + } + } + ] + }, + { + "pvalues_vs_nes_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*pvalues_vs_nes_plot.png": { + "type": "file", + "description": "Plot showing FDR q-value by normalised enrichment score", + "pattern": "pvalues_vs_nes_plot" + } + }, + { + "ues_vs_nes_plot": { + "type": "file", + "description": "Plot showing FDR q-value by normalised enrichment score", + "pattern": "pvalues_vs_nes_plot" + } + } + ] + }, + { + "ranked_list_corr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*ranked_list_corr_2.png": { + "type": "file", + "description": "Ranked Gene List Correlation Profile", + "pattern": "ranked_list_corr_2.png" + } + } + ] + }, + { + "butterfly_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*butterfly_plot.png": { + "type": "file", + "description": "Butterfly plot with gene rank plotted against score", + "pattern": "butterfly_plot.png" + } + } + ] + }, + { + "gene_set_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv": { + "type": "list", + "description": "Where -make_sets is not set to false, TSV files, one file for each gene set, with detail on enrichment for each gene", + "pattern": "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" + } + } + ] + }, + { + "gene_set_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html": { + "type": "list", + "description": "Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene", + "pattern": "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" + } + } + ] + }, + { + "gene_set_heatmap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png": { + "type": "list", + "description": "Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene", + "pattern": "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" + } + } + ] + }, + { + "snapshot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*_snapshot*.html": { + "type": "list", + "description": "HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot", + "pattern": "*_snapshot*.html" + } + } + ] + }, + { + "gene_set_enplot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*enplot*.png": { + "type": "list", + "description": "Where -make_sets is not set to false, PNG-format enrichment (barcode) plots, one file for each gene set, showing how genes contribute to enrichment.", + "pattern": "enplot*.png" + } + } + ] + }, + { + "gene_set_dist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*gset_rnd_es_dist*.png": { + "type": "list", + "description": "Where -make_sets is not set to false, PNG-format enrichment score distributions plots, one file for each gene set.", + "pattern": "gset_rnd_es_dist*.png" + } + } + ] + }, + { + "archive": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]\n" + } + }, + { + "*.zip": { + "type": "file", + "description": "Where -zip_report is set, a zip archive containing all outputs", + "pattern": "*.zip" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63206,108 +78797,201 @@ "doi": "10.1186/s12864-020-07123-7", "licence": [ "GNU GPL3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A sorted BAM or sam file of aligned reads", - "pattern": "*.{bam,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "A fasta file of the genome used for the mapping", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "a bed12 format file containing the final collapsed version of your transcriptome", - "pattern": "*.bed" - } - }, - { - "bed_trans_reads": { - "type": "file", - "description": "This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models.", - "pattern": "*_trans_read.bed" - } - }, - { - "local_density_error": { - "type": "file", - "description": "This file contains the log of filtering for local density error around the splice junctions (\"-lde\")", - "pattern": "*_local_density_error.txt" - } - }, - { - "polya": { - "type": "file", - "description": "This file contains the reads with potential poly A truncation.", - "pattern": "*_polya.txt" - } - }, - { - "read": { - "type": "file", - "description": "This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file", - "pattern": "*_read.txt" - } - }, - { - "strand_check": { - "type": "file", - "description": "This file shows instances where the sam flag strand information contrasted the GMAP strand information.", - "pattern": "*_strand_check.txt" - } - }, - { - "trans_report": { - "type": "file", - "description": "This file contains collapsing information for each transcript.", - "pattern": "*_trans_report.txt" - } - }, - { - "varcov": { - "type": "file", - "description": "This file contains the coverage information for each variant detected.", - "pattern": "*_varcov.txt" - } - }, - { - "variants": { - "type": "file", - "description": "This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo.", - "pattern": "*_variants.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A sorted BAM or sam file of aligned reads", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "A fasta file of the genome used for the mapping", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_collapsed.bed": { + "type": "file", + "description": "a bed12 format file containing the final collapsed version of your transcriptome", + "pattern": "*.bed" + } + } + ] + }, + { + "bed_trans_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_trans_read.bed": { + "type": "file", + "description": "This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models.", + "pattern": "*_trans_read.bed" + } + } + ] + }, + { + "local_density_error": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_local_density_error.txt": { + "type": "file", + "description": "This file contains the log of filtering for local density error around the splice junctions (\"-lde\")", + "pattern": "*_local_density_error.txt" + } + } + ] + }, + { + "polya": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_polya.txt": { + "type": "file", + "description": "This file contains the reads with potential poly A truncation.", + "pattern": "*_polya.txt" + } + } + ] + }, + { + "read": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_read.txt": { + "type": "file", + "description": "This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file", + "pattern": "*_read.txt" + } + } + ] + }, + { + "strand_check": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_strand_check.txt": { + "type": "file", + "description": "This file shows instances where the sam flag strand information contrasted the GMAP strand information.", + "pattern": "*_strand_check.txt" + } + } + ] + }, + { + "trans_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_trans_report.txt": { + "type": "file", + "description": "This file contains collapsing information for each transcript.", + "pattern": "*_trans_report.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "varcov": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_varcov.txt": { + "type": "file", + "description": "This file contains the coverage information for each variant detected.", + "pattern": "*_varcov.txt" + } + } + ] + }, + { + "variants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_variants.txt": { + "type": "file", + "description": "This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo.", + "pattern": "*_variants.txt" + } + } + ] } ], "authors": [ @@ -63351,66 +79035,115 @@ "doi": "10.1186/s12864-020-07123-7", "licence": [ "GPL v3 License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "bed12 file generated by TAMA collapse", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta.", - "pattern": "*.bed" - } - }, - { - "gene_report": { - "type": "file", - "description": "This contains a report of the genes from the merged file. \"num_clusters\" refers to the number of source transcripts that were used to make this gene model. \"num_final_trans\" refers to the number of transcripts in the final gene model.", - "pattern": "*_gene_report.txt" - } - }, - { - "merge": { - "type": "file", - "description": "This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the \"txt\" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix.", - "pattern": "*_merge.txt" - } - }, - { - "trans_report": { - "type": "file", - "description": "This contains the source information for each merged transcript.", - "pattern": "*_trans_report.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "bed12 file generated by TAMA collapse", + "pattern": "*.bed" + } + } + ], + [ + { + "filelist": { + "type": "file", + "description": "list of files" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta.", + "pattern": "*.bed" + } + } + ] + }, + { + "gene_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_gene_report.txt": { + "type": "file", + "description": "This contains a report of the genes from the merged file. \"num_clusters\" refers to the number of source transcripts that were used to make this gene model. \"num_final_trans\" refers to the number of transcripts in the final gene model.", + "pattern": "*_gene_report.txt" + } + } + ] + }, + { + "merge": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_merge.txt": { + "type": "file", + "description": "This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the \"txt\" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix.", + "pattern": "*_merge.txt" + } + } + ] + }, + { + "trans_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_trans_report.txt": { + "type": "file", + "description": "This contains the source information for each merged transcript.", + "pattern": "*_trans_report.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63453,59 +79186,90 @@ "doi": "10.1186/s12864-020-07123-7", "licence": [ "GPL v3 License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Full Length Non Chimeric reads in fasta format", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip.", - "pattern": "*_tama.fa.gz" - } - }, - { - "report": { - "type": "file", - "description": "A text file describing the number of polyA tails removed and their length. Compressed with gzip.", - "pattern": "*_tama_polya_flnc_report.txt.gz" - } - }, - { - "tails": { - "type": "file", - "description": "A gzip compressed FASTA file of trimmed polyA tails.", - "pattern": "*_tama_tails.fa.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Full Length Non Chimeric reads in fasta format", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tama.fa.gz": { + "type": "file", + "description": "The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip.", + "pattern": "*_tama.fa.gz" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tama_polya_flnc_report.txt.gz": { + "type": "file", + "description": "A text file describing the number of polyA tails removed and their length. Compressed with gzip.", + "pattern": "*_tama_polya_flnc_report.txt.gz" + } + } + ] + }, + { + "tails": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tama_tails.fa.gz": { + "type": "file", + "description": "A gzip compressed FASTA file of trimmed polyA tails.", + "pattern": "*_tama_tails.fa.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63544,52 +79308,73 @@ "doi": "10.1109/TCBB.2013.68", "licence": [ "ISC" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Input gff3 file", - "pattern": "*.{gff,gff3}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gt_gff3": { - "type": "file", - "description": "Parsed gff3 file produced only if there is no parsing error", - "pattern": "*.gt.gff3" - } - }, - { - "error_log": { - "type": "file", - "description": "Error log if gt-gff3 failed to parse the input gff3 file", - "pattern": "*.error.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "gff3": { + "type": "file", + "description": "Input gff3 file", + "pattern": "*.{gff,gff3}" + } + } + ] + ], + "output": [ + { + "gt_gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.gt.gff3": { + "type": "file", + "description": "Parsed gff3 file produced only if there is no parsing error", + "pattern": "*.gt.gff3" + } + } + ] + }, + { + "error_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.error.log": { + "type": "file", + "description": "Error log if gt-gff3 failed to parse the input gff3 file", + "pattern": "*.error.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63623,52 +79408,73 @@ "doi": "10.1109/TCBB.2013.68", "licence": [ "ISC" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Input gff3 file", - "pattern": "*.{gff,gff3}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "success_log": { - "type": "file", - "description": "Log file for successful validation", - "pattern": "*.success.log" - } - }, - { - "error_log": { - "type": "file", - "description": "Log file for failed validation", - "pattern": "*.error.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "gff3": { + "type": "file", + "description": "Input gff3 file", + "pattern": "*.{gff,gff3}" + } + } + ] + ], + "output": [ + { + "success_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.success.log": { + "type": "file", + "description": "Log file for successful validation", + "pattern": "*.success.log" + } + } + ] + }, + { + "error_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.error.log": { + "type": "file", + "description": "Log file for failed validation", + "pattern": "*.error.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63704,66 +79510,107 @@ "doi": "10.1109/TCBB.2013.68", "licence": [ "ISC" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the suffixerator index files", - "pattern": "suffixerator" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tabout": { - "type": "file", - "description": "Old tabular output by default or when `-tabout yes` argument is present", - "pattern": "*.tabout" - } - }, - { - "gff3": { - "type": "file", - "description": "GFF3 output when `-tabout no` argument is present", - "pattern": "*.gff3" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA output when `-out` argument is present", - "pattern": "*.{fa,fsa,fasta}" - } - }, - { - "inner_fasta": { - "type": "file", - "description": "FASTA output for inner regions when `-outinner` argument is present", - "pattern": "*.{fa,fsa,fasta}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "index": { + "type": "directory", + "description": "Folder containing the suffixerator index files", + "pattern": "suffixerator" + } + } + ] + ], + "output": [ + { + "tabout": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tabout": { + "type": "file", + "description": "Old tabular output by default or when `-tabout yes` argument is present", + "pattern": "*.tabout" + } + } + ] + }, + { + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "GFF3 output when `-tabout no` argument is present", + "pattern": "*.gff3" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "$out_name": { + "type": "file", + "description": "FASTA output when `-out` argument is present", + "pattern": "*.{fa,fsa,fasta}" + } + } + ] + }, + { + "inner_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "$outinner_name": { + "type": "file", + "description": "FASTA output for inner regions when `-outinner` argument is present", + "pattern": "*.{fa,fsa,fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63798,45 +79645,56 @@ "doi": "10.1109/TCBB.2013.68", "licence": [ "ISC" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Input gff3 file", - "pattern": "*.{gff,gff3}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "gff3": { + "type": "file", + "description": "Input gff3 file", + "pattern": "*.{gff,gff3}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "stats": { - "type": "file", - "description": "Stats file in yaml format", - "pattern": "*.yml" - } + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.yml": { + "type": "file", + "description": "Stats file in yaml format", + "pattern": "*.yml" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63870,51 +79728,64 @@ "doi": "10.1109/TCBB.2013.68", "licence": [ "ISC" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file to index", - "pattern": "*.{fsa,fa,fasta}" - } - }, - { - "mode": { - "type": "string", - "description": "Mode must be one of 'dna', or 'protein'" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the suffixerator index files", - "pattern": "suffixerator" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file to index", + "pattern": "*.{fsa,fa,fasta}" + } + } + ], + [ + { + "mode": { + "type": "string", + "description": "Mode must be one of 'dna', or 'protein'" + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "$prefix": { + "type": "directory", + "description": "Folder containing the suffixerator index files", + "pattern": "suffixerator" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -63951,121 +79822,222 @@ "doi": "10.1093/bioinformatics/btz848", "licence": [ "GNU General Public v3 (GPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n" - } - }, - { - "bins": { - "type": "file", - "description": "The binned fasta files from the assembler", - "pattern": "*.{fasta,fa}" - } - }, - { - "database": { - "type": "file", - "description": "The local copy of the taxonomic database used by GTDB-tk (unzipped copy)", - "pattern": "*" - } - }, - { - "use_pplacer_scratch_dir": { - "type": "boolean", - "description": "Set to true to reduce pplacer memory usage by writing to disk (slower)" - } - }, - { - "mash_db": { - "type": "file", - "description": "The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional)", - "pattern": "*.msh" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "summary": { - "type": "file", - "description": "A TSV summary file for the classification", - "pattern": "*.{summary.tsv}" - } - }, - { - "tree": { - "type": "file", - "description": "NJ or UPGMA tree in Newick format produced from a multiple sequence alignment", - "pattern": "*.{classify.tree.gz}" - } - }, - { - "markers": { - "type": "file", - "description": "A TSV summary file lineage markers used for the classification.", - "pattern": "*.{markers_summary.tsv}" - } - }, - { - "msa": { - "type": "file", - "description": "Multiple sequence alignments file.", - "pattern": "*.{msa.fasta.gz}" - } - }, - { - "user_msa": { - "type": "file", - "description": "Multiple sequence alignments file for the user-provided files.", - "pattern": "*.{user_msa.fasta.gz}" - } - }, - { - "filtered": { - "type": "file", - "description": "A list of genomes with an insufficient number of amino acids in MSA..", - "pattern": "*.{filtered.tsv}" - } - }, - { - "log": { - "type": "file", - "description": "GTDB-tk log file", - "pattern": "*.{log}" - } - }, - { - "warnings": { - "type": "file", - "description": "GTDB-tk warnings log file", - "pattern": "*.{warnings.log}" - } - }, - { - "failed": { - "type": "file", - "description": "A TSV summary of the genomes which GTDB-tk failed to classify.", - "pattern": "*.{failed_genomes.tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, assembler:'spades' ]\n" + } + }, + { + "\"bins/*\"": { + "type": "file", + "description": "bins" + } + } + ], + [ + { + "db_name": { + "type": "string", + "description": "The name of the GTDB database to use." + } + }, + { + "\"database/*\"": { + "type": "file", + "description": "GTDB database" + } + } + ], + [ + { + "use_pplacer_scratch_dir": { + "type": "boolean", + "description": "Set to true to reduce pplacer memory usage by writing to disk (slower)" + } + } + ], + [ + { + "mash_db": { + "type": "file", + "description": "The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional)", + "pattern": "*.msh" + } + } + ] + ], + "output": [ + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.*.summary.tsv": { + "type": "file", + "description": "A TSV summary file for the classification", + "pattern": "*.{summary.tsv}" + } + } + ] + }, + { + "tree": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.*.classify.tree.gz": { + "type": "file", + "description": "NJ or UPGMA tree in Newick format produced from a multiple sequence alignment", + "pattern": "*.{classify.tree.gz}" + } + } + ] + }, + { + "markers": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.*.markers_summary.tsv": { + "type": "file", + "description": "A TSV summary file lineage markers used for the classification.", + "pattern": "*.{markers_summary.tsv}" + } + } + ] + }, + { + "msa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.*.msa.fasta.gz": { + "type": "file", + "description": "Multiple sequence alignments file.", + "pattern": "*.{msa.fasta.gz}" + } + } + ] + }, + { + "user_msa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.*.user_msa.fasta.gz": { + "type": "file", + "description": "Multiple sequence alignments file for the user-provided files.", + "pattern": "*.{user_msa.fasta.gz}" + } + } + ] + }, + { + "filtered": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.*.filtered.tsv": { + "type": "file", + "description": "A list of genomes with an insufficient number of amino acids in MSA..", + "pattern": "*.{filtered.tsv}" + } + } + ] + }, + { + "failed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.failed_genomes.tsv": { + "type": "file", + "description": "A TSV summary of the genomes which GTDB-tk failed to classify.", + "pattern": "*.{failed_genomes.tsv}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.log": { + "type": "file", + "description": "GTDB-tk log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "warnings": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtdbtk.${prefix}.warnings.log": { + "type": "file", + "description": "GTDB-tk warnings log file", + "pattern": "*.{warnings.log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64109,33 +80081,44 @@ "tool_dev_url": "https://github.com/alejandrogzi/gtfsort", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "gtf": { - "type": "file", - "description": "Unsorted GTF/GFF file.", - "pattern": "*.gtf" + [ + { + "gtf": { + "type": "file", + "description": "Unsorted GTF/GFF file.", + "pattern": "*.gtf" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "gtf": [ + { + "*.sorted.gtf": { + "type": "file", + "description": "Sorted GTF file", + "pattern": "*.gtf" + } + } + ] }, { - "gtf": { - "type": "file", - "description": "Sorted GTF file", - "pattern": "*.gtf" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64166,89 +80149,132 @@ "gubbins": { "description": "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.", "homepage": "https://sanger-pathogens.github.io/gubbins/", - "documentation": "https://sanger-pathogens.github.io/gubbins/" - } - } - ], - "input": [ - { - "alignment": { - "type": "file", - "description": "fasta alignment file", - "pattern": "*.{fasta,fas,fa,aln}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Filtered variant alignment in fasta format", - "pattern": "*.{fasta}" - } - }, - { - "embl_predicted": { - "type": "file", - "description": "Recombination predictions in embl format", - "pattern": "*.{recombination_predictions.embl}" - } - }, - { - "gff": { - "type": "file", - "description": "Recombination predictions in gff format", - "pattern": "*.{gff}" - } - }, - { - "embl_branch": { - "type": "file", - "description": "Branch base reconstruction", - "pattern": "*.{branch_base_reconstruction.embl}" - } - }, - { - "vcf": { - "type": "file", - "description": "SNP distribution", - "pattern": "*.{vcf}" - } - }, - { - "stats": { - "type": "file", - "description": "Per branch statistics", - "pattern": "*.{csv}" - } - }, - { - "phylip": { - "type": "file", - "description": "Filtered variant alignment in phylip format", - "pattern": "*.{phylip}" - } - }, - { - "tree": { - "type": "file", - "description": "Recombination removed RAxML phylogenetic tree", - "pattern": "*.{final_tree.tre}" - } - }, - { - "tree_labelled": { - "type": "file", - "description": "Recombination removed RAxML phylogenetic tree (nodes labelled)", - "pattern": "*.{node_labelled.final_tree.tre}" - } + "documentation": "https://sanger-pathogens.github.io/gubbins/", + "identifier": "biotools:gubbins" + } + } + ], + "input": [ + [ + { + "alignment": { + "type": "file", + "description": "fasta alignment file", + "pattern": "*.{fasta,fas,fa,aln}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "*.fasta": { + "type": "file", + "description": "Filtered variant alignment in fasta format", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "gff": [ + { + "*.gff": { + "type": "file", + "description": "Recombination predictions in gff format", + "pattern": "*.{gff}" + } + } + ] + }, + { + "vcf": [ + { + "*.vcf": { + "type": "file", + "description": "SNP distribution", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "stats": [ + { + "*.csv": { + "type": "file", + "description": "Per branch statistics", + "pattern": "*.{csv}" + } + } + ] + }, + { + "phylip": [ + { + "*.phylip": { + "type": "file", + "description": "Filtered variant alignment in phylip format", + "pattern": "*.{phylip}" + } + } + ] + }, + { + "embl_predicted": [ + { + "*.recombination_predictions.embl": { + "type": "file", + "description": "Recombination predictions in embl format", + "pattern": "*.{recombination_predictions.embl}" + } + } + ] + }, + { + "embl_branch": [ + { + "*.branch_base_reconstruction.embl": { + "type": "file", + "description": "Branch base reconstruction", + "pattern": "*.{branch_base_reconstruction.embl}" + } + } + ] + }, + { + "tree": [ + { + "*.final_tree.tre": { + "type": "file", + "description": "Recombination removed RAxML phylogenetic tree", + "pattern": "*.{final_tree.tre}" + } + } + ] + }, + { + "tree_labelled": [ + { + "*.node_labelled.final_tree.tre": { + "type": "file", + "description": "Recombination removed RAxML phylogenetic tree (nodes labelled)", + "pattern": "*.{node_labelled.final_tree.tre}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64284,33 +80310,44 @@ "doi": "10.1186/s13059-021-02393-0", "licence": [ "GNU General Public v3 or later (GPL v3+)" - ] + ], + "identifier": "biotools:gunc" } } ], "input": [ - { - "db_name": { - "type": "string", - "description": "Which database to download. Options: progenomes or gtdb", - "pattern": "progenomes|gtdb" + [ + { + "db_name": { + "type": "string", + "description": "Which database to download. Options: progenomes or gtdb", + "pattern": "progenomes|gtdb" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "*.dmnd": { + "type": "file", + "description": "GUNC database file", + "pattern": "*.dmnd" + } + } + ] }, { - "db": { - "type": "file", - "description": "GUNC database file", - "pattern": "*.dmnd" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64354,52 +80391,63 @@ "doi": "10.1186/s13059-021-02393-0", "licence": [ "GNU General Public v3 or later (GPL v3+)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gunc_file": { - "type": "file", - "description": "Path of a gunc_scores.tsv file (mandatory)", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "checkm_file": { - "type": "file", - "description": "Output TSV from CheckM qa (ideally with -o 2 extended format) (mandatory)", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "Merged checkm/gunc results in TSV format", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:gunc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gunc_file": { + "type": "file", + "description": "Path of a gunc_scores.tsv file (mandatory)", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "checkm_file": { + "type": "file", + "description": "Output TSV from CheckM qa (ideally with -o 2 extended format) (mandatory)", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Merged checkm/gunc results in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64440,59 +80488,82 @@ "doi": "10.1186/s13059-021-02393-0", "licence": [ "GNU General Public v3 or later (GPL v3+)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing contig (bins)", - "pattern": "*.fa" - } - }, - { - "db": { - "type": "file", - "description": "GUNC database file", - "pattern": "*.dmnd" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "maxcss_levels_tsv": { - "type": "file", - "description": "Output file with scores for a taxonomic level with the highest CSS score", - "pattern": "*.tsv" - } - }, - { - "all_levels_tsv": { - "type": "file", - "description": "Optional output file with results for each taxonomic level", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:gunc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing contig (bins)", + "pattern": "*.fa" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "GUNC database file", + "pattern": "*.dmnd" + } + } + ] + ], + "output": [ + { + "maxcss_level_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*maxCSS_level.tsv": { + "type": "file", + "description": "Output file with results for the maximum CSS level", + "pattern": "*.tsv" + } + } + ] + }, + { + "all_levels_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*all_levels.tsv": { + "type": "file", + "description": "Optional output file with results for each taxonomic level", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64528,39 +80599,57 @@ "documentation": "https://www.gnu.org/software/gzip/manual/gzip.html", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Optional groovy Map containing meta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "archive": { - "type": "file", - "description": "File to be compressed/uncompressed", - "pattern": "*.*" + [ + { + "meta": { + "type": "map", + "description": "Optional groovy Map containing meta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "archive": { + "type": "file", + "description": "File to be compressed/uncompressed", + "pattern": "*.*" + } } - } + ] ], "output": [ { - "gunzip": { - "type": "file", - "description": "Compressed/uncompressed file", - "pattern": "*.*" - } + "gunzip": [ + { + "meta": { + "type": "file", + "description": "Compressed/uncompressed file", + "pattern": "*.*" + } + }, + { + "$gunzip": { + "type": "file", + "description": "Compressed/uncompressed file", + "pattern": "*.*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64721,45 +80810,56 @@ "tool_dev_url": "https://github.com/sequencing/gvcftools", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gvcf": { - "type": "file", - "description": "GVCF file", - "pattern": "*.{g.vcf,gvcf}.gz" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gvcf": { + "type": "file", + "description": "GVCF file", + "pattern": "*.{g.vcf,gvcf}.gz" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Converted variant-only VCF file", + "pattern": "*.vcf.gz" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "Converted variant-only VCF file", - "pattern": "*.vcf.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64792,73 +80892,100 @@ "tool_dev_url": "https://github.com/pha4ge/hAMRonization", "licence": [ "GNU Lesser General Public v3 (LGPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Output TSV or CSV file from ABRicate", - "pattern": "*.{csv,tsv}" - } - }, - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" - } - }, - { - "software_version": { - "type": "string", - "description": "Version of ABRicate used", - "pattern": "[0-9].[0-9].[0-9]" - } - }, - { - "reference_db_version": { - "type": "string", - "description": "Database version of ABRicate used", - "pattern": "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json" - } - }, - { - "tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.json" - } + ], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output TSV or CSV file from ABRicate", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + } + ], + [ + { + "software_version": { + "type": "string", + "description": "Version of ABRicate used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ], + [ + { + "reference_db_version": { + "type": "string", + "description": "Database version of ABRicate used", + "pattern": "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -64899,73 +81026,100 @@ "tool_dev_url": "https://github.com/pha4ge/hAMRonization", "licence": [ "GNU Lesser General Public v3 (LGPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Output .tsv file from AMRfinderPlus", - "pattern": "*.tsv" - } - }, - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" - } - }, - { - "software_version": { - "type": "string", - "description": "Version of AMRfinder used", - "pattern": "[0-9].[0-9].[0-9]" - } - }, - { - "reference_db_version": { - "type": "string", - "description": "Database version of ncbi_AMRfinder used", - "pattern": "[0-9]-[0-9]-[0-9].[0-9]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json" - } - }, - { - "tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .tsv file from AMRfinderPlus", + "pattern": "*.tsv" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + } + ], + [ + { + "software_version": { + "type": "string", + "description": "Version of AMRfinder used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ], + [ + { + "reference_db_version": { + "type": "string", + "description": "Database version of ncbi_AMRfinder used", + "pattern": "[0-9]-[0-9]-[0-9].[0-9]" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65004,73 +81158,100 @@ "tool_dev_url": "https://github.com/pha4ge/hAMRonization", "licence": [ "GNU Lesser General Public v3 (LGPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Output .mapping.ARG file from DeepARG", - "pattern": "*.mapping.ARG" - } - }, - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" - } - }, - { - "software_version": { - "type": "string", - "description": "Version of DeepARG used", - "pattern": "[0-9].[0-9].[0-9]" - } - }, - { - "reference_db_version": { - "type": "integer", - "description": "Database version of DeepARG used", - "pattern": "[0-9]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json" - } - }, - { - "tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.json" - } + ], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .mapping.ARG file from DeepARG", + "pattern": "*.mapping.ARG" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + } + ], + [ + { + "software_version": { + "type": "string", + "description": "Version of DeepARG used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ], + [ + { + "reference_db_version": { + "type": "integer", + "description": "Database version of DeepARG used", + "pattern": "[0-9]" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65111,73 +81292,100 @@ "tool_dev_url": "https://github.com/pha4ge/hAMRonization", "licence": [ "GNU Lesser General Public v3 (LGPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Output .txt file from fARGene", - "pattern": "*.txt" - } - }, - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" - } - }, - { - "software_version": { - "type": "string", - "description": "Version of fARGene used", - "pattern": "[0-9].[0-9].[0-9]" - } - }, - { - "reference_db_version": { - "type": "string", - "description": "Database version of fARGene used", - "pattern": "[0-9].[0-9].[0-9]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json" - } - }, - { - "tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.json" - } + ], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .txt file from fARGene", + "pattern": "*.txt" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + } + ], + [ + { + "software_version": { + "type": "string", + "description": "Version of fARGene used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ], + [ + { + "reference_db_version": { + "type": "string", + "description": "Database version of fARGene used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65218,73 +81426,100 @@ "tool_dev_url": "https://github.com/pha4ge/hAMRonization", "licence": [ "GNU Lesser General Public v3 (LGPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "Output .txt file from RGI", - "pattern": "*.txt" - } - }, - { - "format": { - "type": "string", - "description": "Type of report file to be produced", - "pattern": "tsv|json" - } - }, - { - "software_version": { - "type": "string", - "description": "Version of DeepARG used", - "pattern": "[0-9].[0-9].[0-9]" - } - }, - { - "reference_db_version": { - "type": "string", - "description": "Database version of DeepARG used", - "pattern": "[0-9].[0-9].[0-9]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "hAMRonised report in JSON format", - "pattern": "*.json" - } - }, - { - "tsv": { - "type": "file", - "description": "hAMRonised report in TSV format", - "pattern": "*.json" - } + ], + "identifier": "biotools:hamronization" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "report": { + "type": "file", + "description": "Output .txt file from RGI", + "pattern": "*.txt" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Type of report file to be produced", + "pattern": "tsv|json" + } + } + ], + [ + { + "software_version": { + "type": "string", + "description": "Version of DeepARG used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ], + [ + { + "reference_db_version": { + "type": "string", + "description": "Database version of DeepARG used", + "pattern": "[0-9].[0-9].[0-9]" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "hAMRonised report in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "hAMRonised report in TSV format", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65322,54 +81557,75 @@ "tool_dev_url": "https://github.com/pha4ge/hAMRonization", "licence": [ "GNU Lesser General Public v3 (LGPL v3)" - ] + ], + "identifier": "biotools:hamronization" } } ], "input": [ - { - "reports": { - "type": "file", - "description": "List of multiple hAMRonization reports in either JSON or TSV format", - "pattern": "*.{json,tsv}" + [ + { + "reports": { + "type": "file", + "description": "List of multiple hAMRonization reports in either JSON or TSV format", + "pattern": "*.{json,tsv}" + } } - }, - { - "format": { - "type": "string", - "description": "Type of final combined report file to be produced", - "pattern": "tsv|json|interactive" + ], + [ + { + "format": { + "type": "string", + "description": "Type of final combined report file to be produced", + "pattern": "tsv|json|interactive" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "json": [ + { + "hamronization_combined_report.json": { + "type": "file", + "description": "hAMRonised summary in JSON format", + "pattern": "*.json" + } + } + ] }, { - "json": { - "type": "file", - "description": "hAMRonised summary in JSON format", - "pattern": "*.json" - } + "tsv": [ + { + "hamronization_combined_report.tsv": { + "type": "file", + "description": "hAMRonised summary in TSV format", + "pattern": "*.json" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "hAMRonised summary in TSV format", - "pattern": "*.json" - } + "html": [ + { + "hamronization_combined_report.html": { + "type": "file", + "description": "hAMRonised summary in HTML format", + "pattern": "*.html" + } + } + ] }, { - "html": { - "type": "file", - "description": "hAMRonised summary in HTML format", - "pattern": "*.html" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65407,73 +81663,108 @@ "doi": "10.1016/j.ajhg.2020.02.010", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "phased VCF file with a GT FORMAT subfield with no missing alleles", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "map": { - "type": "file", - "description": "genetic map with cM units in PLINK format", - "pattern": "*.{map,map.gz,map.zip}" - } - }, - { - "exclude": { - "type": "file", - "description": "text file containing samples one sample per line to be excluded from the analysis", - "pattern": "*.*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hbd": { - "type": "file", - "description": "contains HBD segments within individuals", - "pattern": "*.hbd.gz" - } - }, - { - "ibd": { - "type": "file", - "description": "contains IBD segments shared between individuals", - "pattern": "*.ibd.gz" - } - }, - { - "log": { - "type": "file", - "description": "contains a summary of the analysis which includes the analysis parameters the number of markers the number of samples the number of output HBD and IBD segments and the mean number of HBD and IBD segments per sample", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "phased VCF file with a GT FORMAT subfield with no missing alleles", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "map": { + "type": "file", + "description": "genetic map with cM units in PLINK format", + "pattern": "*.{map,map.gz,map.zip}" + } + } + ], + [ + { + "exclude": { + "type": "file", + "description": "text file containing samples one sample per line to be excluded from the analysis", + "pattern": "*.*" + } + } + ] + ], + "output": [ + { + "hbd": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.hbd.gz": { + "type": "file", + "description": "contains HBD segments within individuals", + "pattern": "*.hbd.gz" + } + } + ] + }, + { + "ibd": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.ibd.gz": { + "type": "file", + "description": "contains IBD segments shared between individuals", + "pattern": "*.ibd.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing cohort information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "contains a summary of the analysis which includes the analysis parameters the number of markers the number of samples the number of output HBD and IBD segments and the mean number of HBD and IBD segments per sample", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65506,52 +81797,73 @@ "doi": "10.1101/gr.256545.119", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Raw report in txt format", - "pattern": "*.{txt}" - } - }, - { - "html": { - "type": "file", - "description": "Haplocheck HTML report", - "pattern": "*.{html}" - } + ], + "identifier": "biotools:haplocheck" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Raw report in txt format", + "pattern": "*.{txt}" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "Haplocheck HTML report", + "pattern": "*.{html}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65593,51 +81905,64 @@ "tool_dev_url": "https://github.com/seppinho/haplogrep-cmd", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "inputfile": { - "type": "file", - "description": "valid options are hsd, vcf, or fasta files", - "pattern": "*.{vcf,vcf.gz,fasta,hsd}" - } - }, - { - "format": { - "type": "string", - "description": "either \"vcf\", \"fasta\" or \"hsd\"" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "text file with classification information", - "pattern": "*.{txt}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputfile": { + "type": "file", + "description": "valid options are hsd, vcf, or fasta files", + "pattern": "*.{vcf,vcf.gz,fasta,hsd}" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "either \"vcf\", \"fasta\" or \"hsd\"" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "text file with classification information", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65676,92 +82001,107 @@ "tool_dev_url": "https://github.com/Illumina/hap.py", "licence": [ "BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to process", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "regions_bed": { - "type": "file", - "description": "BED file. Restrict analysis to given (sparse) regions.", - "pattern": "*.bed" - } - }, - { - "targets_bed": { - "type": "file", - "description": "Restrict analysis to given (dense) regions.", - "pattern": "*.bed" - } - }, - { - "bam": { - "type": "file", - "description": "Pass one or more BAM files for feature table extraction", - "pattern": "*.bam" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "features": { - "type": "file", - "description": "Fuature table", - "pattern": "*.csv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to process", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "regions_bed": { + "type": "file", + "description": "BED file. Restrict analysis to given (sparse) regions.", + "pattern": "*.bed" + } + }, + { + "targets_bed": { + "type": "file", + "description": "Restrict analysis to given (dense) regions.", + "pattern": "*.bed" + } + }, + { + "bam": { + "type": "file", + "description": "Pass one or more BAM files for feature table extraction", + "pattern": "*.bam" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "features": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Fuature table", + "pattern": "*.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -65794,230 +82134,351 @@ "tool_dev_url": "https://github.com/Illumina/hap.py", "licence": [ "BSD-2-clause" - ] - } + ], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "VCF/GVCF file to query", + "pattern": "*.{gvcf,vcf}.gz" + } + }, + { + "truth_vcf": { + "type": "file", + "description": "gold standard VCF file", + "pattern": "*.{gvcf,vcf}.gz" + } + }, + { + "regions_bed": { + "type": "file", + "description": "Sparse regions to restrict the analysis to", + "pattern": "*.bed" + } + }, + { + "targets_bed": { + "type": "file", + "description": "Dense regions to restrict the analysis to", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" + } + }, + { + "false_positives_bed": { + "type": "file", + "description": "False positive / confident call regions. Calls outside these regions will be labelled as UNK.", + "pattern": "*.{bed,bed.gz}" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing stratification_tsv file information\ne.g. [ id:'test5']\n" + } + }, + { + "stratification_tsv": { + "type": "file", + "description": "Stratification file list in TSV format", + "pattern": "*.tsv" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing stratification_beds file information\ne.g. [ id:'test6']\n" + } + }, + { + "stratification_beds": { + "type": "file", + "description": "One or more BED files used for stratification (these should be referenced in the stratification TSV)", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "summary_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary.csv": { + "type": "file", + "description": "A CSV file containing the summary of the benchmarking", + "pattern": "*.summary.csv" + } + } + ] + }, + { + "roc_all_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.all.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all variants", + "pattern": "*.roc.all.csv.gz" + } + } + ] + }, + { + "roc_indel_locations_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.INDEL.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all indels", + "pattern": "*.roc.Locations.INDEL.csv.gz" + } + } + ] + }, + { + "roc_indel_locations_pass_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.INDEL.PASS.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all indels that passed all filters", + "pattern": "*.roc.Locations.INDEL.PASS.csv.gz" + } + } + ] + }, + { + "roc_snp_locations_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.SNP.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all SNPs", + "pattern": "*.roc.Locations.SNP.csv.gz" + } + } + ] + }, + { + "roc_snp_locations_pass_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.roc.Locations.SNP.PASS.csv.gz": { + "type": "file", + "description": "A CSV file containing ROC values for all SNPs that passed all filters", + "pattern": "*.roc.Locations.SNP.PASS.csv.gz" + } + } + ] + }, + { + "extended_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.extended.csv": { + "type": "file", + "description": "A CSV file containing extended info of the benchmarking", + "pattern": "*.extended.csv" + } + } + ] + }, + { + "runinfo": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.runinfo.json": { + "type": "file", + "description": "A JSON file containing the benchmarking metrics", + "pattern": "*.metrics.json.gz" + } + } + ] + }, + { + "metrics_json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.json.gz": { + "type": "file", + "description": "A JSON file containing the run info", + "pattern": "*.runinfo.json" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "An annotated VCF", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "The index of the annotated VCF", + "pattern": "*.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing stratification_tsv file information\ne.g. [ id:'test5']\n" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing stratification_beds file information\ne.g. [ id:'test6']\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "VCF/GVCF file to query", - "pattern": "*.{gvcf,vcf}.gz" - } - }, - { - "truth_vcf": { - "type": "file", - "description": "gold standard VCF file", - "pattern": "*.{gvcf,vcf}.gz" - } - }, - { - "regions_bed": { - "type": "file", - "description": "Sparse regions to restrict the analysis to", - "pattern": "*.bed" - } - }, - { - "targets_bed": { - "type": "file", - "description": "Dense regions to restrict the analysis to", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai" - } - }, - { - "false_positives_bed": { - "type": "file", - "description": "False positive / confident call regions. Calls outside these regions will be labelled as UNK.", - "pattern": "*.{bed,bed.gz}" - } - }, - { - "stratification_tsv": { - "type": "file", - "description": "Stratification file list in TSV format", - "pattern": "*.tsv" - } - }, - { - "stratification_beds": { - "type": "file", - "description": "One or more BED files used for stratification (these should be referenced in the stratification TSV)", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "summary_csv": { - "type": "file", - "description": "A CSV file containing the summary of the benchmarking", - "pattern": "*.summary.csv" - } - }, - { - "roc_all_csv": { - "type": "file", - "description": "A CSV file containing ROC values for all variants", - "pattern": "*.roc.all.csv.gz" - } - }, - { - "roc_indel_locations_csv": { - "type": "file", - "description": "A CSV file containing ROC values for all indels", - "pattern": "*.roc.Locations.INDEL.csv.gz" - } - }, - { - "roc_indel_locations_pass_csv": { - "type": "file", - "description": "A CSV file containing ROC values for all indels that passed all filters", - "pattern": "*.roc.Locations.INDEL.PASS.csv.gz" - } - }, - { - "roc_snp_locations_csv": { - "type": "file", - "description": "A CSV file containing ROC values for all SNPs", - "pattern": "*.roc.Locations.SNP.csv.gz" - } - }, - { - "roc_snp_locations_pass_csv": { - "type": "file", - "description": "A CSV file containing ROC values for all SNPs that passed all filters", - "pattern": "*.roc.Locations.SNP.PASS.csv.gz" - } - }, - { - "extended_csv": { - "type": "file", - "description": "A CSV file containing extended info of the benchmarking", - "pattern": "*.extended.csv" - } - }, - { - "metrics_json": { - "type": "file", - "description": "A JSON file containing the run info", - "pattern": "*.runinfo.json" - } - }, - { - "runinfo": { - "type": "file", - "description": "A JSON file containing the benchmarking metrics", - "pattern": "*.metrics.json.gz" - } - }, - { - "vcf": { - "type": "file", - "description": "An annotated VCF", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "The index of the annotated VCF", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@nvnieuwk" - ], - "maintainers": [ - "@nvnieuwk" - ] - }, - "pipelines": [ - { - "name": "variantbenchmarking", - "version": "dev" - } - ] - }, - { - "name": "happy_prepy", - "path": "modules/nf-core/happy/prepy/meta.yml", - "type": "module", - "meta": { - "name": "happy_prepy", - "description": "Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py", - "keywords": [ - "happy", - "benchmark", - "haplotype" - ], - "tools": [ + "authors": [ + "@nvnieuwk" + ], + "maintainers": [ + "@nvnieuwk" + ] + }, + "pipelines": [ + { + "name": "variantbenchmarking", + "version": "dev" + } + ] + }, + { + "name": "happy_prepy", + "path": "modules/nf-core/happy/prepy/meta.yml", + "type": "module", + "meta": { + "name": "happy_prepy", + "description": "Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py", + "keywords": [ + "happy", + "benchmark", + "haplotype" + ], + "tools": [ { "happy": { "description": "Haplotype VCF comparison tools", @@ -66026,78 +82487,93 @@ "tool_dev_url": "https://github.com/Illumina/hap.py", "licence": [ "BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to preprocess", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "A preprocessed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to preprocess", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for reference fasta\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information for reference fai\ne.g. [ id:'test3' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "preprocessed_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Preprocessed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66138,145 +82614,186 @@ "tool_dev_url": "https://github.com/Illumina/hap.py", "licence": [ "BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing ambiguous_beds file information\ne.g. [ id:'test5']\n" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing bam file information\ne.g. [ id:'test6']\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "VCF/GVCF file to query", - "pattern": "*.{gvcf,vcf}.gz" - } - }, - { - "truth_vcf": { - "type": "file", - "description": "gold standard VCF file", - "pattern": "*.{gvcf,vcf}.gz" - } - }, - { - "regions_bed": { - "type": "file", - "description": "Sparse regions to restrict the analysis to", - "pattern": "*.bed" - } - }, - { - "targets_bed": { - "type": "file", - "description": "Dense regions to restrict the analysis to", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of the reference genome", - "pattern": "*.{fa,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA", - "pattern": "*.fai" - } - }, - { - "false_positives_bed": { - "type": "file", - "description": "False positive / confident call regions. Calls outside these regions will be labelled as UNK.", - "pattern": "*.{bed,bed.gz}" - } - }, - { - "stratification_tsv": { - "type": "file", - "description": "Ambiguous region bed file(s)", - "pattern": "*.bed" - } - }, - { - "bams": { - "type": "file", - "description": "one or more BAM files for feature table extraction", - "pattern": "*.bam" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "features": { - "type": "file", - "description": "One or more than one (if AF count is on ) CSV file containing feature information", - "pattern": "*.features.csv" - } - }, - { - "metrics": { - "type": "file", - "description": "One or more than one (if AF count is on ) JSON file with metrics", - "pattern": "*.metrics.json" - } - }, - { - "stats": { - "type": "file", - "description": "One or more than one (if AF count is on ) CSV file with benchmark stats", - "pattern": "*.stats.csv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:happy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "VCF/GVCF file to query", + "pattern": "*.{gvcf,vcf}.gz" + } + }, + { + "truth_vcf": { + "type": "file", + "description": "gold standard VCF file", + "pattern": "*.{gvcf,vcf}.gz" + } + }, + { + "regions_bed": { + "type": "file", + "description": "Sparse regions to restrict the analysis to", + "pattern": "*.bed" + } + }, + { + "targets_bed": { + "type": "file", + "description": "Dense regions to restrict the analysis to", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta file information\ne.g. [ id:'test2']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of the reference genome", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fai file information\ne.g. [ id:'test3']\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing false_positives_bed file information\ne.g. [ id:'test4']\n" + } + }, + { + "false_positives_bed": { + "type": "file", + "description": "False positive / confident call regions. Calls outside these regions will be labelled as UNK.", + "pattern": "*.{bed,bed.gz}" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing ambiguous_beds file information\ne.g. [ id:'test5']\n" + } + }, + { + "ambiguous_beds": { + "type": "file", + "description": "Ambiguous regions", + "pattern": "*.{bed,bed.gz}" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing bam file information\ne.g. [ id:'test6']\n" + } + }, + { + "bams": { + "type": "file", + "description": "one or more BAM files for feature table extraction", + "pattern": "*.bam" + } + } + ] + ], + "output": [ + { + "features": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.features.csv": { + "type": "file", + "description": "One or more than one (if AF count is on ) CSV file containing feature information", + "pattern": "*.features.csv" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.json": { + "type": "file", + "description": "One or more than one (if AF count is on ) JSON file with metrics", + "pattern": "*.metrics.json" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats.csv": { + "type": "file", + "description": "One or more than one (if AF count is on ) CSV file with benchmark stats", + "pattern": "*.stats.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66312,73 +82829,108 @@ "doi": "10.1128/JCM.00190-19", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA formatted assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - }, - { - "database_dir": { - "type": "directory", - "description": "Optional - Directory containing locus database", - "pattern": "*/*" - } - }, - { - "model_fp": { - "type": "file", - "description": "Optional - Prodigal model to use for gene prediction", - "pattern": "*.{bin}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gbk": { - "type": "file", - "description": "GenBank file and cap locus annotations", - "pattern": "*.gbk" - } - }, - { - "svg": { - "type": "file", - "description": "Visualization of annotated cap locus", - "pattern": "*.svg" - } - }, - { - "tsv": { - "type": "file", - "description": "Detailed summary of cap locus annotations", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA formatted assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + } + ], + [ + { + "database_dir": { + "type": "directory", + "description": "Optional - Directory containing locus database", + "pattern": "*/*" + } + } + ], + [ + { + "model_fp": { + "type": "file", + "description": "Optional - Prodigal model to use for gene prediction", + "pattern": "*.{bin}" + } + } + ] + ], + "output": [ + { + "gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gbk": { + "type": "file", + "description": "GenBank file and cap locus annotations", + "pattern": "*.gbk" + } + } + ] + }, + { + "svg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Visualization of annotated cap locus", + "pattern": "*.svg" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Detailed summary of cap locus annotations", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66411,55 +82963,86 @@ "doi": "10.1038/s41467-017-02525-w", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" - } - }, - { - "matrix": { - "type": "file", - "description": "HiCExplorer matrix in h5 format" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "file", - "description": "Outputs of hicPCA" - } - }, - { - "pca1": { - "type": "file", - "description": "PCA1 file" - } - }, - { - "pca2": { - "type": "file", - "description": "PCA2 file" - } + ], + "identifier": "biotools:hicexplorer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" + } + }, + { + "matrix": { + "type": "file", + "description": "HiCExplorer matrix in h5 format" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" + } + }, + { + "${prefix}_*": { + "type": "file", + "description": "Outputs of hicPCA" + } + } + ] + }, + { + "pca1": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" + } + }, + { + "${prefix}_pca1.$format": { + "type": "file", + "description": "PCA1 file" + } + } + ] + }, + { + "pca2": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', bin:50000 ]\n" + } + }, + { + "${prefix}_pca2.$format": { + "type": "file", + "description": "PCA2 file" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66495,138 +83078,258 @@ "doi": "10.1038/s41592-020-01056-5", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ file with PacBio HiFi reads", - "pattern": "*.{fastq}" - } - }, - { - "paternal_kmer_dump": { - "type": "file", - "description": "Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension." - } - }, - { - "maternal_kmer_dump": { - "type": "file", - "description": "Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension." - } - }, - { - "use_parental_kmers": { - "type": "boolean", - "description": "A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps." - } - }, - { - "hic_read1": { - "type": "file", - "description": "Hi-C data Forward reads." - } - }, - { - "hic_read2": { - "type": "file", - "description": "Hi-C data Reverse reads." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "raw_unitigs": { - "type": "file", - "description": "Raw unitigs", - "pattern": "*.r_utg.gfa" - } - }, - { - "processed_unitigs": { - "type": "file", - "description": "Processed unitigs", - "pattern": "*.p_utg.gfa" - } - }, - { - "primary_contigs": { - "type": "file", - "description": "Primary contigs", - "pattern": "*.asm.p_ctg.gfa" - } - }, - { - "alternate_contigs": { - "type": "file", - "description": "Alternative contigs", - "pattern": "*.asm.a_ctg.gfa" - } - }, - { - "paternal_contigs": { - "type": "file", - "description": "Paternal contigs", - "pattern": "*.hap1.p_ctg.gfa" - } - }, - { - "maternal_contigs": { - "type": "file", - "description": "Maternal contigs", - "pattern": "*.hap2.p_ctg.gfa" - } - }, - { - "corrected_reads": { - "type": "file", - "description": "Corrected reads", - "pattern": "*.ec.bin" - } - }, - { - "source_overlaps": { - "type": "file", - "description": "Source overlaps", - "pattern": "*.ovlp.source.bin" - } - }, - { - "reverse_overlaps": { - "type": "file", - "description": "Reverse overlaps", - "pattern": "*.ovlp.reverse.bin" - } - }, - { - "log": { - "type": "file", - "description": "Stderr log", - "pattern": "*.log" - } + ], + "identifier": "biotools:hifiasm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ file with PacBio HiFi reads", + "pattern": "*.{fastq}" + } + } + ], + [ + { + "paternal_kmer_dump": { + "type": "file", + "description": "Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension." + } + } + ], + [ + { + "maternal_kmer_dump": { + "type": "file", + "description": "Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension." + } + } + ], + [ + { + "hic_read1": { + "type": "file", + "description": "Hi-C data Forward reads." + } + } + ], + [ + { + "hic_read2": { + "type": "file", + "description": "Hi-C data Reverse reads." + } + } + ] + ], + "output": [ + { + "raw_unitigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.r_utg.gfa": { + "type": "file", + "description": "Raw unitigs", + "pattern": "*.r_utg.gfa" + } + } + ] + }, + { + "corrected_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ec.bin": { + "type": "file", + "description": "Corrected reads", + "pattern": "*.ec.bin" + } + } + ] + }, + { + "source_overlaps": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ovlp.source.bin": { + "type": "file", + "description": "Source overlaps", + "pattern": "*.ovlp.source.bin" + } + } + ] + }, + { + "reverse_overlaps": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ovlp.reverse.bin": { + "type": "file", + "description": "Reverse overlaps", + "pattern": "*.ovlp.reverse.bin" + } + } + ] + }, + { + "processed_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bp.p_ctg.gfa": { + "type": "file", + "description": "Processed contigs", + "pattern": "*.bp.p_ctg.gfa" + } + } + ] + }, + { + "processed_unitigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.p_utg.gfa": { + "type": "file", + "description": "Processed unitigs", + "pattern": "*.p_utg.gfa" + } + } + ] + }, + { + "primary_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.asm.p_ctg.gfa": { + "type": "file", + "description": "Primary contigs", + "pattern": "*.asm.p_ctg.gfa" + } + } + ] + }, + { + "alternate_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.asm.a_ctg.gfa": { + "type": "file", + "description": "Alternative contigs", + "pattern": "*.asm.a_ctg.gfa" + } + } + ] + }, + { + "paternal_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap1.p_ctg.gfa": { + "type": "file", + "description": "Paternal contigs", + "pattern": "*.hap1.p_ctg.gfa" + } + } + ] + }, + { + "maternal_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap2.p_ctg.gfa": { + "type": "file", + "description": "Maternal contigs", + "pattern": "*.hap2.p_ctg.gfa" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Stderr log", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66662,77 +83365,119 @@ "doi": "10.1038/s41587-019-0201-4", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "HISAT2 genome index file", - "pattern": "*.ht2" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "splicesites": { - "type": "file", - "description": "Splices sites in gtf file", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "summary": { - "type": "file", - "description": "Aligment log", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:hisat2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "HISAT2 genome index file", + "pattern": "*.ht2" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "splicesites": { + "type": "file", + "description": "Splices sites in gtf file", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Aligment log", + "pattern": "*.log" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Output FastQ file", + "pattern": "*fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66782,71 +83527,86 @@ "doi": "10.1038/s41587-019-0201-4", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Reference gtf annotation file", - "pattern": "*.{gtf}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "splicesites": { - "type": "file", - "description": "Splices sites in gtf file", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "HISAT2 genome index file", - "pattern": "*.ht2" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:hisat2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Reference gtf annotation file", + "pattern": "*.{gtf}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "splicesites": { + "type": "file", + "description": "Splices sites in gtf file", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "hisat2": { + "type": "file", + "description": "HISAT2 genome index file", + "pattern": "*.ht2" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66893,45 +83653,56 @@ "doi": "10.1038/s41587-019-0201-4", "licence": [ "MIT" - ] + ], + "identifier": "biotools:hisat2" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Reference gtf annotation file", - "pattern": "*.{gtf}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Reference gtf annotation file", + "pattern": "*.{gtf}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "*.splice_sites.txt": { + "type": "file", + "description": "Splice sites in txt file", + "pattern": "*.txt" + } + } + ] }, { - "splicesites": { - "type": "file", - "description": "Splices sites in gtf file", - "pattern": "*.{splice_sites.txt}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -66981,31 +83752,54 @@ "doi": "10.1093/bioinformatics/btz235", "licence": [ "GPL" - ] + ], + "identifier": "" } } ], "input": [ - { - "graph": { - "type": "directory", - "description": "PRG graph directory" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "directory", + "description": "PRG graph directory" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "graph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${graph}": { + "type": "directory", + "description": "PRG graph directory" + } + } + ] }, { - "folder": { - "type": "directory", - "description": "Directory containing indexed graph" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67039,50 +83833,186 @@ "doi": "10.1093/bioinformatics/btz235", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "graph": { - "type": "directory", - "description": "Path to prepared graph with hla-la --acton prepareGraph" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "folder": { - "type": "directory", - "description": "Folder containing the HLA typing output" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}" + } + }, + { + "graph": { + "type": "directory", + "description": "Path to prepared graph with hla-la --acton prepareGraph" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}": { + "type": "file", + "description": "results file" + } + } + ] + }, + { + "extraction": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/extraction.bam*": { + "type": "file", + "description": "Extraction BAM file", + "pattern": "*.bam*" + } + } + ] + }, + { + "extraction_mapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/extraction_mapped.bam": { + "type": "file", + "description": "Extraction mapped BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "extraction_unmpapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/extraction_unmapped.bam": { + "type": "file", + "description": "Extraction unmapped BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "hla": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/hla/*": { + "type": "file", + "description": "HLA results" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/*.fastq": { + "type": "file", + "description": "Fastq file", + "pattern": "*.fastq" + } + } + ] + }, + { + "reads_per_level": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/reads_per_level.txt": { + "type": "file", + "description": "Reads per level", + "pattern": "*.txt" + } + } + ] + }, + { + "remapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}/remapped_with_a.bam*": { + "type": "file", + "description": "Remapped BAM file", + "pattern": "*.bam*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67114,44 +84044,55 @@ "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:hmmcopy" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "wig file containing gc content of each window of the genome", + "pattern": "*.wig" + } + } + ] }, { - "wig": { - "type": "file", - "description": "wig file containing gc content of each window of the genome", - "pattern": "*.wig" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67185,44 +84126,55 @@ "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:hmmcopy" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bigwig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bw": { + "type": "file", + "description": "bigwig file containing the mappability of the genome", + "pattern": "*.bw" + } + } + ] }, { - "bigwig": { - "type": "file", - "description": "bigwig file containing the mappability of the genome", - "pattern": "*.bw" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67256,45 +84208,56 @@ "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:hmmcopy" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bigwig": { - "type": "file", - "description": "BigWig file with the mappability score of the genome, for instance made with generateMap function.", - "pattern": "*.wig" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bigwig": { + "type": "file", + "description": "BigWig file with the mappability score of the genome, for instance made with generateMap function.", + "pattern": "*.wig" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "wig file containing mappability of each window of the genome", + "pattern": "*.wig" + } + } + ] }, { - "wig": { - "type": "file", - "description": "wig file containing mappability of each window of the genome", - "pattern": "*.wig" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67326,45 +84289,63 @@ "tool_dev_url": "https://github.com/shahcompbio/hmmcopy_utils", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "wig": { - "type": "file", - "description": "A wig file with the number of reads lying within each window in each chromosome", - "pattern": "*.wig" - } + ], + "identifier": "biotools:hmmcopy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}" + } + } + ] + ], + "output": [ + { + "wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "A wig file with the number of reads lying within each window in each chromosome", + "pattern": "*.wig" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67396,130 +84377,167 @@ "doi": "10.1371/journal.pcbi.1002195", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "unmaskedaln": { - "type": "file", - "description": "multiple sequence alignment, Stockholm or other formats", - "pattern": "*" - } - }, - { - "fmask_rf": { - "type": "boolean", - "description": "Flag to output optional file with final mask of non-gap RF len" - } - }, - { - "fmask_all": { - "type": "boolean", - "description": "Flag to output optional file with final mask of full aln len" - } - }, - { - "gmask_rf": { - "type": "boolean", - "description": "Flag to output optional file gap-based 0/1 mask of non-gap RF len" - } - }, - { - "gmask_all": { - "type": "boolean", - "description": "Flag to output optional file gap-based 0/1 mask of full aln len" - } - }, - { - "pmask_rf": { - "type": "boolean", - "description": "Flag to output optional file with PP-based 0/1 mask of non-gap RF len" - } - }, - { - "pmask_all": { - "type": "boolean", - "description": "Flag to output optional file with PP-based 0/1 mask of full aln len" - } - }, - { - "maskfile": { - "type": "file", - "description": "mask file, see program documentation", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "maskedaln": { - "type": "file", - "description": "Masked alignment in gzipped Stockholm format", - "pattern": "*.sthlm.gz" - } - }, - { - "fmask_rf": { - "type": "file", - "description": "File with final mask of non-gap RF len", - "pattern": "*.fmask-rf.gz" - } - }, - { - "fmask_all": { - "type": "file", - "description": "File with final mask of full aln len", - "pattern": "*.fmask-all.gz" - } - }, - { - "gmask_rf": { - "type": "file", - "description": "File with gap-based 0/1 mask of non-gap RF len", - "pattern": "*.gmask-rf.gz" - } - }, - { - "gmask_all": { - "type": "file", - "description": "File with gap-based 0/1 mask of full aln len", - "pattern": "*.gmask-all.gz" - } - }, - { - "pmask_rf": { - "type": "file", - "description": "File with PP-based 0/1 mask of non-gap RF len", - "pattern": "*.pmask-rf.gz" - } - }, - { - "pmask_all": { - "type": "file", - "description": "File with PP-based 0/1 mask of full aln len", - "pattern": "*.pmask-all.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "unmaskedaln": { + "type": "file", + "description": "multiple sequence alignment, Stockholm or other formats", + "pattern": "*" + } + }, + { + "fmask_rf": { + "type": "boolean", + "description": "Flag to output optional file with final mask of non-gap RF len" + } + }, + { + "fmask_all": { + "type": "boolean", + "description": "Flag to output optional file with final mask of full aln len" + } + }, + { + "gmask_rf": { + "type": "boolean", + "description": "Flag to output optional file gap-based 0/1 mask of non-gap RF len" + } + }, + { + "gmask_all": { + "type": "boolean", + "description": "Flag to output optional file gap-based 0/1 mask of full aln len" + } + }, + { + "pmask_rf": { + "type": "boolean", + "description": "Flag to output optional file with PP-based 0/1 mask of non-gap RF len" + } + }, + { + "pmask_all": { + "type": "boolean", + "description": "Flag to output optional file with PP-based 0/1 mask of full aln len" + } + } + ], + [ + { + "maskfile": { + "type": "file", + "description": "mask file, see program documentation", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "maskedaln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.masked.sthlm.gz": { + "type": "file", + "description": "Masked alignment in gzipped Stockholm format", + "pattern": "*.sthlm.gz" + } + } + ] + }, + { + "fmask_rf": [ + { + "*.fmask-rf.gz": { + "type": "file", + "description": "File with final mask of non-gap RF len", + "pattern": "*.fmask-rf.gz" + } + } + ] + }, + { + "fmask_all": [ + { + "*.fmask-all.gz": { + "type": "file", + "description": "File with final mask of full aln len", + "pattern": "*.fmask-all.gz" + } + } + ] + }, + { + "gmask_rf": [ + { + "*.gmask-rf.gz": { + "type": "file", + "description": "File with gap-based 0/1 mask of non-gap RF len", + "pattern": "*.gmask-rf.gz" + } + } + ] + }, + { + "gmask_all": [ + { + "*.gmask-all.gz": { + "type": "file", + "description": "File with gap-based 0/1 mask of full aln len", + "pattern": "*.gmask-all.gz" + } + } + ] + }, + { + "pmask_rf": [ + { + "*.pmask-rf.gz": { + "type": "file", + "description": "File with PP-based 0/1 mask of non-gap RF len", + "pattern": "*.pmask-rf.gz" + } + } + ] + }, + { + "pmask_all": [ + { + "*.pmask-all.gz": { + "type": "file", + "description": "File with PP-based 0/1 mask of full aln len", + "pattern": "*.pmask-all.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67561,45 +84579,56 @@ "doi": "10.1371/journal.pcbi.1002195", "licence": [ "BSD-3-Clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "seqfile": { + "type": "file", + "description": "Sequences, aligned or not, in any supported format", + "pattern": "*" + } } - }, - { - "seqfile": { - "type": "file", - "description": "Sequences, aligned or not, in any supported format", - "pattern": "*" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "seqreformated": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.*.gz": { + "type": "file", + "description": "Reformated sequence file", + "pattern": "*.*.gz" + } + } + ] }, { - "seqreformated": { - "type": "file", - "description": "Reformated sequence file", - "pattern": "*.*.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67643,52 +84672,65 @@ "doi": "10.1371/journal.pcbi.1002195", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Amino acid or nucleotide gzipped compressed fasta file", - "pattern": "*.{fna.gz,faa.gz,fasta.gz,fa.gz}" - } - }, - { - "hmm": { - "type": "file", - "description": "A gzipped HMM file", - "pattern": "*.hmm.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sthlm": { - "type": "file", - "description": "Multiple alignment in gzipped Stockholm format", - "pattern": "*.sthlm.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Amino acid or nucleotide gzipped compressed fasta file", + "pattern": "*.{fna.gz,faa.gz,fasta.gz,fa.gz}" + } + } + ], + [ + { + "hmm": { + "type": "file", + "description": "A gzipped HMM file", + "pattern": "*.hmm.gz" + } + } + ] + ], + "output": [ + { + "sthlm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sthlm.gz": { + "type": "file", + "description": "Multiple alignment in gzipped Stockholm format", + "pattern": "*.sthlm.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67735,46 +84777,76 @@ "doi": "10.1371/journal.pcbi.1002195", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "multiple sequence alignment in fasta, clustal, stockholm or phylip format", - "pattern": "*" - } - }, - { - "mxfile": { - "type": "file", - "description": "read substitution score matrix, for use when building profiles from single sequences (--singlemx option)", - "pattern": "*" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hmm": { - "type": "file", - "description": "Gzipped HMM file", - "pattern": "*.{hmm.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "multiple sequence alignment in fasta, clustal, stockholm or phylip format", + "pattern": "*" + } + } + ], + [ + { + "mxfile": { + "type": "file", + "description": "read substitution score matrix, for use when building profiles from single sequences (--singlemx option)", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "hmm": [ + { + "meta": { + "type": "file", + "description": "Gzipped HMM file", + "pattern": "*.{hmm.gz}" + } + }, + { + "*.hmm.gz": { + "type": "file", + "description": "Gzipped HMM file", + "pattern": "*.{hmm.gz}" + } + } + ] + }, + { + "hmmbuildout": [ + { + "*.hmmbuild.txt": { + "type": "file", + "description": "HMM build output" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -67818,69 +84890,102 @@ "doi": "10.1371/journal.pcbi.1002195", "licence": [ "BSD" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hmm": { + "type": "file", + "description": "HMM file with multiple HMM models", + "pattern": "*.hmm" + } + } + ], + [ + { + "key": { + "type": "string", + "description": "Name of HMM to extract. Specify either this or keyfile. If none is specified, an index will be built." + } + } + ], + [ + { + "keyfile": { + "type": "file", + "description": "File containing list of HMM models to extract. Specify either this or key. If none is specified, an index will be built.", + "pattern": "*.txt" + } + } + ], + [ + { + "index": { + "type": "file", + "description": "Index file from another run." + } + } + ] + ], + "output": [ + { + "hmm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hmm": { + "type": "file", + "description": "File with one or more HMM models", + "pattern": "selection.hmm" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ssi": { + "type": "file", + "description": "Index for HMM database. Created if neither key nor keyfile is specified.", + "pattern": "*.ssi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hmm": { - "type": "file", - "description": "HMM file with multiple HMM models", - "pattern": "*.hmm" - } - }, - { - "key": { - "type": "string", - "description": "Name of HMM to extract. Specify either this or keyfile. If none is specified, an index will be built." - } - }, - { - "keyfile": { - "type": "file", - "description": "File containing list of HMM models to extract. Specify either this or key. If none is specified, an index will be built.", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hmm": { - "type": "file", - "description": "File with one or more HMM models", - "pattern": "selection.hmm" - } - }, - { - "index": { - "type": "file", - "description": "Index for HMM database. Created if neither key nor keyfile is specified.", - "pattern": "*.ssi" - } - } - ], - "authors": [ - "@erikrikarddaniel" + "authors": [ + "@erikrikarddaniel" ], "maintainers": [ "@erikrikarddaniel" @@ -67909,7 +85014,8 @@ "doi": "10.1371/journal.pcbi.1002195", "licence": [ "BSD" - ] + ], + "identifier": "" } }, { @@ -67919,7 +85025,8 @@ "documentation": "https://www.r-project.org/", "licence": [ "GPL v2" - ] + ], + "identifier": "" } }, { @@ -67931,45 +85038,56 @@ "doi": "10.21105/joss.01686", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tblouts": { - "type": "file", - "description": "table outputs from hmmsearch", - "pattern": "*.tsv.gz" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tblouts": { + "type": "file", + "description": "table outputs from hmmsearch", + "pattern": "*.tsv.gz" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "hmmrank": { - "type": "file", - "description": "TSV file with ranked hmmer results", - "pattern": "*.hmmrank.tsv.gz" - } + "hmmrank": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.hmmrank.tsv.gz": { + "type": "file", + "description": "TSV file with ranked hmmer results", + "pattern": "*.hmmrank.tsv.gz" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68003,91 +85121,132 @@ "doi": "10.1371/journal.pcbi.1002195", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hmmfile": { - "type": "file", - "description": "One or more HMM profiles created with hmmbuild", - "pattern": "*.{hmm,hmm.gz}" - } - }, - { - "seqdb": { - "type": "file", - "description": "Database of sequences in FASTA format", - "pattern": "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}" - } - }, - { - "write_align": { - "type": "boolean", - "description": "Flag to save optional alignment output. Specify with 'true' to save." - } - }, - { - "write_target": { - "type": "boolean", - "description": "Flag to save optional per target summary. Specify with 'true' to save." - } - }, - { - "write_domain": { - "type": "boolean", - "description": "Flag to save optional per domain summary. Specify with 'true' to save." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "Human readable output summarizing hmmsearch results", - "pattern": "*.{txt.gz}" - } - }, - { - "alignments": { - "type": "file", - "description": "Optional multiple sequence alignment (MSA) in Stockholm format", - "pattern": "*.{sto.gz}" - } - }, - { - "target_summary": { - "type": "file", - "description": "Optional tabular (space-delimited) summary of per-target output", - "pattern": "*.{tbl.gz}" - } - }, - { - "domain_summary": { - "type": "file", - "description": "Optional tabular (space-delimited) summary of per-domain output", - "pattern": "*.{domtbl.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hmmfile": { + "type": "file", + "description": "One or more HMM profiles created with hmmbuild", + "pattern": "*.{hmm,hmm.gz}" + } + }, + { + "seqdb": { + "type": "file", + "description": "Database of sequences in FASTA format", + "pattern": "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}" + } + }, + { + "write_align": { + "type": "boolean", + "description": "Flag to save optional alignment output. Specify with 'true' to save." + } + }, + { + "write_target": { + "type": "boolean", + "description": "Flag to save optional per target summary. Specify with 'true' to save." + } + }, + { + "write_domain": { + "type": "boolean", + "description": "Flag to save optional per domain summary. Specify with 'true' to save." + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Human readable output summarizing hmmsearch results", + "pattern": "*.{txt.gz}" + } + } + ] + }, + { + "alignments": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sto.gz": { + "type": "file", + "description": "Optional multiple sequence alignment (MSA) in Stockholm format", + "pattern": "*.{sto.gz}" + } + } + ] + }, + { + "target_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbl.gz": { + "type": "file", + "description": "Optional tabular (space-delimited) summary of per-target output", + "pattern": "*.{tbl.gz}" + } + } + ] + }, + { + "domain_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.domtbl.gz": { + "type": "file", + "description": "Optional tabular (space-delimited) summary of per-domain output", + "pattern": "*.{domtbl.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68129,45 +85288,56 @@ "doi": "10.1101/600619", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.vcf" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.vcf" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "*_annotated.vcf": { + "type": "file", + "description": "annotated vcf", + "pattern": "*_annotated.vcf" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "annotated vcf", - "pattern": "*_annotated.vcf" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68204,66 +85374,90 @@ "doi": "10.1016/j.molcel.2010.05.004.", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "peaks": { - "type": "file", - "description": "The peak files in bed format", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of reference genome", - "pattern": "*.fasta" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file of reference genome", - "pattern": "*.gtf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "annotated_peaks": { - "type": "file", - "description": "The annotated peaks", - "pattern": "*annotatePeaks.txt" - } - }, - { - "annotation_stats": { - "type": "file", - "description": "the annStats file output from -annStats parameter", - "pattern": "*annStats.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:homer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "peak": { + "type": "file", + "description": "Peak file to annotate" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "GTF file of reference genome", + "pattern": "*.gtf" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*annotatePeaks.txt": { + "type": "file", + "description": "Annotated peaks in txt file", + "pattern": "*annotatePeaks.txt" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*annStats.txt": { + "type": "file", + "description": "Annotation statistics in txt file", + "pattern": "*annStats.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68308,45 +85502,56 @@ "doi": "10.1016/j.molcel.2010.05.004.", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:homer" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tagDir": { - "type": "directory", - "description": "The 'Tag Directory'", - "pattern": "tagDir" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tagDir": { + "type": "directory", + "description": "The 'Tag Directory'", + "pattern": "tagDir" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "peaks": { - "type": "file", - "description": "The found peaks", - "pattern": "*.peaks.txt" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.peaks.txt": { + "type": "file", + "description": "Peaks in txt file", + "pattern": "*.peaks.txt" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68384,7 +85589,8 @@ "doi": "10.1016/j.molcel.2010.05.004.", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:homer" } }, { @@ -68395,7 +85601,8 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] + ], + "identifier": "biotools:homer" } }, { @@ -68407,7 +85614,8 @@ "doi": "10.18129/B9.bioc.DESeq2", "licence": [ "LGPL-3.0-or-later" - ] + ], + "identifier": "biotools:homer" } }, { @@ -68419,59 +85627,82 @@ "doi": "10.18129/B9.bioc.edgeR", "licence": [ "GPL >=2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/BED/SAM file", - "pattern": "*.{bam,bed,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of reference genome", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tagdir": { - "type": "directory", - "description": "The \"Tag Directory\"", - "pattern": "*_tagdir" - } - }, - { - "taginfo": { - "type": "directory", - "description": "The tagInfo.txt included to ensure there's proper output", - "pattern": "*_tagdir/tagInfo.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:homer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/BED/SAM file", + "pattern": "*.{bam,bed,sam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "tagdir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tagdir": { + "type": "directory", + "description": "The \"Tag Directory\"", + "pattern": "*_tagdir" + } + } + ] + }, + { + "taginfo": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_tagdir/tagInfo.txt": { + "type": "directory", + "description": "The tagInfo.txt included to ensure there's proper output", + "pattern": "*_tagdir/tagInfo.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68508,45 +85739,56 @@ "doi": "10.1016/j.molcel.2010.05.004.", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:homer" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tagDir": { - "type": "directory", - "description": "The 'Tag Directory'", - "pattern": "tagDir" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tagDir": { + "type": "directory", + "description": "The 'Tag Directory'", + "pattern": "tagDir" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedGraph": { - "type": "file", - "description": "The UCSC bed graph", - "pattern": "*.bedGraph.gz" - } + "bedGraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedGraph.gz": { + "type": "file", + "description": "The UCSC bed graph", + "pattern": "*.bedGraph.gz" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68585,45 +85827,55 @@ "doi": "10.1016/j.molcel.2010.05.004.", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:homer" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tagDir": { - "type": "directory", - "description": "The 'Tag Directory'", - "pattern": "tagDir" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "peaks": { + "type": "file", + "description": "Peak file to convert to BED format" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68661,45 +85913,56 @@ "tool_dev_url": "https://github.com/jimmyliu1326/HpsuisSero", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembly in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited serotype prediction", + "pattern": "*.{tsv}" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited serotype prediction", - "pattern": "*.{tsv}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68732,58 +85995,78 @@ "doi": "10.1093/bioinformatics/btu638", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": ".gtf file information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "index": { - "type": "file", - "description": "Contains indexed bam file", - "pattern": "*.bai" - } - }, - { - "gtf": { - "type": "file", - "description": "Contains the features in the GTF format", - "pattern": "*.gtf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "txt": { - "type": "file", - "description": "File containing feature counts output", - "pattern": ".txt" - } + ], + "identifier": "biotools:htseq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "index": { + "type": "file", + "description": "Contains indexed bam file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": ".gtf file information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Contains the features in the GTF format", + "pattern": "*.gtf" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing feature counts output", + "pattern": ".txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68815,72 +86098,85 @@ "tool_dev_url": "https://github.com/brentp/hts-nim-tools", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The query VCF file", - "pattern": "*.{vcf,vcf.gz,bcf}" - } - }, - { - "tbi": { - "type": "file", - "description": "The index of the query VCF file", - "pattern": "*.{tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing background VCF information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "background_vcf": { - "type": "file", - "description": "The background VCF file", - "pattern": "*.{vcf,vcf.gz,bcf}" - } - }, - { - "background_tbi": { - "type": "file", - "description": "The index of the background VCF file", - "pattern": "*.{tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "A tab-delimited file comparing the variant count of each region in the query VCF and background VCF", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The query VCF file", + "pattern": "*.{vcf,vcf.gz,bcf}" + } + }, + { + "tbi": { + "type": "file", + "description": "The index of the query VCF file", + "pattern": "*.{tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing background VCF information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "background_vcf": { + "type": "file", + "description": "The background VCF file", + "pattern": "*.{vcf,vcf.gz,bcf}" + } + }, + { + "background_tbi": { + "type": "file", + "description": "The index of the background VCF file", + "pattern": "*.{tbi}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A tab-delimited file comparing the variant count of each region in the query VCF and background VCF", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -68914,79 +86210,121 @@ "tool_dev_url": "https://github.com/jfjlaros/HUMID", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Fastq file(s) to deduplicate", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "umis": { - "type": "file", - "description": "Fastq file(s) containing UMIs", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "dedup": { - "type": "file", - "description": "Deduplicated Fastq file(s)", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - }, - { - "annotated": { - "type": "file", - "description": "Annotated Fastq file(s)", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - }, - { - "stats": { - "type": "directory", - "description": "Directory containg statistics file, use for multiqc.", - "pattern": "${prefix}/" - } - }, - { - "log": { - "type": "file", - "description": "Log file of humid, containing progress and errors", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Fastq file(s) to deduplicate", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "umi_file": { + "type": "file", + "description": "UMI file" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "Log file of humid, containing progress and errors", + "pattern": "*.log" + } + } + ] + }, + { + "dedup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_dedup*.fastq.gz": { + "type": "file", + "description": "Deduplicated Fastq file(s)", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } + } + ] + }, + { + "annotated": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_annotated*.fastq.gz": { + "type": "file", + "description": "Annotated Fastq file(s)", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containg statistics file, use for multiqc.", + "pattern": "${prefix}/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69020,75 +86358,94 @@ "doi": "10.1101/2019.12.19.882506", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Short reads file(s). In fastq or fasta, compressed or uncompressed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sr_bam": { - "type": "file", - "description": "Aligned short-read BAM/SAM file. Must have CIGAR information.", - "pattern": "*.{bam,sam}" - } - }, - { - "draft": { - "type": "file", - "description": "Input (fasta) file containing draft contig assembly" - } - }, - { - "genome_size": { - "type": "string", - "description": "Estimated size of the genome. Number or nts or use suffixes k/m/g, e.g. 5m, 3.2g" - } - }, - { - "reads_coverage": { - "type": "integer", - "description": "Appprimate depth of coverage of short reads." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Polished assembly fasta file", - "pattern": "*.fasta" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:hypo" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sr_bam": { + "type": "file", + "description": "Aligned short-read BAM/SAM file. Must have CIGAR information.", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Short reads file(s). In fastq or fasta, compressed or uncompressed" + } + } + ], + [ + { + "draft": { + "type": "file", + "description": "Input (fasta) file containing draft contig assembly" + } + } + ], + [ + { + "genome_size": { + "type": "string", + "description": "Estimated size of the genome. Number or nts or use suffixes k/m/g, e.g. 5m, 3.2g" + } + } + ], + [ + { + "reads_coverage": { + "type": "integer", + "description": "Appprimate depth of coverage of short reads." + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Polished assembly fasta file", + "pattern": "*.fasta" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69124,75 +86481,100 @@ "doi": "10.1038/s41467-017-00965-y", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "wigs": { - "type": "file", - "description": "Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals.", - "pattern": "*.{wig}" - } - }, - { - "gc_wig": { - "type": "file", - "description": "hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window", - "pattern": "*.{wig}" - } - }, - { - "map_wig": { - "type": "file", - "description": "hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window", - "pattern": "*.{wig}" - } - }, - { - "centromere": { - "type": "file", - "description": "Text file giving centromere locations of each genome, to exclude these windows", - "pattern": "*.{txt}" - } - }, - { - "rep_time_wig": { - "type": "file", - "description": "Replication/timing .wig file.", - "pattern": "*.{wig}" - } - }, - { - "exons": { - "type": "file", - "description": "BED file for exon regions to annotate CNA regions.", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "rds": { - "type": "file", - "description": "R data file (.rds) containing panel of normals data, medians of each bin.", - "pattern": "*.rds" - } - }, - { - "txt": { - "type": "file", - "description": "Text file containing panel of normals data, medians of each bin.", - "pattern": "*.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "wigs": { + "type": "file", + "description": "Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals.", + "pattern": "*.{wig}" + } + } + ], + [ + { + "gc_wig": { + "type": "file", + "description": "hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window", + "pattern": "*.{wig}" + } + } + ], + [ + { + "map_wig": { + "type": "file", + "description": "hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window", + "pattern": "*.{wig}" + } + } + ], + [ + { + "centromere": { + "type": "file", + "description": "Text file giving centromere locations of each genome, to exclude these windows", + "pattern": "*.{txt}" + } + } + ], + [ + { + "rep_time_wig": { + "type": "file", + "description": "Replication/timing .wig file.", + "pattern": "*.{wig}" + } + } + ], + [ + { + "exons": { + "type": "file", + "description": "BED file for exon regions to annotate CNA regions.", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "rds": [ + { + "${prefix}*.rds": { + "type": "file", + "description": "R data file (.rds) containing panel of normals data, medians of each bin.", + "pattern": "*.rds" + } + } + ] + }, + { + "txt": [ + { + "${prefix}*.txt": { + "type": "file", + "description": "Text file containing panel of normals data, medians of each bin.", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69227,143 +86609,238 @@ "doi": "10.1038/s41467-017-00965-y", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "wig": { - "type": "file", - "description": "hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window", - "pattern": "*.{wig}" - } - }, - { - "gc_wig": { - "type": "file", - "description": "hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window", - "pattern": "*.{wig}" - } - }, - { - "map_wig": { - "type": "file", - "description": "hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window", - "pattern": "*.{wig}" - } - }, - { - "normal_wig": { - "type": "file", - "description": "hmmcopy/readCounter processed .wig file giving the number of reads in the normal sample, in each genomic window", - "pattern": "*.{wig}" - } - }, - { - "normal_background": { - "type": "file", - "description": "Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc.", - "pattern": "*.{rds}" - } - }, - { - "centromere": { - "type": "file", - "description": "Text file giving centromere locations of each genome, to exclude these windows", - "pattern": "*.{txt}" - } - }, - { - "rep_time_wig": { - "type": "file", - "description": "Replication/timing .wig file.", - "pattern": "*.{wig}" - } - }, - { - "exons": { - "type": "file", - "description": "BED file for exon regions to annotate CNA regions.", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "seg": { - "type": "file", - "description": "Predicted copy number variation per segment", - "pattern": "*.{seg}" - } - }, - { - "seg_txt": { - "type": "file", - "description": "Predicted copy number variation per segment", - "pattern": "*.{seg.txt}" - } - }, - { - "cna_seg": { - "type": "file", - "description": "Predicted copy number variation per segment", - "pattern": "*.{cng.seg}" - } - }, - { - "ichorcna_params": { - "type": "file", - "description": "A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc", - "pattern": "*.{params.txt}" - } - }, - { - "corrected_depth": { - "type": "file", - "description": "A text file with corrected depth per bin", - "pattern": "*.{params.txt}" - } - }, - { - "genome_plot": { - "type": "file", - "description": "A plot with the best-fit genome-wide CNV data", - "pattern": "*.{genomeWide.pdf}" - } - }, - { - "plots": { - "type": "file", - "description": "Plots with e.g. individual chromosomes and different considered ploidy", - "pattern": "*.{pdf}" - } - }, - { - "rdata": { - "type": "file", - "description": "RData file containing all the intermediate R objects", - "pattern": "*.{cng.seg}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "wig": { + "type": "file", + "description": "hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window", + "pattern": "*.{wig}" + } + } + ], + [ + { + "gc_wig": { + "type": "file", + "description": "hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window", + "pattern": "*.{wig}" + } + } + ], + [ + { + "map_wig": { + "type": "file", + "description": "hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window", + "pattern": "*.{wig}" + } + } + ], + [ + { + "normal_wig": { + "type": "file", + "description": "hmmcopy/readCounter processed .wig file giving the number of reads in the normal sample, in each genomic window", + "pattern": "*.{wig}" + } + } + ], + [ + { + "normal_background": { + "type": "file", + "description": "Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc.", + "pattern": "*.{rds}" + } + } + ], + [ + { + "centromere": { + "type": "file", + "description": "Text file giving centromere locations of each genome, to exclude these windows", + "pattern": "*.{txt}" + } + } + ], + [ + { + "rep_time_wig": { + "type": "file", + "description": "Replication/timing .wig file.", + "pattern": "*.{wig}" + } + } + ], + [ + { + "exons": { + "type": "file", + "description": "BED file for exon regions to annotate CNA regions.", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "rdata": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.RData": { + "type": "file", + "description": "RData file containing all the intermediate R objects", + "pattern": "*.{cng.seg}" + } + } + ] + }, + { + "seg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.seg": { + "type": "file", + "description": "Predicted copy number variation per segment", + "pattern": "*.{seg}" + } + } + ] + }, + { + "cna_seg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.cna.seg": { + "type": "file", + "description": "Predicted copy number variation per segment", + "pattern": "*.{cng.seg}" + } + } + ] + }, + { + "seg_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.seg.txt": { + "type": "file", + "description": "Predicted copy number variation per segment", + "pattern": "*.{seg.txt}" + } + } + ] + }, + { + "corrected_depth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.correctedDepth.txt": { + "type": "file", + "description": "A text file with corrected depth per bin", + "pattern": "*.{params.txt}" + } + } + ] + }, + { + "ichorcna_params": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}.params.txt": { + "type": "file", + "description": "A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc", + "pattern": "*.{params.txt}" + } + } + ] + }, + { + "plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "${prefix}/*.pdf": { + "type": "file", + "description": "Plots with e.g. individual chromosomes and different considered ploidy", + "pattern": "*.{pdf}" + } + } + ] + }, + { + "genome_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "**/${prefix}_genomeWide.pdf": { + "type": "file", + "description": "A plot with the best-fit genome-wide CNV data", + "pattern": "*.{genomeWide.pdf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69396,51 +86873,64 @@ "documentation": "https://icount.readthedocs.io/en/latest/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file of crosslinks" - } - }, - { - "segmentation": { - "type": "file", - "description": "A iCount segmentation file", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Metagene table", - "pattern": "*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file of crosslinks" + } + } + ], + [ + { + "segmentation": { + "type": "file", + "description": "A iCount segmentation file", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "metagene_*/*plot_data.tsv": { + "type": "file", + "description": "Metagene table", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69477,52 +86967,63 @@ "doi": "10.1038/nsmb.1838", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file of crosslinks", - "pattern": "*.{bed}" - } - }, - { - "sigxls": { - "type": "file", - "description": "TSV file of sigxls from iCount sigxls", - "pattern": "*.{tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "peaks": { - "type": "file", - "description": "Crosslinks deemed significant by iCount", - "pattern": "*.{bed.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file of crosslinks", + "pattern": "*.{bed}" + } + }, + { + "sigxls": { + "type": "file", + "description": "TSV file of sigxls from iCount sigxls", + "pattern": "*.{tsv}" + } + } + ] + ], + "output": [ + { + "peaks": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.peaks.bed.gz": { + "type": "file", + "description": "Crosslinks deemed significant by iCount", + "pattern": "*.{bed.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69559,46 +87060,82 @@ "doi": "10.1038/nsmb.1838", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "A GTF file to use for the segmentation", - "pattern": "*.{gtf}" - } - }, - { - "fai": { - "type": "file", - "description": "FAI file corresponding to the reference sequence", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "gtf": { - "type": "file", - "description": "Segmented GTF file for use with iCount sigxls", - "pattern": "*.{gtf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "A GTF file to use for the segmentation", + "pattern": "*.{gtf}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "FAI file corresponding to the reference sequence", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_seg.gtf": { + "type": "file", + "description": "Segmented GTF file for use with iCount sigxls", + "pattern": "*.{gtf}" + } + } + ] + }, + { + "regions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information" + } + }, + { + "*_regions.gtf.gz": { + "type": "file", + "description": "Regions file for use with iCount sigxls", + "pattern": "*.{gtf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69636,59 +87173,82 @@ "doi": "10.1038/nsmb.1838", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file of crosslinks", - "pattern": "*.{bam,bam.gz}" - } - }, - { - "segmentation": { - "type": "file", - "description": "A iCount segmentation file", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "peaks": { - "type": "file", - "description": "Crosslinks deemed significant by iCount", - "pattern": "*.{bed.gz}" - } - }, - { - "scores": { - "type": "file", - "description": "Crosslink scores calculated by iCount", - "pattern": "*.{tsv}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file of crosslinks", + "pattern": "*.{bam,bam.gz}" + } + } + ], + [ + { + "segmentation": { + "type": "file", + "description": "A iCount segmentation file", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "sigxls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sigxls.bed.gz": { + "type": "file", + "description": "sigxls bed file", + "pattern": "*.{bed.gz}" + } + } + ] + }, + { + "scores": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.scores.tsv": { + "type": "file", + "description": "Crosslink scores calculated by iCount", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69723,65 +87283,98 @@ "documentation": "https://icount.readthedocs.io/en/latest/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file of crosslinks" - } - }, - { - "segmentation": { - "type": "file", - "description": "A iCount segmentation file", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "summary_type": { - "type": "file", - "description": "Summary type output stats file", - "pattern": "*summary_type.tsv" - } - }, - { - "summary_subtype": { - "type": "file", - "description": "Summary subtype output stats file", - "pattern": "*summary_subtype.tsv" - } - }, - { - "summary_gene": { - "type": "file", - "description": "Summary gene output stats file", - "pattern": "*summary_gene.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file of crosslinks" + } + } + ], + [ + { + "segmentation": { + "type": "file", + "description": "A iCount segmentation file", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "summary_type": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*summary_type.tsv": { + "type": "file", + "description": "Summary type output stats file", + "pattern": "*summary_type.tsv" + } + } + ] + }, + { + "summary_subtype": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*summary_subtype.tsv": { + "type": "file", + "description": "Summary subtype output stats file", + "pattern": "*summary_subtype.tsv" + } + } + ] + }, + { + "summary_gene": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*summary_gene.tsv": { + "type": "file", + "description": "Summary gene output stats file", + "pattern": "*summary_gene.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69817,60 +87410,93 @@ "tool_dev_url": "https://github.com/Lexogen-Tools/idemux", "licence": [ "LEXOGEN" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'NVQ', lane:1 ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files\n", - "pattern": "Undetermined_S*.fastq.gz" - } - }, - { - "samplesheet": { - "type": "file", - "description": "Input samplesheet", - "pattern": "*.{csv}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "*.fastq.gz" - } - }, - { - "undetermined": { - "type": "file", - "description": "Optional undetermined sample FASTQ files", - "pattern": "Undetermined_R?.fastq.gz" - } - }, - { - "stats": { - "type": "file", - "description": "Demultiplexing Stats", - "pattern": "demultipexing_stats.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'NVQ', lane:1 ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files\n", + "pattern": "Undetermined_S*.fastq.gz" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Input samplesheet", + "pattern": "*.{csv}" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "*.fastq.gz" + } + }, + { + "[!undetermined]*.fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "undetermined": [ + { + "meta": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_R?.fastq.gz" + } + }, + { + "undetermined_R?.fastq.gz": { + "type": "file", + "description": "Optional undetermined sample FASTQ files", + "pattern": "Undetermined_R?.fastq.gz" + } + } + ] + }, + { + "stats": [ + { + "demultipexing_stats.tsv": { + "type": "file", + "description": "Demultiplexing Stats", + "pattern": "demultipexing_stats.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69901,60 +87527,83 @@ "tool_dev_url": "https://github.com/kundajelab/idr", "licence": [ "GPL v2" - ] + ], + "identifier": "biotools:idr" } } ], "input": [ - { - "peaks": { - "type": "list", - "description": "BED, narrowPeak or broadPeak files of replicates", - "pattern": "*" + [ + { + "peaks": { + "type": "list", + "description": "BED, narrowPeak or broadPeak files of replicates", + "pattern": "*" + } } - }, - { - "peak_type": { - "type": "string", - "description": "Type of peak file", - "pattern": "{narrowPeak,broadPeak,bed}" + ], + [ + { + "peak_type": { + "type": "string", + "description": "Type of peak file", + "pattern": "{narrowPeak,broadPeak,bed}" + } } - }, - { - "prefix": { - "type": "string", - "description": "Prefix for output files" + ], + [ + { + "prefix": { + "type": "string", + "description": "Prefix for output files" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "idr": [ + { + "*idrValues.txt": { + "type": "file", + "description": "Text file containing IDR values", + "pattern": "*.{txt}" + } + } + ] }, { - "idr": { - "type": "file", - "description": "Text file containing IDR values", - "pattern": "*.{txt}" - } + "log": [ + { + "*log.txt": { + "type": "file", + "description": "Log file", + "pattern": "*.{txt}" + } + } + ] }, { - "log": { - "type": "file", - "description": "Log file", - "pattern": "*.{txt}" - } + "png": [ + { + "*.png": { + "type": "file", + "description": "Plot generated by idr", + "pattern": "*{.png}" + } + } + ] }, { - "png": { - "type": "file", - "description": "Plot generated by idr", - "pattern": "*{.png}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -69990,70 +87639,101 @@ "doi": "10.1093/bioinformatics/btac830", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:igv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "index": { + "type": "file", + "description": "Index of sorted BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + } + ] + ], + "output": [ + { + "browser": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genome-browser.html": { + "type": "file", + "description": "Genome browser HTML file", + "pattern": "*.{html}" + } + } + ] + }, + { + "align_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "Copy of the input sorted BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ] + }, + { + "index_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Copy of the input index of sorted BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "index": { - "type": "file", - "description": "Index of sorted BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "browser": { - "type": "file", - "description": "Genome browser HTML file", - "pattern": "*.{html}" - } - }, - { - "align_files": { - "type": "file", - "description": "Copy of the input sorted BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "index_files": { - "type": "file", - "description": "Copy of the input index of sorted BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@mirpedrol" + "authors": [ + "@mirpedrol" ], "maintainers": [ "@mirpedrol" @@ -70082,70 +87762,90 @@ "doi": "10.1093/bioinformatics/btac830", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sites": { - "type": "file", - "description": "VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites\n" - } - }, - { - "tracks": { - "type": "file", - "description": "List of any set of files of the types that IGV can display,\neg BAM/CRAM, GTF/GFF, VCF, BED, etc\n" - } - }, - { - "tracks_indices": { - "type": "file", - "description": "Track index files, eg bai/crai files. This may not be required,\nbut for some file types, eg BAM/CRAM, they are. They are not used in the\nigvreports cmds, but may need to exist in the working directory\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing genome information\ne.g. [ id:'genome_name' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fasta file index", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "report": { - "type": "file", - "description": "html report with a table of genomic sites and an embedded\nIGV genome browser for viewing data for each site\n", - "pattern": "*.{html}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sites": { + "type": "file", + "description": "VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites\n" + } + }, + { + "tracks": { + "type": "file", + "description": "List of any set of files of the types that IGV can display,\neg BAM/CRAM, GTF/GFF, VCF, BED, etc\n" + } + }, + { + "tracks_indicies": { + "type": "file", + "description": "List of indices for the tracks\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing genome information\ne.g. [ id:'genome_name' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fasta,fa}" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fasta file index", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "file", + "description": "html report with a table of genomic sites and an embedded\nIGV genome browser for viewing data for each site\n", + "pattern": "*.{html}" + } + }, + { + "*.html": { + "type": "file", + "description": "html report with a table of genomic sites and an embedded\nIGV genome browser for viewing data for each site\n", + "pattern": "*.{html}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70177,71 +87877,86 @@ "tool_dev_url": "https://github.com/ilastik/ilastik", "license": [ "GPL3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "h5": { - "type": "file", - "description": "h5 file containing image stack to classify file", - "pattern": "*.{h5,hdf5}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ilp": { - "type": "file", - "description": "Trained ilastik .ilp project file", - "pattern": "*.{ilp}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "probs": { - "type": "file", - "description": "Probability map for boundary based segmentation", - "pattern": "*.{h5,,hdf5}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "out_tiff": { - "type": "file", - "description": "Multicut segmentation mask output.", - "pattern": "*.{tiff}" - } + ], + "identifier": "biotools:ilastik" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "h5": { + "type": "file", + "description": "h5 file containing image stack to classify file", + "pattern": "*.{h5,hdf5}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ilp": { + "type": "file", + "description": "Trained ilastik .ilp project file", + "pattern": "*.{ilp}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "probs": { + "type": "file", + "description": "Probability map for boundary based segmentation", + "pattern": "*.{h5,,hdf5}" + } + } + ] + ], + "output": [ + { + "out_tiff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tiff": { + "type": "file", + "description": "Multicut segmentation mask output.", + "pattern": "*.{tiff}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70283,56 +87998,69 @@ "tool_dev_url": "https://github.com/ilastik/ilastik", "licence": [ "GPL3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information for h5 file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_img": { - "type": "file", - "description": "Input img file containing image stack to classify" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for ilp file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ilp": { - "type": "file", - "description": "Trained ilastik pixel classification .ilp project file", - "pattern": "*.{ilp}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "Output file from ilastik pixel classification." - } + ], + "identifier": "biotools:ilastik" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information for h5 file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_img": { + "type": "file", + "description": "Input img file containing image stack to classify" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for ilp file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ilp": { + "type": "file", + "description": "Trained ilastik pixel classification .ilp project file", + "pattern": "*.{ilp}" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${suffix}": { + "type": "file", + "description": "Output file from ilastik pixel classification." + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70377,87 +88105,140 @@ "doi": "10.1038/s41587-020-00797-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "profiles": { - "type": "directory", - "description": "InStrain profile folders", - "pattern": "*.IS/" - } - }, - { - "bams": { - "type": "file", - "description": "Path to .bam files that were profiled", - "pattern": "*.{bam,sam}" - } - }, - { - "stb_file": { - "type": "file", - "description": "Path to .stb (scaffold to bin) file that was profiled", - "pattern": "*.stb" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "compare": { - "type": "directory", - "description": "inStrain compare folders", - "pattern": "*.IS_compare/" - } - }, - { - "comparisons_table": { - "type": "file", - "description": "Comparisons table", - "pattern": "*.tsv" - } - }, - { - "pooled_snv": { - "type": "file", - "description": "Pooled SNV", - "pattern": "*.tsv" - } - }, - { - "snv_info": { - "type": "file", - "description": "SNV information", - "pattern": "*.tsv" - } - }, - { - "snv_keys": { - "type": "file", - "description": "SNV keys", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:instrain" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bams": { + "type": "file", + "description": "Path to .bam files that were profiled", + "pattern": "*.{bam,sam}" + } + }, + { + "profiles": { + "type": "directory", + "description": "InStrain profile folders", + "pattern": "*.IS/" + } + } + ], + [ + { + "stb_file": { + "type": "file", + "description": "Path to .stb (scaffold to bin) file that was profiled", + "pattern": "*.stb" + } + } + ] + ], + "output": [ + { + "compare": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare": { + "type": "directory", + "description": "inStrain compare folders", + "pattern": "*.IS_compare/" + } + } + ] + }, + { + "comparisons_table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_comparisonsTable.tsv": { + "type": "file", + "description": "Comparisons table", + "pattern": "*.tsv" + } + } + ] + }, + { + "pooled_snv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_pooled_SNV_data.tsv": { + "type": "file", + "description": "Pooled SNV", + "pattern": "*.tsv" + } + } + ] + }, + { + "snv_keys": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_pooled_SNV_data_keys.tsv": { + "type": "file", + "description": "SNV keys", + "pattern": "*.tsv" + } + } + ] + }, + { + "snv_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.IS_compare/output/*.IS_compare_pooled_SNV_info.tsv": { + "type": "file", + "description": "SNV information", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70499,108 +88280,185 @@ "doi": "10.1038/s41587-020-00797-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test']" - } - }, - { - "bam": { - "type": "file", - "description": "Path to .bam file to be profiled", - "pattern": "*.{bam,sam}" - } - }, - { - "genome_fasta": { - "type": "file", - "description": "Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "genes_fasta": { - "type": "file", - "description": "Path to .fna file of genes to be profiled (OPTIONAL)", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "stb_file": { - "type": "file", - "description": "Path to .stb (scaffold to bin) file to be profiled (OPTIONAL)", - "pattern": "*.stb" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "profile": { - "type": "directory", - "description": "InStrain profile folder", - "pattern": "*.IS/" - } - }, - { - "gene_info": { - "type": "file", - "description": "Gene information", - "pattern": "*.tsv" - } - }, - { - "genome_info": { - "type": "file", - "description": "Genome information", - "pattern": "*.tsv" - } - }, - { - "linkage": { - "type": "file", - "description": "Linkage information", - "pattern": "*.tsv" - } - }, - { - "mapping_info": { - "type": "file", - "description": "Mapping information", - "pattern": "*.tsv" - } - }, - { - "scaffold_info": { - "type": "file", - "description": "Scaffold information", - "pattern": "*.tsv" - } - }, - { - "snvs": { - "type": "file", - "description": "SNVs", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:instrain" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test']" + } + }, + { + "bam": { + "type": "file", + "description": "Path to .bam file to be profiled", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "genome_fasta": { + "type": "file", + "description": "Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "genes_fasta": { + "type": "file", + "description": "Path to .fna file of genes to be profiled (OPTIONAL)", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "stb_file": { + "type": "file", + "description": "Path to .stb (scaffold to bin) file to be profiled (OPTIONAL)", + "pattern": "*.stb" + } + } + ] + ], + "output": [ + { + "profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS": { + "type": "directory", + "description": "InStrain profile folder", + "pattern": "*.IS/" + } + } + ] + }, + { + "snvs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_SNVs.tsv": { + "type": "file", + "description": "SNVs", + "pattern": "*.tsv" + } + } + ] + }, + { + "gene_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_gene_info.tsv": { + "type": "file", + "description": "Gene information", + "pattern": "*.tsv" + } + } + ] + }, + { + "genome_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_genome_info.tsv": { + "type": "file", + "description": "Genome information", + "pattern": "*.tsv" + } + } + ] + }, + { + "linkage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_linkage.tsv": { + "type": "file", + "description": "Linkage information", + "pattern": "*.tsv" + } + } + ] + }, + { + "mapping_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_mapping_info.tsv": { + "type": "file", + "description": "Mapping information", + "pattern": "*.tsv" + } + } + ] + }, + { + "scaffold_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.IS/output/*.IS_scaffold_info.tsv": { + "type": "file", + "description": "Scaffold information", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70641,66 +88499,119 @@ "doi": "10.1093/bioinformatics/btu031", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing the amino acid or dna query sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "interproscan_database": { - "type": "directory", - "description": "Path to the interproscan database (untarred http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz)" - } - } - ], - "output": [ - { - "tsv": { - "type": "file", - "description": "Tab separated file containing with detailed hits", - "pattern": "*.{tsv}" - } - }, - { - "xml": { - "type": "file", - "description": "XML file containing with detailed hits", - "pattern": "*.{xml}" - } - }, - { - "gff3": { - "type": "file", - "description": "GFF3 file containing with detailed hits", - "pattern": "*.{gff3}" - } - }, - { - "json": { - "type": "file", - "description": "JSON file containing with detailed hits", - "pattern": "*.{json}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing the amino acid or dna query sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "interproscan_database": { + "type": "directory", + "description": "Path to the interproscan database (untarred http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz)" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "file", + "description": "Tab separated file containing with detailed hits", + "pattern": "*.{tsv}" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab separated file containing with detailed hits", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "xml": [ + { + "meta": { + "type": "file", + "description": "XML file containing with detailed hits", + "pattern": "*.{xml}" + } + }, + { + "*.xml": { + "type": "file", + "description": "XML file containing with detailed hits", + "pattern": "*.{xml}" + } + } + ] + }, + { + "gff3": [ + { + "meta": { + "type": "file", + "description": "GFF3 file containing with detailed hits", + "pattern": "*.{gff3}" + } + }, + { + "*.gff3": { + "type": "file", + "description": "GFF3 file containing with detailed hits", + "pattern": "*.{gff3}" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "file", + "description": "JSON file containing with detailed hits", + "pattern": "*.{json}" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file containing with detailed hits", + "pattern": "*.{json}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70740,24 +88651,33 @@ "doi": "10.1371/journal.pbio.3002083", "licence": [ "Modified GPL v3" - ] + ], + "identifier": "" } } ], "output": [ { - "iphop_db": { - "type": "directory", - "description": "Directory containing downloaded and md5 checked iPHoP database", - "pattern": "iphop_db/" - } + "iphop_db": [ + { + "iphop_db/": { + "type": "directory", + "description": "Directory containing downloaded and md5 checked iPHoP database", + "pattern": "iphop_db/" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70800,65 +88720,98 @@ "doi": "10.1371/journal.pbio.3002083", "licence": [ "Modified GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing phage contigs/scaffolds/chromosomes", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "iphop_db": { - "type": "directory", - "description": "Directory pointing to iPHoP database" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "iphop_genus": { - "type": "file", - "description": "File containing integrated host predictions at genus level, with a minimum score defined by the `--min_score` argument", - "pattern": "Host_prediction_to_genus_m*.csv" - } - }, - { - "iphop_genome": { - "type": "file", - "description": "File containing integrated host predictions at host genome level, with a minimum score defined by the `--min_score` argument", - "pattern": "Host_prediction_to_genome_m*.csv" - } - }, - { - "iphop_detailed_output": { - "type": "file", - "description": "File containing each phage's top 5 hits via each method", - "pattern": "Detailed_output_by_tool.csv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing phage contigs/scaffolds/chromosomes", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "iphop_db": { + "type": "directory", + "description": "Directory pointing to iPHoP database" + } + } + ] + ], + "output": [ + { + "iphop_genus": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "Host_prediction_to_genus_m*.csv": { + "type": "file", + "description": "File containing integrated host predictions at genus level, with a minimum score defined by the `--min_score` argument", + "pattern": "Host_prediction_to_genus_m*.csv" + } + } + ] + }, + { + "iphop_genome": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "Host_prediction_to_genome_m*.csv": { + "type": "file", + "description": "File containing integrated host predictions at host genome level, with a minimum score defined by the `--min_score` argument", + "pattern": "Host_prediction_to_genome_m*.csv" + } + } + ] + }, + { + "iphop_detailed_output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "Detailed_output_by_tool.csv": { + "type": "file", + "description": "File containing each phage's top 5 hits via each method", + "pattern": "Detailed_output_by_tool.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -70897,381 +88850,676 @@ "doi": "10.1093/molbev/msaa015", "licence": [ "GPL v2-or-later" - ] - } + ], + "identifier": "biotools:iqtree" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy map containing sample information for the\nalignment/tree file, e.g. [ id: 'test' ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "Input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format (-s)", + "pattern": "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}" + } + }, + { + "tree": { + "type": "file", + "description": "File containing one or multiple phylogenetic trees (-t): - Single tree used e.g. as starting tree for tree search - Set of trees used e.g. for distance computation, consensus tree construction", + "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + } + } + ], + [ + { + "tree_te": { + "type": "file", + "description": "File containing single phylogenetic tree (-te) Use cases: - fixed user tree to skip tree search - ancestral sequence reconstruction", + "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + } + } + ], + [ + { + "lmclust": { + "type": "file", + "description": "NEXUS file containing taxon clusters for quartet mapping analysis (-lmclust)", + "pattern": "*.nex{us}" + } + } + ], + [ + { + "mdef": { + "type": "file", + "description": "NEXUS model file defining new models (-mdef)", + "pattern": "*.nex{us}" + } + } + ], + [ + { + "partitions_equal": { + "type": "file", + "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-q)", + "pattern": "*.{nex,nexus,tre,tree,treefile}" + } + } + ], + [ + { + "partitions_proportional": { + "type": "file", + "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-spp)", + "pattern": "*.{nex,nexus,tre,tree,treefile}" + } + } + ], + [ + { + "partitions_unlinked": { + "type": "file", + "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-sp)", + "pattern": "*.{nex,nexus,tre,tree,treefile}" + } + } + ], + [ + { + "guide_tree": { + "type": "file", + "description": "File containing guide tree for inference of site frequency profiles (-ft)", + "pattern": "*.{nex,nexus,tre,tree,treefile}" + } + } + ], + [ + { + "sitefreq_in": { + "type": "file", + "description": "Site frequency file (-fs)", + "pattern": "*.sitefreq" + } + } + ], + [ + { + "constraint_tree": { + "type": "file", + "description": "File containing opological constraint tree in NEWICK format. The constraint tree can be a multifurcating tree and need not to include all taxa. (-g)", + "pattern": "*.{nwk,newick}" + } + } + ], + [ + { + "trees_z": { + "type": "file", + "description": "File containing a set of trees for which log-likelihoods should be computed (-z)" + } + } + ], + [ + { + "suptree": { + "type": "file", + "description": "File containing input “target” tree, support values are extracted from trees passed via -t, and mapped onto the target tree (-sup)" + } + } + ], + [ + { + "trees_rf": { + "type": "file", + "description": "File containing a second tree set (-rf). Used for computing the distance to the primary tree set (`tree`)", + "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + } + } + ] + ], + "output": [ + { + "phylogeny": [ + { + "meta": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{treefile}" + } + }, + { + "*.treefile": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{treefile}" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "file", + "description": "Main report file containing computational\nresults as well as a textual visualization\nof the final tree\n", + "pattern": "*.{iqtree}" + } + }, + { + "*.iqtree": { + "type": "file", + "description": "Main report file containing computational\nresults as well as a textual visualization\nof the final tree\n", + "pattern": "*.{iqtree}" + } + } + ] + }, + { + "mldist": [ + { + "meta": { + "type": "file", + "description": "File containing the pairwise maximum\nlikelihood distances as a matrix\n", + "pattern": "*.{mldist}" + } + }, + { + "*.mldist": { + "type": "file", + "description": "File containing the pairwise maximum\nlikelihood distances as a matrix\n", + "pattern": "*.{mldist}" + } + } + ] + }, + { + "lmap_svg": [ + { + "meta": { + "type": "file", + "description": "File containing likelihood mapping analysis\nresults in .svg format (-lmap/-lmclust)\n", + "pattern": "*.lmap.svg" + } + }, + { + "*.lmap.svg": { + "type": "file", + "description": "File containing likelihood mapping analysis\nresults in .svg format (-lmap/-lmclust)\n", + "pattern": "*.lmap.svg" + } + } + ] + }, + { + "lmap_eps": [ + { + "meta": { + "type": "file", + "description": "File containing likelihood mapping analysis\nresults in .eps format (-lmap/-lmclust)\n", + "pattern": "*.lmap.eps" + } + }, + { + "*.lmap.eps": { + "type": "file", + "description": "File containing likelihood mapping analysis\nresults in .eps format (-lmap/-lmclust)\n", + "pattern": "*.lmap.eps" + } + } + ] + }, + { + "lmap_quartetlh": [ + { + "meta": { + "type": "file", + "description": "File containing quartet log-likelihoods (-wql)\n", + "pattern": "*.lmap.quartetlh" + } + }, + { + "*.lmap.quartetlh": { + "type": "file", + "description": "File containing quartet log-likelihoods (-wql)\n", + "pattern": "*.lmap.quartetlh" + } + } + ] + }, + { + "sitefreq_out": [ + { + "meta": { + "type": "file", + "description": "File containing site frequency profiles (-ft)\n", + "pattern": "*.sitefreq" + } + }, + { + "*.sitefreq": { + "type": "file", + "description": "File containing site frequency profiles (-ft)\n", + "pattern": "*.sitefreq" + } + } + ] + }, + { + "bootstrap": [ + { + "meta": { + "type": "file", + "description": "File containing all bootstrap trees (-wbt/-wbtl)\n", + "pattern": "*.ufboot" + } + }, + { + "*.ufboot": { + "type": "file", + "description": "File containing all bootstrap trees (-wbt/-wbtl)\n", + "pattern": "*.ufboot" + } + } + ] + }, + { + "state": [ + { + "meta": { + "type": "file", + "description": "File containing ancestral sequences for all\nnodes of the tree by empirical Bayesian method (-asr)\n", + "pattern": "*.{state}" + } + }, + { + "*.state": { + "type": "file", + "description": "File containing ancestral sequences for all\nnodes of the tree by empirical Bayesian method (-asr)\n", + "pattern": "*.{state}" + } + } + ] + }, + { + "contree": [ + { + "meta": { + "type": "file", + "description": "File containing consensus tree (-con/-bb)\n", + "pattern": "*.{contree}" + } + }, + { + "*.contree": { + "type": "file", + "description": "File containing consensus tree (-con/-bb)\n", + "pattern": "*.{contree}" + } + } + ] + }, + { + "nex": [ + { + "meta": { + "type": "file", + "description": "File containing consensus network (-net/-bb)\n", + "pattern": "*.{nex}" + } + }, + { + "*.nex": { + "type": "file", + "description": "File containing consensus network (-net/-bb)\n", + "pattern": "*.{nex}" + } + } + ] + }, + { + "splits": [ + { + "meta": { + "type": "file", + "description": "File containing consensus network in star-dot format (-wsplits)\n", + "pattern": "*.{splits}" + } + }, + { + "*.splits": { + "type": "file", + "description": "File containing consensus network in star-dot format (-wsplits)\n", + "pattern": "*.{splits}" + } + } + ] + }, + { + "suptree": [ + { + "meta": { + "type": "file", + "description": "File containing tree with assigned support\nvalues based on supplied \"target\" tree (-sup)\n", + "pattern": "*.{suptree}" + } + }, + { + "*.suptree": { + "type": "file", + "description": "File containing tree with assigned support\nvalues based on supplied \"target\" tree (-sup)\n", + "pattern": "*.{suptree}" + } + } + ] + }, + { + "alninfo": [ + { + "meta": { + "type": "file", + "description": "File containing alignment site statistics (-alninfo)\n", + "pattern": "*.{alninfo}" + } + }, + { + "*.alninfo": { + "type": "file", + "description": "File containing alignment site statistics (-alninfo)\n", + "pattern": "*.{alninfo}" + } + } + ] + }, + { + "partlh": [ + { + "meta": { + "type": "file", + "description": "File containing partition log-likelihoods (-wpl)\n", + "pattern": "*.{partlh}" + } + }, + { + "*.partlh": { + "type": "file", + "description": "File containing partition log-likelihoods (-wpl)\n", + "pattern": "*.{partlh}" + } + } + ] + }, + { + "siteprob": [ + { + "meta": { + "type": "file", + "description": "File containing site posterior probabilities (-wspr/-wspm/-wspmr)\n", + "pattern": "*.{siteprob}" + } + }, + { + "*.siteprob": { + "type": "file", + "description": "File containing site posterior probabilities (-wspr/-wspm/-wspmr)\n", + "pattern": "*.{siteprob}" + } + } + ] + }, + { + "sitelh": [ + { + "meta": { + "type": "file", + "description": "File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr)\n", + "pattern": "*.{sitelh}" + } + }, + { + "*.sitelh": { + "type": "file", + "description": "File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr)\n", + "pattern": "*.{sitelh}" + } + } + ] + }, + { + "treels": [ + { + "meta": { + "type": "file", + "description": "File containing all locally optimal trees (-wt)\n", + "pattern": "*.{treels}" + } + }, + { + "*.treels": { + "type": "file", + "description": "File containing all locally optimal trees (-wt)\n", + "pattern": "*.{treels}" + } + } + ] + }, + { + "rate": [ + { + "meta": { + "type": "file", + "description": "File containing inferred site-specific\nevolutionary rates (-wsr)\n", + "pattern": "*.{rate}" + } + }, + { + "*.rate ": { + "type": "file", + "description": "File containing inferred site-specific\nevolutionary rates (-wsr)\n", + "pattern": "*.{rate}" + } + } + ] + }, + { + "mlrate": [ + { + "meta": { + "type": "file", + "description": "File containing site-specific subtitution\nrates determined by maximum likelihood (--mlrate)\n", + "pattern": "*.{mlrate}" + } + }, + { + "*.mlrate": { + "type": "file", + "description": "File containing site-specific subtitution\nrates determined by maximum likelihood (--mlrate)\n", + "pattern": "*.{mlrate}" + } + } + ] + }, + { + "exch_matrix": [ + { + "meta": { + "type": "file", + "description": "File containing the exchangeability matrix obtained from the optimization (--link-exchange-rates)", + "pattern": "GTRPMIX.nex" + } + }, + { + "GTRPMIX.nex": { + "type": "file", + "description": "File containing the exchangeability matrix obtained from the optimization (--link-exchange-rates)", + "pattern": "GTRPMIX.nex" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log file of entire run", + "pattern": "*.{log}" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of entire run", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy map containing sample information for the\nalignment/tree file, e.g. [ id: 'test' ]\n" - } - }, + "authors": [ + "@avantonder", + "@aunderwo" + ], + "maintainers": [ + "@avantonder", + "@aunderwo" + ] + }, + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "reportho", + "version": "1.0.1" + } + ] + }, + { + "name": "islandpath", + "path": "modules/nf-core/islandpath/meta.yml", + "type": "module", + "meta": { + "name": "islandpath", + "description": "Genomic island prediction in bacterial and archaeal genomes", + "keywords": [ + "genomes", + "genomic islands", + "prediction" + ], + "tools": [ { - "alignment": { - "type": "file", - "description": "Input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format (-s)", - "pattern": "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}" + "islandpath": { + "description": "IslandPath-DIMOB is a standalone software to predict genomic islands (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes.", + "homepage": "https://github.com/brinkmanlab/islandpath", + "documentation": "https://github.com/brinkmanlab/islandpath#readme", + "tool_dev_url": "https://github.com/brinkmanlab/islandpath", + "doi": "10.1093/bioinformatics/bty095", + "licence": [ + "GPL v3" + ], + "identifier": "biotools:islandpath" } - }, - { - "tree": { - "type": "file", - "description": "File containing one or multiple phylogenetic trees (-t): - Single tree used e.g. as starting tree for tree search - Set of trees used e.g. for distance computation, consensus tree construction", - "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genome": { + "type": "file", + "description": "Genome file in .gbk or .embl format.\npattern: \"*.{gbk, embl, gbff}\"\n" + } } - }, + ] + ], + "output": [ { - "tree_te": { - "type": "file", - "description": "File containing single phylogenetic tree (-te) Use cases: - fixed user tree to skip tree search - ancestral sequence reconstruction", - "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}" - } + "gff": [ + { + "meta": { + "type": "file", + "description": "GFF file listing the predicted genomic islands and their coordinates", + "pattern": "*.gff" + } + }, + { + "*.gff": { + "type": "file", + "description": "GFF file listing the predicted genomic islands and their coordinates", + "pattern": "*.gff" + } + } + ] }, { - "lmclust": { - "type": "file", - "description": "NEXUS file containing taxon clusters for quartet mapping analysis (-lmclust)", - "pattern": "*.nex{us}" - } + "log": [ + { + "Dimob.log": { + "type": "file", + "description": "Log file of the islandpath run", + "pattern": "*.log" + } + } + ] }, { - "mdef": { - "type": "file", - "description": "NEXUS model file defining new models (-mdef)", - "pattern": "*.nex{us}" - } - }, - { - "partitions_equal": { - "type": "file", - "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-q)", - "pattern": "*.{nex,nexus,tre,tree,treefile}" - } - }, - { - "partitions_proportional": { - "type": "file", - "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-spp)", - "pattern": "*.{nex,nexus,tre,tree,treefile}" - } - }, - { - "partitions_unlinked": { - "type": "file", - "description": "Partition file for edge-equal partition model, all partitions share same set of branch lengths (-sp)", - "pattern": "*.{nex,nexus,tre,tree,treefile}" - } - }, - { - "guide_tree": { - "type": "file", - "description": "File containing guide tree for inference of site frequency profiles (-ft)", - "pattern": "*.{nex,nexus,tre,tree,treefile}" - } - }, - { - "sitefreq_in": { - "type": "file", - "description": "Site frequency file (-fs)", - "pattern": "*.sitefreq" - } - }, - { - "constraint_tree": { - "type": "file", - "description": "File containing opological constraint tree in NEWICK format. The constraint tree can be a multifurcating tree and need not to include all taxa. (-g)", - "pattern": "*.{nwk,newick}" - } - }, - { - "trees_z": { - "type": "file", - "description": "File containing a set of trees for which log-likelihoods should be computed (-z)" - } - }, - { - "suptree": { - "type": "file", - "description": "File containing input “target” tree, support values are extracted from trees passed via -t, and mapped onto the target tree (-sup)" - } - }, - { - "trees_rf": { - "type": "file", - "description": "File containing a second tree set (-rf). Used for computing the distance to the primary tree set (`tree`)", - "pattern": "*.{tre,tree,treefile,newick,nwk,nex,nexus}" - } - } - ], - "output": [ - { - "phylogeny": { - "type": "file", - "description": "A phylogeny in Newick format", - "pattern": "*.{treefile}" - } - }, - { - "report": { - "type": "file", - "description": "Main report file containing computational\nresults as well as a textual visualization\nof the final tree\n", - "pattern": "*.{iqtree}" - } - }, - { - "mldist": { - "type": "file", - "description": "File containing the pairwise maximum\nlikelihood distances as a matrix\n", - "pattern": "*.{mldist}" - } - }, - { - "lmap_svg": { - "type": "file", - "description": "File containing likelihood mapping analysis\nresults in .svg format (-lmap/-lmclust)\n", - "pattern": "*.lmap.svg" - } - }, - { - "lmap_eps": { - "type": "file", - "description": "File containing likelihood mapping analysis\nresults in .eps format (-lmap/-lmclust)\n", - "pattern": "*.lmap.eps" - } - }, - { - "lmap_quartetlh": { - "type": "file", - "description": "File containing quartet log-likelihoods (-wql)\n", - "pattern": "*.lmap.quartetlh" - } - }, - { - "sitefreq_out": { - "type": "file", - "description": "File containing site frequency profiles (-ft)\n", - "pattern": "*.sitefreq" - } - }, - { - "bootstrap": { - "type": "file", - "description": "File containing all bootstrap trees (-wbt/-wbtl)\n", - "pattern": "*.ufboot" - } - }, - { - "state": { - "type": "file", - "description": "File containing ancestral sequences for all\nnodes of the tree by empirical Bayesian method (-asr)\n", - "pattern": "*.{state}" - } - }, - { - "contree": { - "type": "file", - "description": "File containing consensus tree (-con/-bb)\n", - "pattern": "*.{contree}" - } - }, - { - "nex": { - "type": "file", - "description": "File containing consensus network (-net/-bb)\n", - "pattern": "*.{nex}" - } - }, - { - "splits": { - "type": "file", - "description": "File containing consensus network in star-dot format (-wsplits)\n", - "pattern": "*.{splits}" - } - }, - { - "suptree": { - "type": "file", - "description": "File containing tree with assigned support\nvalues based on supplied \"target\" tree (-sup)\n", - "pattern": "*.{suptree}" - } - }, - { - "alninfo": { - "type": "file", - "description": "File containing alignment site statistics (-alninfo)\n", - "pattern": "*.{alninfo}" - } - }, - { - "partlh": { - "type": "file", - "description": "File containing partition log-likelihoods (-wpl)\n", - "pattern": "*.{partlh}" - } - }, - { - "siteprob": { - "type": "file", - "description": "File containing site posterior probabilities (-wspr/-wspm/-wspmr)\n", - "pattern": "*.{siteprob}" - } - }, - { - "sitelh": { - "type": "file", - "description": "File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr)\n", - "pattern": "*.{sitelh}" - } - }, - { - "treels": { - "type": "file", - "description": "File containing all locally optimal trees (-wt)\n", - "pattern": "*.{treels}" - } - }, - { - "rate": { - "type": "file", - "description": "File containing inferred site-specific\nevolutionary rates (-wsr)\n", - "pattern": "*.{rate}" - } - }, - { - "mlrate": { - "type": "file", - "description": "File containing site-specific subtitution\nrates determined by maximum likelihood (--mlrate)\n", - "pattern": "*.{mlrate}" - } - }, - { - "exch_matrix": { - "type": "file", - "description": "File containing the exchangeability matrix obtained from the optimization (--link-exchange-rates)", - "pattern": "GTRPMIX.nex" - } - }, - { - "log": { - "type": "file", - "description": "Log file of entire run", - "pattern": "*.{log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@avantonder", - "@aunderwo" - ], - "maintainers": [ - "@avantonder", - "@aunderwo" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "dev" - }, - { - "name": "reportho", - "version": "1.0.1" - } - ] - }, - { - "name": "islandpath", - "path": "modules/nf-core/islandpath/meta.yml", - "type": "module", - "meta": { - "name": "islandpath", - "description": "Genomic island prediction in bacterial and archaeal genomes", - "keywords": [ - "genomes", - "genomic islands", - "prediction" - ], - "tools": [ - { - "islandpath": { - "description": "IslandPath-DIMOB is a standalone software to predict genomic islands (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes.", - "homepage": "https://github.com/brinkmanlab/islandpath", - "documentation": "https://github.com/brinkmanlab/islandpath#readme", - "tool_dev_url": "https://github.com/brinkmanlab/islandpath", - "doi": "10.1093/bioinformatics/bty095", - "licence": [ - "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genome": { - "type": "file", - "description": "Genome file in .gbk or .embl format.\npattern: \"*.{gbk, embl, gbff}\"\n" - } - } - ], - "output": [ - { - "gff": { - "type": "file", - "description": "GFF file listing the predicted genomic islands and their coordinates", - "pattern": "*.gff" - } - }, - { - "log": { - "type": "file", - "description": "Log file of the islandpath run", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@jvfe" - ], - "maintainers": [ - "@jvfe" - ] - } - }, - { - "name": "ismapper", - "path": "modules/nf-core/ismapper/meta.yml", - "type": "module", - "meta": { - "name": "ismapper", - "description": "Identify insertion sites positions in bacterial genomes", - "keywords": [ - "fastq", - "insertion", - "bacteria" - ], - "tools": [ + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@jvfe" + ], + "maintainers": [ + "@jvfe" + ] + } + }, + { + "name": "ismapper", + "path": "modules/nf-core/ismapper/meta.yml", + "type": "module", + "meta": { + "name": "ismapper", + "description": "Identify insertion sites positions in bacterial genomes", + "keywords": [ + "fastq", + "insertion", + "bacteria" + ], + "tools": [ { "ismapper": { "description": "A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes.", @@ -71281,59 +89529,70 @@ "doi": "10.1186/s12864-015-1860-2", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "A set of paired-end FASTQ files", - "pattern": "*.{fastq.gz,fq.gz}" - } - }, - { - "reference": { - "type": "file", - "description": "Reference genome in GenBank format", - "pattern": "*.{gbk}" - } - }, - { - "query": { - "type": "file", - "description": "Insertion sequences to query in FASTA format", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "directory", - "description": "Directory containing ISMapper result files", - "pattern": "*/*" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "A set of paired-end FASTQ files", + "pattern": "*.{fastq.gz,fq.gz}" + } + }, + { + "reference": { + "type": "file", + "description": "Reference genome in GenBank format", + "pattern": "*.{gbk}" + } + }, + { + "query": { + "type": "file", + "description": "Insertion sequences to query in FASTA format", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*": { + "type": "directory", + "description": "Directory containing ISMapper result files", + "pattern": "*/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72098,59 +90357,82 @@ "tool_dev_url": "https://github.com/PacificBiosciences/IsoSeq/tree/master", "licence": [ "BSD-3-clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file, one full-length CCS file generated by lima", - "pattern": "*.5p--3p.bam" - } - }, - { - "design": { - "type": "string", - "description": "Barcoding design. Specifies which bases to use as cell/molecular barcodes.", - "pattern": "^(?:\\d{1,2}[UBGX]-)+T$|^(?:\\d{1,2}[UBGX]-)+T(?:-\\d{1,2}[UBGX])+$|^T(?:-\\d{1,2}[UBGX])+$" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with full-length tagged reads", - "pattern": "*.flt.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "Pacbio index file of full-length tagged reads", - "pattern": "*.flt.bam.pbi" - } + ], + "identifier": "biotools:isoseq3" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file, one full-length CCS file generated by lima", + "pattern": "*.5p--3p.bam" + } + } + ], + [ + { + "design": { + "type": "string", + "description": "Barcoding design. Specifies which bases to use as cell/molecular barcodes.", + "pattern": "^(?:\\d{1,2}[UBGX]-)+T$|^(?:\\d{1,2}[UBGX]-)+T(?:-\\d{1,2}[UBGX])+$|^T(?:-\\d{1,2}[UBGX])+$" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.flt.bam": { + "type": "file", + "description": "BAM file with full-length tagged reads", + "pattern": "*.flt.bam" + } + } + ] + }, + { + "pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.flt.bam.pbi": { + "type": "file", + "description": "Pacbio index file of full-length tagged reads", + "pattern": "*.flt.bam.pbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72183,115 +90465,226 @@ "tool_dev_url": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", "licence": [ "BSD-3-Clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file generated by isoseq refine", - "pattern": "*.bam" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file of clustered consensus", - "pattern": "*.transcripts.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "Pacbio Index of consensus reads generated by clustering", - "pattern": "*.transcripts.bam.pbi" - } - }, - { - "cluster": { - "type": "file", - "description": "A two columns (from, to) file describing original read name to new read name", - "pattern": "*.transcripts.cluster" - } - }, - { - "cluster_report": { - "type": "file", - "description": "A table files clusters (transcripts) members (read)", - "pattern": "*.transcripts.cluster_report.csv" - } - }, - { - "transcriptset": { - "type": "file", - "description": "A metadata xml file which contains full paths to data files", - "pattern": "*.transcripts.transcriptset.xml" - } - }, - { - "hq_bam": { - "type": "file", - "description": "High quality reads (when --use-qvs is set)", - "pattern": "*.transcripts.hq.bam" - } - }, - { - "hq_pbi": { - "type": "file", - "description": "Pacbio index of high quality reads (when --use-qvs is set)", - "pattern": "*.transcripts.hq.bam.pbi" - } - }, - { - "lq_bam": { - "type": "file", - "description": "Low quality reads (when --use-qvs is set)", - "pattern": "*.transcripts.lq.bam" - } - }, - { - "lq_pbi": { - "type": "file", - "description": "Pacbio index of low quality reads (when --use-qvs is set)", - "pattern": "*.transcripts.lq.bam.pbi" - } - }, - { - "singletons_bam": { - "type": "file", - "description": "Unclustered reads (when --singletons is set)", - "pattern": "*.transcripts.singletons.bam" - } - }, - { - "singletons_pbi": { - "type": "file", - "description": "Pacbio index of unclustered reads (when --singletons is set)", - "pattern": "*.transcripts.singletons.bam.pbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file generated by isoseq refine", + "pattern": "*.bam" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.bam": { + "type": "file", + "description": "BAM file of clustered consensus", + "pattern": "*.transcripts.bam" + } + } + ] + }, + { + "pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.bam.pbi": { + "type": "file", + "description": "Pacbio Index of consensus reads generated by clustering", + "pattern": "*.transcripts.bam.pbi" + } + } + ] + }, + { + "cluster": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.cluster": { + "type": "file", + "description": "A two columns (from, to) file describing original read name to new read name", + "pattern": "*.transcripts.cluster" + } + } + ] + }, + { + "cluster_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.cluster_report.csv": { + "type": "file", + "description": "A table files clusters (transcripts) members (read)", + "pattern": "*.transcripts.cluster_report.csv" + } + } + ] + }, + { + "transcriptset": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.transcriptset.xml": { + "type": "file", + "description": "A metadata xml file which contains full paths to data files", + "pattern": "*.transcripts.transcriptset.xml" + } + } + ] + }, + { + "hq_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.hq.bam": { + "type": "file", + "description": "High quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.hq.bam" + } + } + ] + }, + { + "hq_pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.hq.bam.pbi": { + "type": "file", + "description": "Pacbio index of high quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.hq.bam.pbi" + } + } + ] + }, + { + "lq_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.lq.bam": { + "type": "file", + "description": "Low quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.lq.bam" + } + } + ] + }, + { + "lq_pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.lq.bam.pbi": { + "type": "file", + "description": "Pacbio index of low quality reads (when --use-qvs is set)", + "pattern": "*.transcripts.lq.bam.pbi" + } + } + ] + }, + { + "singletons_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.singletons.bam": { + "type": "file", + "description": "Unclustered reads (when --singletons is set)", + "pattern": "*.transcripts.singletons.bam" + } + } + ] + }, + { + "singletons_pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.singletons.bam.pbi": { + "type": "file", + "description": "Pacbio index of unclustered reads (when --singletons is set)", + "pattern": "*.transcripts.singletons.bam.pbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72325,80 +90718,133 @@ "tool_dev_url": "https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md", "licence": [ "BSD-3-Clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file, cleaned ccs generated by lima", - "pattern": "*.bam" - } - }, - { - "primers": { - "type": "file", - "description": "fasta file of primers", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Set of complete reads (with polyA tail), where the polyA has been trimmed", - "pattern": "*.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "Pacbio index file from polyA trimmed reads", - "pattern": "*.pbi" - } - }, - { - "consensusreadset": { - "type": "file", - "description": "Metadata about read library", - "pattern": "*.xml" - } - }, - { - "summary": { - "type": "file", - "description": "json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads", - "pattern": "*.json" - } - }, - { - "report": { - "type": "file", - "description": "Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)", - "pattern": "*.csv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file, cleaned ccs generated by lima", + "pattern": "*.bam" + } + } + ], + [ + { + "primers": { + "type": "file", + "description": "fasta file of primers", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Set of complete reads (with polyA tail), where the polyA has been trimmed", + "pattern": "*.bam" + } + } + ] + }, + { + "pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam.pbi": { + "type": "file", + "description": "Pacbio index file from polyA trimmed reads", + "pattern": "*.pbi" + } + } + ] + }, + { + "consensusreadset": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.consensusreadset.xml": { + "type": "file", + "description": "Metadata about read library", + "pattern": "*.xml" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.filter_summary.report.json": { + "type": "file", + "description": "json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads", + "pattern": "*.json" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.report.csv": { + "type": "file", + "description": "Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)", + "pattern": "*.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72435,73 +90881,108 @@ "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", - "pattern": "*.bam" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference sequence used for mapping and generating the BAM file", - "pattern": "*.fa" - } - }, - { - "save_mpileup": { - "type": "boolean", - "description": "Save mpileup file generated by ivar consensus", - "patter": "*.mpileup" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "iVar generated consensus sequence", - "pattern": "*.fa" - } - }, - { - "qual": { - "type": "file", - "description": "iVar generated quality file", - "pattern": "*.qual.txt" - } - }, - { - "mpileup": { - "type": "file", - "description": "mpileup output from samtools mpileup [OPTIONAL]", - "pattern": "*.mpileup" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:andersen-lab_ivar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", + "pattern": "*.bam" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference sequence used for mapping and generating the BAM file", + "pattern": "*.fa" + } + } + ], + [ + { + "save_mpileup": { + "type": "boolean", + "description": "Save mpileup file generated by ivar consensus", + "patter": "*.mpileup" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "iVar generated consensus sequence", + "pattern": "*.fa" + } + } + ] + }, + { + "qual": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.qual.txt": { + "type": "file", + "description": "iVar generated quality file", + "pattern": "*.qual.txt" + } + } + ] + }, + { + "mpileup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup": { + "type": "file", + "description": "mpileup output from samtools mpileup [OPTIONAL]", + "pattern": "*.mpileup" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72540,66 +91021,89 @@ "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Co-ordinate sorted BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Index file for co-ordinate sorted BAM file", - "pattern": "*.bai" - } - }, - { - "bed": { - "type": "file", - "description": "BED file with primer labels and positions", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "iVar generated trimmed bam file (unsorted)", - "pattern": "*.bam" - } - }, - { - "log": { - "type": "file", - "description": "Log file generated by iVar for use with MultiQC", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:andersen-lab_ivar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Co-ordinate sorted BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "Index file for co-ordinate sorted BAM file", + "pattern": "*.bai" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "BED file with primer labels and positions", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "iVar generated trimmed bam file (unsorted)", + "pattern": "*.bam" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file generated by iVar for use with MultiQC", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72638,80 +91142,109 @@ "documentation": "https://andersen-lab.github.io/ivar/html/manualpage.html", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", - "pattern": "*.bam" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference sequence used for mapping and generating the BAM file", - "pattern": "*.fa" - } - }, - { - "fai": { - "type": "file", - "description": "The index for the reference sequence used for mapping and generating the BAM file", - "pattern": "*.fai" - } - }, - { - "gff": { - "type": "file", - "description": "A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.", - "patter": "*.gff" - } - }, - { - "save_mpileup": { - "type": "boolean", - "description": "Save mpileup file generated by ivar variants", - "patter": "*.mpileup" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "iVar generated TSV file with the variants", - "pattern": "*.tsv" - } - }, - { - "mpileup": { - "type": "file", - "description": "mpileup output from samtools mpileup [OPTIONAL]", - "pattern": "*.mpileup" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:andersen-lab_ivar" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "A sorted (with samtools sort) and trimmed (with iVar trim) bam file", + "pattern": "*.bam" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference sequence used for mapping and generating the BAM file", + "pattern": "*.fa" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "The index for the reference sequence used for mapping and generating the BAM file", + "pattern": "*.fai" + } + } + ], + [ + { + "gff": { + "type": "file", + "description": "A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.", + "patter": "*.gff" + } + } + ], + [ + { + "save_mpileup": { + "type": "boolean", + "description": "Save mpileup file generated by ivar variants", + "patter": "*.mpileup" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "iVar generated TSV file with the variants", + "pattern": "*.tsv" + } + } + ] + }, + { + "mpileup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup": { + "type": "file", + "description": "mpileup output from samtools mpileup [OPTIONAL]", + "pattern": "*.mpileup" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72753,92 +91286,109 @@ "tool_dev_url": "https://github.com/mkirsche/Jasmine", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "The VCF files that need to be merged\n", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "bams": { - "type": "list", - "description": "Optional - The BAM files from which the VCFs were created", - "pattern": "*.bam" - } - }, - { - "sample_dists": { - "type": "file", - "description": "Optional - A txt file containing the distance thresholds for each sample", - "pattern": "*.txt" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional - The reference FASTA file used to create the VCFs", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Optional - The index of the reference FASTA file used to create the VCFs", - "pattern": "*.fai" - } - }, - { - "chr_norm": { - "type": "file", - "description": "Optional - A txt file containing the chromosomes and their aliases for normalization", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The merged VCF file", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "The VCF files that need to be merged\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "bams": { + "type": "list", + "description": "Optional - The BAM files from which the VCFs were created", + "pattern": "*.bam" + } + }, + { + "sample_dists": { + "type": "file", + "description": "Optional - A txt file containing the distance thresholds for each sample", + "pattern": "*.txt" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Optional - The reference FASTA file used to create the VCFs", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Optional - The index of the reference FASTA file used to create the VCFs", + "pattern": "*.fai" + } + } + ], + [ + { + "chr_norm": { + "type": "file", + "description": "Optional - A txt file containing the chromosomes and their aliases for normalization", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The merged VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -72873,7 +91423,8 @@ "tool_dev_url": "https://github.com/mwouts/jupytext/", "license": [ "MIT" - ] + ], + "identifier": "" } }, { @@ -72884,7 +91435,8 @@ "tool_dev_url": "https://github.com/nteract/papermill", "license": [ "BSD 3-clause" - ] + ], + "identifier": "" } }, { @@ -72895,65 +91447,322 @@ "tool_dev_url": "https://github.com/jupyter/nbconvert", "license": [ "BSD 3-clause" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "notebook": { + "type": "file", + "description": "Jupyter notebook or jupytext representation thereof", + "pattern": "*.{ipynb,py,md,Rmd,myst}" + } + } + ], + [ + { + "parameters": { + "type": "map", + "description": "Groovy map with notebook parameters which will be passed\nto papermill in order to create parametrized reports.\n" + } + } + ], + [ + { + "input_files": { + "type": "file", + "description": "One or multiple files serving as input data for the notebook.", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML report generated from Jupyter notebook", + "pattern": "*.html" + } + } + ] + }, + { + "artifacts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "artifacts/": { + "type": "directory", + "description": "Directory containing all artifacts generated by the notebook", + "pattern": "artifacts/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, + "authors": [ + "@grst" + ], + "maintainers": [ + "@grst" + ] + } + }, + { + "name": "jvarkit_vcffilterjdk", + "path": "modules/nf-core/jvarkit/vcffilterjdk/meta.yml", + "type": "module", + "meta": { + "name": "jvarkit_vcffilterjdk", + "description": "Filtering VCF with dynamically-compiled java expressions", + "keywords": [ + "vcf", + "bcf", + "filter", + "variant", + "java", + "script" + ], + "tools": [ { - "notebook": { - "type": "file", - "description": "Jupyter notebook or jupytext representation thereof", - "pattern": "*.{ipynb,py,md,Rmd,myst}" + "jvarkit": { + "description": "Java utilities for Bioinformatics.", + "homepage": "https://github.com/lindenb/jvarkit", + "documentation": "https://jvarkit.readthedocs.io/", + "tool_dev_url": "https://github.com/lindenb/jvarkit", + "doi": "10.1093/bioinformatics/btx734 ", + "licence": [ + "MIT License" + ], + "args_id": "$args2", + "identifier": "" } }, { - "parameters": { - "type": "map", - "description": "Groovy map with notebook parameters which will be passed\nto papermill in order to create parametrized reports.\n" - } - }, - { - "input_files": { - "type": "file", - "description": "One or multiple files serving as input data for the notebook.", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "HTML report generated from Jupyter notebook", - "pattern": "*.html" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bcftools": { + "description": "View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF\n", + "homepage": "http://samtools.github.io/bcftools/bcftools.html", + "documentation": "http://www.htslib.org/doc/bcftools.html", + "doi": "10.1093/bioinformatics/btp352", + "licence": [ + "MIT" + ], + "args_id": [ + "$args1", + "$args3" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF/BCF file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "Optional VCF/BCF index file", + "pattern": "*.{tbi,csi}" + } + }, + { + "regions_file": { + "type": "file", + "description": "Optional. Restrict to regions listed in a file", + "pattern": "*.{bed,bed.gz,txt,tsv}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta reference file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta.fai information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Fasta file index", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing fasta.dict information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing code information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "code": { + "type": "file", + "description": "File containing custom user code . May be empty if script if provided via `task.ext.args2`.", + "pattern": "*.{code,script,txt,tsv,java,js}" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing pedigree information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "pedigree": { + "type": "file", + "description": "Optional jvarkit pedigree.", + "pattern": "*.{tsv,ped,pedigree}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF filtered output file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ - "@grst" + "@lindenb" ], "maintainers": [ - "@grst" + "@lindenb" ] } }, @@ -72967,10 +91776,8 @@ "keywords": [ "vcf", "bcf", - "variant", "annotation", - "repeats", - "polyx" + "repeats" ], "tools": [ { @@ -72983,7 +91790,7 @@ "licence": [ "MIT License" ], - "args_id": "$args2" + "identifier": "" } }, { @@ -72995,115 +91802,134 @@ "licence": [ "MIT" ], - "args_id": [ - "$args1", - "$args3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta.fai information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing fasta.dict information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Groovy Map containing reference genome information for vcf", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "Optional VCF/BCF index file", - "pattern": "*.{tbi,csi}" - } - }, - { - "regions_file": { - "type": "file", - "description": "Optional. Restrict to regions listed in a file", - "pattern": "*.{bed,bed.gz,txt,tsv}" - } - }, - { - "fasta": { - "type": "file", - "description": "Groovy Map containing reference genome information for fai reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Groovy Map containing reference genome information for fai", - "pattern": "*.fasta.fai" - } - }, - { - "dict": { - "type": "file", - "description": "Groovy Map containing reference genome information for GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF filtered output file", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "csi": { - "type": "file", - "description": "Default VCF file index", - "pattern": "*.csi" - } - }, - { - "tbi": { - "type": "file", - "description": "Alternative VCF file index", - "pattern": "*.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Groovy Map containing reference genome information for vcf", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Groovy Map containing reference genome information for fai reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta.fai information\n" + } + }, + { + "fai": { + "type": "file", + "description": "Groovy Map containing reference genome information for fai", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing fasta.dict information\n" + } + }, + { + "dict": { + "type": "file", + "description": "Groovy Map containing reference genome information for GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${extension}": { + "type": "file", + "description": "VCF filtered output file", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Alternative VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing VCF information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Default VCF file index", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73140,91 +91966,108 @@ "doi": "10.6084/m9.figshare.1425030", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fai information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference dict information\ne.g. [ id:'test_reference' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing Sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output": { - "type": "file", - "description": "Output SVG file", - "pattern": "*.svg" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fai information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference dict information\ne.g. [ id:'test_reference' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing Sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Output SVG file", + "pattern": "*.svg" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73258,51 +92101,64 @@ "doi": "10.1038/ncomms11257", "licence": [ "GNU GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}" - } - }, - { - "db": { - "type": "directory", - "description": "List containing the database and nodes files for Kaiju\ne.g. [ 'database.fmi', 'nodes.dmp' ]\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "file", - "description": "Results with taxonomic classification of each read", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "List containing the database and nodes files for Kaiju\ne.g. [ 'database.fmi', 'nodes.dmp' ]\n" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results with taxonomic classification of each read", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73346,45 +92202,64 @@ "doi": "10.1038/ncomms11257", "licence": [ "GNU GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Kaiju tab-separated output file", - "pattern": "*.{tsv,txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Krona text-based input file converted from Kaiju report", - "pattern": "*.{txt,krona}" - } + ], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tsv": { + "type": "file", + "description": "Kaiju tab-separated output file", + "pattern": "*.{tsv,txt}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Kaiju database file" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Krona text-based input file converted from Kaiju report", + "pattern": "*.{txt,krona}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73423,51 +92298,71 @@ "doi": "10.1038/ncomms11257", "licence": [ "GNU GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "file", - "description": "File containing the kaiju classification results", - "pattern": "*.{txt}" - } - }, - { - "taxon_rank": { - "type": "string", - "description": "Taxonomic rank to display in report\npattern: \"phylum|class|order|family|genus|species\"\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "file", - "description": "Summary table for a given taxonomic rank\n", - "pattern": "*.{tsv}" - } + ], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Kaiju input file" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Kaiju database" + } + } + ], + [ + { + "taxon_rank": { + "type": "string", + "description": "Taxonomic rank to display in report\npattern: \"phylum|class|order|family|genus|species\"\n" + } + } + ] + ], + "output": [ + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Kaiju output file", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73511,57 +92406,70 @@ "doi": "10.1038/ncomms11257", "licence": [ "GNU GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "kaiju": { - "type": "file", - "description": "Results with taxonomic classification of each read from Kaiju\n" - } - }, - { - "kraken": { - "type": "file", - "description": "Results with taxonomic classification of each read from Kraken\n", - "pattern": "*.{tsv}" - } - }, - { - "db": { - "type": "directory", - "description": "List containing the database and nodes files for Kaiju\ne.g. [ 'database.fmi', 'nodes.dmp' ]\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "merged": { - "type": "file", - "description": "Results with merged taxonomic classification of each read based on the given strategy '1', '2', 'lca' [default] or 'lowest'", - "pattern": "*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:kaiju" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kaiju": { + "type": "file", + "description": "Results with taxonomic classification of each read from Kaiju\n" + } + }, + { + "kraken": { + "type": "file", + "description": "Results with taxonomic classification of each read from Kraken\n", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "List containing the database and nodes files for Kaiju\ne.g. [ 'database.fmi', 'nodes.dmp' ]\n" + } + } + ] + ], + "output": [ + { + "merged": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results with merged taxonomic classification of each read based on the given strategy '1', '2', 'lca' [default] or 'lowest'", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73597,45 +92505,56 @@ "doi": "10.1038/ncomms11257", "licence": [ "GNU GPL v3" - ] + ], + "identifier": "biotools:kaiju" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Uncompressed Protein FASTA file (mandatory)", - "pattern": "*.{fa,faa,fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Uncompressed Protein FASTA file (mandatory)", + "pattern": "*.{fa,faa,fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fmi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fmi": { + "type": "file", + "description": "Kaiju FM-index file", + "pattern": "*.{fmi}" + } + } + ] }, { - "fmi": { - "type": "file", - "description": "Kaiju FM-index file", - "pattern": "*.{fmi}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73671,51 +92590,64 @@ "doi": "10.1093/bioinformatics/btz795", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Alignment file. May be gzipped or uncompressed, depending on if `compress` is set to `true` or `false`.", - "pattern": "*.{aln}{.gz,}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:kalign" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file. May be gzipped or uncompressed, depending on if `compress` is set to `true` or `false`.", + "pattern": "*.{aln}{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73755,45 +92687,56 @@ "tool_dev_url": "https://github.com/pachterlab/kallisto", "licence": [ "BSD-2-Clause" - ] + ], + "identifier": "biotools:kallisto" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "genome fasta file", - "pattern": "*.{fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "genome fasta file", + "pattern": "*.{fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Kallisto genome index", - "pattern": "*.idx" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "kallisto": { + "type": "directory", + "description": "Kallisto genome index", + "pattern": "*.idx" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -73836,103 +92779,142 @@ "doi": "10.1038/nbt.3519", "licence": [ "BSD_2_clause" - ] - } + ], + "identifier": "biotools:kallisto" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fastq,fastq.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "Kallisto genome index.", + "pattern": "*.idx" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "Optional gtf file for translation of transcripts into genomic coordinates.", + "pattern": "*.gtf" + } + } + ], + [ + { + "chromosomes": { + "type": "file", + "description": "Optional tab separated file with chromosome names and lengths.", + "pattern": "*.tsv" + } + } + ], + [ + { + "fragment_length": { + "type": "integer", + "description": "For single-end mode only, the estimated average fragment length." + } + } + ], + [ + { + "fragment_length_sd": { + "type": "integer", + "description": "For single-end mode only, the estimated standard deviation of the fragment length." + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Kallisto output file" + } + } + ] + }, + { + "json_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.run_info.json": { + "type": "file", + "description": "JSON file containing information about the run", + "pattern": "*.run_info.json" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File containing log information from running kallisto quant", + "pattern": "*.log.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "*.{fastq,fastq.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Kallisto genome index.", - "pattern": "*.idx" - } - }, - { - "gtf": { - "type": "file", - "description": "Optional gtf file for translation of transcripts into genomic coordinates.", - "pattern": "*.gtf" - } - }, - { - "chromosomes": { - "type": "file", - "description": "Optional tab separated file with chromosome names and lengths.", - "pattern": "*.tsv" - } - }, - { - "fragment_length": { - "type": "integer", - "description": "For single-end mode only, the estimated average fragment length." - } - }, - { - "fragment_length_sd": { - "type": "integer", - "description": "For single-end mode only, the estimated standard deviation of the fragment length." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "File containing log information from running kallisto quant", - "pattern": "*.log.txt" - } - }, - { - "abundance": { - "type": "file", - "description": "Plaintext file of the abundance estimates", - "pattern": "abundance.tsv" - } - }, - { - "abundance_hdf5": { - "type": "file", - "description": "A HDF5 binary file containing run info, abundance estimates, bootstrap\nestimates, and transcript length information\n", - "pattern": "abundance.h5" - } - }, - { - "run_info": { - "type": "file", - "description": "A json file containing information about the run", - "pattern": "run_info.json" - } - } - ], - "authors": [ - "@anoronh4" + "authors": [ + "@anoronh4" ], "maintainers": [ "@anoronh4" @@ -73972,86 +92954,120 @@ "tool_dev_url": "https://github.com/pachterlab/kb_python", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "index": { - "type": "file", - "description": "kb-ref index file (.idx)", - "pattern": "*.{idx}" - } - }, - { - "t2g": { - "type": "file", - "description": "t2g file from kallisto", - "pattern": "*t2g.txt" - } - }, - { - "t1c": { - "type": "file", - "description": "kb ref's c1 cdna_t2c file", - "pattern": "*.{cdna_t2c.txt}" - } - }, - { - "t2c": { - "type": "file", - "description": "kb ref's c2 intron_t2c file", - "pattern": "*.{intron_t2c.txt}" - } - }, - { - "workflow_mode": { - "type": "string", - "description": "String value defining workflow to use, can be one of \"standard\", \"nac\", \"lamanno\" (obsolete)", - "pattern": "{standard,lamanno,nac}" - } - }, - { - "technology": { - "type": "string", - "description": "String value defining the sequencing technology used.", - "pattern": "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "count": { - "type": "file", - "description": "kb count output folder", - "pattern": "*.{count}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "index": { + "type": "file", + "description": "kb-ref index file (.idx)", + "pattern": "*.{idx}" + } + } + ], + [ + { + "t2g": { + "type": "file", + "description": "t2g file from kallisto", + "pattern": "*t2g.txt" + } + } + ], + [ + { + "t1c": { + "type": "file", + "description": "kb ref's c1 cdna_t2c file", + "pattern": "*.{cdna_t2c.txt}" + } + } + ], + [ + { + "t2c": { + "type": "file", + "description": "kb ref's c2 intron_t2c file", + "pattern": "*.{intron_t2c.txt}" + } + } + ], + [ + { + "technology": { + "type": "string", + "description": "String value defining the sequencing technology used.", + "pattern": "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" + } + } + ], + [ + { + "workflow_mode": { + "type": "string", + "description": "String value defining workflow to use, can be one of \"standard\", \"nac\", \"lamanno\" (obsolete)", + "pattern": "{standard,lamanno,nac}" + } + } + ] + ], + "output": [ + { + "count": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.count": { + "type": "file", + "description": "kb count output folder", + "pattern": "*.{count}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "matrix": [ + { + "*.count/*/*.mtx": { + "type": "file", + "description": "file containing the count matrix", + "pattern": "*.mtx" + } + } + ] } ], "authors": [ @@ -74093,82 +93109,117 @@ "doi": "10.22002/D1.1876", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Genomic DNA fasta file", - "pattern": "*.{fasta,fasta.gz}" - } - }, - { - "gtf": { - "type": "file", - "description": "Genomic gtf file", - "pattern": "*.{gtf,gtf.gz}" - } - }, - { - "workflow_mode": { - "type": "string", - "description": "String value defining workflow to use, can be one of \"standard\", \"nac\", \"lamanno\" (obsolete)", - "pattern": "{standard,lamanno,nac}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "kb_ref_idx": { - "type": "file", - "description": "Index file from kb ref.", - "pattern": "*.{idx}" - } - }, - { - "t2g": { - "type": "file", - "description": "Transcript to gene table", - "pattern": "*t2g.{txt}" - } - }, - { - "cdna": { - "type": "file", - "description": "cDNA fasta file", - "pattern": "*cdna.{fa}" - } - }, - { - "intron": { - "type": "file", - "description": "Intron fasta file", - "pattern": "*intron.{fa}" - } - }, - { - "cdna_t2c": { - "type": "file", - "description": "cDNA transcript to capture file", - "pattern": "*cdna_t2c.{txt}" - } - }, - { - "intron_t2c": { - "type": "file", - "description": "Intron transcript to capture file", - "pattern": "*intron_t2c.{txt}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "fasta": { + "type": "file", + "description": "Genomic DNA fasta file", + "pattern": "*.{fasta,fasta.gz}" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "Genomic gtf file", + "pattern": "*.{gtf,gtf.gz}" + } + } + ], + [ + { + "workflow_mode": { + "type": "string", + "description": "String value defining workflow to use, can be one of \"standard\", \"nac\", \"lamanno\" (obsolete)", + "pattern": "{standard,lamanno,nac}" + } + } + ] + ], + "output": [ + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "index": [ + { + "kb_ref_out.idx": { + "type": "file", + "description": "kb ref index file", + "pattern": "*kb_ref_out.idx" + } + } + ] + }, + { + "t2g": [ + { + "t2g.txt": { + "type": "file", + "description": "Transcript to gene table", + "pattern": "*t2g.{txt}" + } + } + ] + }, + { + "cdna": [ + { + "cdna.fa": { + "type": "file", + "description": "cDNA fasta file", + "pattern": "*cdna.{fa}" + } + } + ] + }, + { + "intron": [ + { + "intron.fa": { + "type": "file", + "description": "Intron fasta file", + "pattern": "*intron.{fa}" + } + } + ] + }, + { + "cdna_t2c": [ + { + "cdna_t2c.txt": { + "type": "file", + "description": "cDNA transcript to capture file", + "pattern": "*cdna_t2c.{txt}" + } + } + ] + }, + { + "intron_t2c": [ + { + "intron_t2c.txt": { + "type": "file", + "description": "Intron transcript to capture file", + "pattern": "*intron_t2c.{txt}" + } + } + ] } ], "authors": [ @@ -74207,79 +93258,140 @@ "doi": "10.1093/bioinformatics/btw663", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hist": { - "type": "file", - "description": "KAT histogram of k-mer counts", - "pattern": "*.hist" - } - }, - { - "json": { - "type": "file", - "description": "KAT histogram summary of distance analysis", - "pattern": "*.hist.dist_analysis.json" - } - }, - { - "png": { - "type": "file", - "description": "KAT plot of k-mer histogram in PNG format", - "pattern": "*.png" - } - }, - { - "ps": { - "type": "file", - "description": "KAT plot of k-mer histogram in PS format", - "pattern": "*.ps" - } - }, - { - "pdf": { - "type": "file", - "description": "KAT plot of k-mer histogram in PDF format", - "pattern": "*.pdf" - } - }, - { - "jellyfish_hash": { - "type": "file", - "description": "Jellyfish hash file", - "pattern": "*-hist.jf*" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ] + ], + "output": [ + { + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "KAT histogram of k-mer counts", + "pattern": "*.hist" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist.dist_analysis.json": { + "type": "file", + "description": "KAT histogram summary of distance analysis", + "pattern": "*.hist.dist_analysis.json" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "KAT plot of k-mer histogram in PNG format", + "pattern": "*.png" + } + } + ] + }, + { + "ps": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ps": { + "type": "file", + "description": "KAT plot of k-mer histogram in PS format", + "pattern": "*.ps" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "KAT plot of k-mer histogram in PDF format", + "pattern": "*.pdf" + } + } + ] + }, + { + "jellyfish_hash": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-hash.jf*": { + "type": "file", + "description": "Jellyfish hash file", + "pattern": "*-hist.jf*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74312,46 +93424,61 @@ "doi": "10.12688/f1000research.6924.1", "licence": [ "BSD License" - ] + ], + "identifier": "biotools:khmer" } } ], "input": [ - { - "pe_reads": { - "type": "file", - "description": "Paired-end interleaved fastq files", - "pattern": "*.{fq,fastq}.gz" + [ + { + "pe_reads": { + "type": "file", + "description": "Paired-end interleaved fastq files", + "pattern": "*.{fq,fastq}.gz" + } } - }, - { - "se_reads": { - "type": "file", - "description": "Single-end fastq files", - "pattern": "*.{fq,fastq}.gz" + ], + [ + { + "se_reads": { + "type": "file", + "description": "Single-end fastq files", + "pattern": "*.{fq,fastq}.gz" + } } - }, - { - "name": { - "type": "string", - "description": "filename for output file(s); \".fastq.gz\" will be appended" + ], + [ + { + "name": { + "type": "string", + "description": "filename for output file(s); \".fastq.gz\" will be appended" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "reads": [ + { + "${name}.fastq.gz": { + "type": "file", + "description": "Interleaved fastq files", + "pattern": "*.{fq,fastq}.gz" + } + } + ] }, { - "reads": { - "type": "file", - "description": "Interleaved fastq files", - "pattern": "*.{fq,fastq}.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74384,46 +93511,63 @@ "doi": "10.12688/f1000research.6924.1", "licence": [ "BSD License" - ] + ], + "identifier": "biotools:khmer" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fa,fasta}" + [ + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fa,fasta}" + } } - }, - { - "kmer_size": { - "type": "integer", - "description": "k-mer size to use" + ], + [ + { + "kmer_size": { + "type": "integer", + "description": "k-mer size to use" + } } - } + ] ], "output": [ { - "report": { - "type": "file", - "description": "Text file containing unique-kmers.py execution report", - "pattern": "report.txt" - } + "report": [ + { + "report.txt": { + "type": "file", + "description": "Text file containing unique-kmers.py execution report", + "pattern": "report.txt" + } + } + ] }, { - "kmers": { - "type": "file", - "description": "Text file containing number of kmers", - "pattern": "kmers.txt" - } + "kmers": [ + { + "kmers.txt": { + "type": "file", + "description": "Text file containing number of kmers", + "pattern": "kmers.txt" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74467,45 +93611,56 @@ "doi": "10.1038/s41467-021-24448-3", "licence": [ "GPL v3 or later (GPL v3+)" - ] + ], + "identifier": "biotools:kleborate" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastas": { - "type": "list", - "description": "Klebsiella genome assemblies to be screened", - "pattern": "*.fasta" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastas": { + "type": "list", + "description": "Klebsiella genome assemblies to be screened", + "pattern": "*.fasta" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Result file generated after screening", + "pattern": "*.txt" + } + } + ] }, { - "txt": { - "type": "file", - "description": "Result file generated after screening", - "pattern": "*.txt" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74543,52 +93698,73 @@ "doi": "10.1093/bioinformatics/btac845", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "fasta file, or a directory containing FASTA files", - "pattern": "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "outdir": { - "type": "directory", - "description": "Output directory containing all .unik files and a summary file in .txt format. Every .unik file contains the sequence/reference ID,chunk index, number of chunks, and genome size of reference.", - "pattern": "*/" - } - }, - { - "info": { - "type": "file", - "description": "Summary file that is generated for later use", - "pattern": "*_info.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "fasta file, or a directory containing FASTA files", + "pattern": "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" + } + } + ] + ], + "output": [ + { + "outdir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Output directory containing all .unik files and a summary file in .txt format. Every .unik file contains the sequence/reference ID,chunk index, number of chunks, and genome size of reference.", + "pattern": "*/" + } + } + ] + }, + { + "info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/_info.txt": { + "type": "file", + "description": "Summary file that is generated for later use", + "pattern": "*_info.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74625,52 +93801,73 @@ "doi": "10.1093/bioinformatics/btac845", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "compute_dir": { - "type": "directory", - "description": "Output directory generated by \"kmcp compute\"", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "kmcp": { - "type": "directory", - "description": "Output directory containing the database from k-mer files.", - "pattern": "*/" - } - }, - { - "log": { - "type": "file", - "description": "A log of kmcp/index output", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "compute_dir": { + "type": "directory", + "description": "Output directory generated by \"kmcp compute\"", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "kmcp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Output directory containing the database from k-mer files.", + "pattern": "*/" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "A log of kmcp/index output", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74706,45 +93903,56 @@ "doi": "10.1093/bioinformatics/btac845", "license": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "search_out": { - "type": "file", - "description": "The output file created by kmcp search", - "pattern": "*.gz" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "search_out": { + "type": "file", + "description": "The output file created by kmcp search", + "pattern": "*.gz" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "Output file in gzipped format", + "pattern": "*.gz" + } + } + ] }, { - "result": { - "type": "file", - "description": "Output file in gzipped format", - "pattern": "*.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74781,51 +93989,64 @@ "doi": "10.1093/bioinformatics/btac845", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "search_results": { - "type": "file", - "description": "Gzipped file output from kmcp search module", - "pattern": "*.gz" - } - }, - { - "db": { - "type": "directory", - "description": "Database directory containing taxdump files and taxid file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "profile": { - "type": "file", - "description": "Tab-delimited format file with 17 columns.", - "pattern": "*.profile" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "search_results": { + "type": "file", + "description": "Gzipped file output from kmcp search module", + "pattern": "*.gz" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Database directory containing taxdump files and taxid file" + } + } + ] + ], + "output": [ + { + "profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.profile": { + "type": "file", + "description": "Tab-delimited format file with 17 columns.", + "pattern": "*.profile" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74867,52 +94088,65 @@ "doi": "10.1093/bioinformatics/btac845", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "gzipped fasta or fastq files", - "pattern": "*.{fq.gz,fastq.gz,fa.gz}" - } - }, - { - "db": { - "type": "directory", - "description": "Database directory created by \"kmcp index\"", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "result": { - "type": "file", - "description": "Output file in tab-delimited format with 15 columns", - "pattern": "*.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "gzipped fasta or fastq files", + "pattern": "*.{fq.gz,fastq.gz,fa.gz}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Database directory created by \"kmcp index\"", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "Output file in tab-delimited format with 15 columns", + "pattern": "*.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -74951,60 +94185,93 @@ "doi": "10.1093/bioinformatics/btz859", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing query sequences", - "pattern": "*.{fa,fasta}" - } - }, - { - "profiles": { - "type": "directory", - "description": "Directory containing the Profiles database", - "pattern": "*" - } - }, - { - "ko_list": { - "type": "file", - "description": "File containing list of KO entries with their data", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "txt": { - "type": "file", - "description": "Application-specific text file with hits information", - "pattern": "*.{txt}" - } - }, - { - "tsv": { - "type": "file", - "description": "Tab separated file containing with detailed hits", - "pattern": "*.{tsv}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:kofamscan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing query sequences", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "profiles": { + "type": "directory", + "description": "Directory containing the Profiles database", + "pattern": "*" + } + } + ], + [ + { + "ko_list": { + "type": "file", + "description": "File containing list of KO entries with their data", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "file", + "description": "Application-specific text file with hits information", + "pattern": "*.{txt}" + } + }, + { + "*.txt": { + "type": "file", + "description": "Application-specific text file with hits information", + "pattern": "*.{txt}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "file", + "description": "Tab separated file containing with detailed hits", + "pattern": "*.{tsv}" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab separated file containing with detailed hits", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75040,66 +94307,83 @@ "doi": "10.1186/s13059-019-1891-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file that will be added to the database", - "pattern": "*.{fa,fasta,fna,ffn}" - } - }, - { - "taxonomy_names": { - "type": "file", - "description": "used for associating sequences with taxonomy IDs", - "pattern": "*.dmp" - } - }, - { - "taxonomy_nodes": { - "type": "file", - "description": "tree nodes using NCBI taxonomy nomenclature", - "pattern": "*.dmp" - } - }, - { - "accession2taxid": { - "type": "file", - "description": "associates sequence accession IDs to taxonomy IDs", - "pattern": "*.accession2taxid" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "contains required files to build the database", - "pattern": "*/" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:kraken2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file that will be added to the database", + "pattern": "*.{fa,fasta,fna,ffn}" + } + } + ], + [ + { + "taxonomy_names": { + "type": "file", + "description": "used for associating sequences with taxonomy IDs", + "pattern": "*.dmp" + } + } + ], + [ + { + "taxonomy_nodes": { + "type": "file", + "description": "tree nodes using NCBI taxonomy nomenclature", + "pattern": "*.dmp" + } + } + ], + [ + { + "accession2taxid": { + "type": "file", + "description": "associates sequence accession IDs to taxonomy IDs", + "pattern": "*.accession2taxid" + } + } + ] + ], + "output": [ + { + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$prefix": { + "type": "directory", + "description": "contains required files to build the database", + "pattern": "*/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75141,51 +94425,64 @@ "licence": [ "MIT" ], - "args_id": "$args" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "contains required files to build the database", - "pattern": "*/" - } - }, - { - "cleaning": { - "type": "boolean", - "description": "activate or deactivate (true or false) cleaning of intermediate files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "contains the database that can be used to perform taxonomic classification", - "pattern": "*/" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "args_id": "$args", + "identifier": "biotools:kraken2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "db": { + "type": "directory", + "description": "contains required files to build the database", + "pattern": "*/" + } + } + ], + [ + { + "cleaning": { + "type": "boolean", + "description": "activate or deactivate (true or false) cleaning of intermediate files" + } + } + ] + ], + "output": [ + { + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$prefix": { + "type": "directory", + "description": "contains the database that can be used to perform taxonomic classification", + "pattern": "*/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75229,32 +94526,43 @@ "licence": [ "MIT" ], - "args_id": "$args" + "args_id": "$args", + "identifier": "biotools:kraken2" } } ], "input": [ - { - "cleaning": { - "type": "boolean", - "description": "activate or deactivate (true or false) cleaning of intermediate files" + [ + { + "cleaning": { + "type": "boolean", + "description": "activate or deactivate (true or false) cleaning of intermediate files" + } } - } + ] ], "output": [ { - "db": { - "type": "directory", - "description": "Directory containing the Kraken2 'standard' database that can be used to perform taxonomic classification", - "pattern": "*/" - } + "db": [ + { + "$prefix": { + "type": "directory", + "description": "Directory containing the Kraken2 'standard' database that can be used to perform taxonomic classification", + "pattern": "*/" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75287,82 +94595,129 @@ "doi": "10.1186/s13059-019-1891-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "db": { - "type": "directory", - "description": "Kraken2 database" - } - }, - { - "save_output_fastqs": { - "type": "string", - "description": "If true, optional commands are added to save classified and unclassified reads\nas fastq files\n" - } - }, - { - "save_reads_assignment": { - "type": "string", - "description": "If true, an optional command is added to save a file reporting the taxonomic\nclassification of each input read\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "classified_reads_fastq": { - "type": "file", - "description": "Reads classified as belonging to any of the taxa\non the Kraken2 database.\n", - "pattern": "*{fastq.gz}" - } - }, - { - "unclassified_reads_fastq": { - "type": "file", - "description": "Reads not classified to any of the taxa\non the Kraken2 database.\n", - "pattern": "*{fastq.gz}" - } - }, - { - "classified_reads_assignment": { - "type": "file", - "description": "Kraken2 output file indicating the taxonomic assignment of\neach input read\n" - } - }, - { - "report": { - "type": "file", - "description": "Kraken2 report containing stats about classified\nand not classifed reads.\n", - "pattern": "*.{report.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:kraken2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "Kraken2 database" + } + } + ], + [ + { + "save_output_fastqs": { + "type": "string", + "description": "If true, optional commands are added to save classified and unclassified reads\nas fastq files\n" + } + } + ], + [ + { + "save_reads_assignment": { + "type": "string", + "description": "If true, an optional command is added to save a file reporting the taxonomic\nclassification of each input read\n" + } + } + ] + ], + "output": [ + { + "classified_reads_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.classified{.,_}*": { + "type": "file", + "description": "Reads classified as belonging to any of the taxa\non the Kraken2 database.\n", + "pattern": "*{fastq.gz}" + } + } + ] + }, + { + "unclassified_reads_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unclassified{.,_}*": { + "type": "file", + "description": "Reads not classified to any of the taxa\non the Kraken2 database.\n", + "pattern": "*{fastq.gz}" + } + } + ] + }, + { + "classified_reads_assignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*classifiedreads.txt": { + "type": "file", + "description": "Kraken2 output file indicating the taxonomic assignment of\neach input read\n" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "Kraken2 report containing stats about classified\nand not classifed reads.\n", + "pattern": "*.{report.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75427,45 +94782,56 @@ "homepage": "https://github.com/jenniferlu717/KrakenTools", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:krakentools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "kreports": { - "type": "file", - "description": "List of kraken-style report files", - "pattern": "*.{txt,kreport}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kreports": { + "type": "file", + "description": "List of kraken-style report files", + "pattern": "*.{txt,kreport}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Combined kreport file of all input files", + "pattern": "*.txt" + } + } + ] }, { - "txt": { - "type": "file", - "description": "Combined kreport file of all input files", - "pattern": "*.txt" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75504,65 +94870,94 @@ "doi": "10.1038/s41596-022-00738-y", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "taxid": { - "type": "string", - "description": "A list of taxid separated by spaces" - } - }, - { - "classified_reads_assignment": { - "type": "file", - "description": "A file contains the taxonomic classification of each input read.", - "pattern": "*.{classifiedreads.txt}" - } - }, - { - "classified_reads_fastq": { - "type": "file", - "description": "Classified reads as belonging to any of the taxa on the kraken2 database.", - "pattern": "*.{fastq.gz}" - } - }, - { - "report": { - "type": "file", - "description": "Optional Kraken2 report containing stats about classified and not classifed reads.", - "pattern": "*.{report.txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "extracted_kraken2_reads": { - "type": "file", - "description": "Reads assigned to a taxid list.", - "pattern": "*.{fastq,fasta}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:krakentools" + } + } + ], + "input": [ + [ + { + "taxid": { + "type": "string", + "description": "A list of taxid separated by spaces" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "classified_reads_assignment": { + "type": "file", + "description": "A file contains the taxonomic classification of each input read.", + "pattern": "*.{classifiedreads.txt}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "classified_reads_fastq": { + "type": "file", + "description": "Classified reads as belonging to any of the taxa on the kraken2 database.", + "pattern": "*.{fastq.gz}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "report": { + "type": "file", + "description": "Optional Kraken2 report containing stats about classified and not classifed reads.", + "pattern": "*.{report.txt}" + } + } + ] + ], + "output": [ + { + "extracted_kraken2_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{fastq,fasta}": { + "type": "file", + "description": "Reads assigned to a taxid list.", + "pattern": "*.{fastq,fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75593,45 +94988,56 @@ "homepage": "https://github.com/jenniferlu717/KrakenTools", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:krakentools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "kreport": { - "type": "file", - "description": "Kraken report", - "pattern": "*.{txt,kreport}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "kreport": { + "type": "file", + "description": "Kraken report", + "pattern": "*.{txt,kreport}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Krona text-based input file converted from Kraken report", + "pattern": "*.{txt,krona}" + } + } + ] }, { - "txt": { - "type": "file", - "description": "Krona text-based input file converted from Kraken report", - "pattern": "*.{txt,krona}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75676,52 +95082,69 @@ "doi": "10.1186/s13059-018-1568-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "custom_library_dir": { - "type": "directory", - "description": "Optional directory containing custom fasta files for database build", - "pattern": "*" - } - }, - { - "custom_taxonomy_dir": { - "type": "directory", - "description": "Optional directory containing custom taxonomy files for database build", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing KrakenUniq database", - "pattern": "*/" - } + ], + "identifier": "biotools:KrakenUniq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "custom_library_dir": { + "type": "directory", + "description": "Optional directory containing custom fasta files for database build", + "pattern": "*" + } + }, + { + "custom_taxonomy_dir": { + "type": "directory", + "description": "Optional directory containing custom taxonomy files for database build", + "pattern": "*" + } + }, + { + "custom_seqid2taxid": { + "type": "file", + "description": "custom seqid2taxid" + } + } + ] + ], + "output": [ + { + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "$prefix/": { + "type": "directory", + "description": "Directory containing KrakenUniq database", + "pattern": "*/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75762,43 +95185,42 @@ "doi": "10.1186/s13059-018-1568-0", "licence": [ "MIT" - ] + ], + "identifier": "biotools:KrakenUniq" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "pattern": { + "type": "string", + "description": "Pattern indicating what type of NCBI data to download. See KrakenUniq documnation for possibilities." + } } - }, - { - "pattern": { - "type": "string", - "description": "Pattern indicating what type of NCBI data to download. See KrakenUniq documnation for possibilities." - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "output": [ + { + "${pattern}/": { + "type": "directory", + "description": "Directory containing downloaded data with directory naming being the user provided pattern." + } + } + ] }, { - "output": { - "type": "directory", - "description": "Directory containing downloaded data with directory naming being the user provided pattern." - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75832,103 +95254,156 @@ "doi": "10.1186/s13059-018-1568-0", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "List of input files containing sequences. All of them must be either in FASTA or FASTQ format." - } - }, - { - "sequence_type": { - "type": "string", - "description": "Format of all given sequencing files as literal string, either 'fasta' or 'fastq'.", - "pattern": "{fasta,fastq}" - } - }, - { - "db": { - "type": "directory", - "description": "KrakenUniq database" - } - }, - { - "ram_chunk_size": { - "type": "string", - "description": "Amount of maximum amount of RAM each chunk of database that should be loaded at any one time", - "pattern": "*GB" - } - }, - { - "save_output_reads": { - "type": "boolean", - "description": "Optionally, commands are added to save classified and unclassified reads\nas FASTQ or FASTA files depending on the input format. When the input\nis paired-end, the single output FASTQ contains merged reads.\n" - } - }, - { - "report_file": { - "type": "boolean", - "description": "Whether to generate a report of relative abundances." - } - }, - { - "save_output": { - "type": "boolean", - "description": "Whether to save a file reporting the taxonomic classification of each input read." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "classified_reads": { - "type": "file", - "description": "Reads classified as belonging to any of the taxa\nin the KrakenUniq reference database.\n", - "pattern": "*.classified.{fastq,fasta}.gz" - } - }, - { - "unclassified_reads": { - "type": "file", - "description": "Reads not classified to any of the taxa\nin the KrakenUniq reference database.\n", - "pattern": "*.unclassified.{fastq,fasta}.gz" - } - }, - { - "classified_assignment": { - "type": "file", - "description": "KrakenUniq output file indicating the taxonomic assignment of\neach input read ## DOUBLE CHECK!!\n", - "pattern": "*.krakenuniq.classified.txt" - } - }, - { - "report": { - "type": "file", - "description": "KrakenUniq report containing statistics about classified\nand unclassified reads.\n", - "pattern": "*.krakenuniq.report.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:KrakenUniq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "List of input files containing sequences. All of them must be either in FASTA or FASTQ format." + } + } + ], + [ + { + "sequence_type": { + "type": "string", + "description": "Format of all given sequencing files as literal string, either 'fasta' or 'fastq'.", + "pattern": "{fasta,fastq}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "KrakenUniq database" + } + } + ], + [ + { + "ram_chunk_size": { + "type": "string", + "description": "Amount of maximum amount of RAM each chunk of database that should be loaded at any one time", + "pattern": "*GB" + } + } + ], + [ + { + "save_output_reads": { + "type": "boolean", + "description": "Optionally, commands are added to save classified and unclassified reads\nas FASTQ or FASTA files depending on the input format. When the input\nis paired-end, the single output FASTQ contains merged reads.\n" + } + } + ], + [ + { + "report_file": { + "type": "boolean", + "description": "Whether to generate a report of relative abundances." + } + } + ], + [ + { + "save_output": { + "type": "boolean", + "description": "Whether to save a file reporting the taxonomic classification of each input read." + } + } + ] + ], + "output": [ + { + "classified_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.classified.${sequence_type}.gz": { + "type": "file", + "description": "Reads classified as belonging to any of the taxa\nin the KrakenUniq reference database.\n", + "pattern": "*.classified.{fastq,fasta}.gz" + } + } + ] + }, + { + "unclassified_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unclassified.${sequence_type}.gz": { + "type": "file", + "description": "Reads not classified to any of the taxa\nin the KrakenUniq reference database.\n", + "pattern": "*.unclassified.{fastq,fasta}.gz" + } + } + ] + }, + { + "classified_assignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.krakenuniq.classified.txt": { + "type": "file", + "description": "KrakenUniq output file indicating the taxonomic assignment of\neach input read ## DOUBLE CHECK!!\n", + "pattern": "*.krakenuniq.classified.txt" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.krakenuniq.report.txt": { + "type": "file", + "description": "KrakenUniq report containing statistics about classified\nand unclassified reads.\n", + "pattern": "*.krakenuniq.report.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -75965,24 +95440,33 @@ "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", "documentation": "https://github.com/marbl/Krona/wiki/Installing", - "doi": "10.1186/1471-2105-12-385" + "doi": "10.1186/1471-2105-12-385", + "identifier": "biotools:krona" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "taxonomy/taxonomy.tab": { + "type": "file", + "description": "A TAB separated file that contains a taxonomy database.", + "pattern": "*.{tab}" + } + } + ] }, { - "db": { - "type": "file", - "description": "A TAB separated file that contains a taxonomy database.", - "pattern": "*.{tab}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76020,46 +95504,66 @@ "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", "documentation": "http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html", - "doi": "10.1186/1471-2105-12-385" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "taxonomy": { - "type": "file", - "description": "Path to a Krona taxonomy .tab file normally downloaded and generated by\nkrona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but\nmust end in `.tab`.\n", - "pattern": "*tab" - } - }, - { - "report": { - "type": "file", - "description": "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored.", - "pattern": "*.{tsv}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "html": { - "type": "file", - "description": "A html file containing an interactive krona plot.", - "pattern": "*.{html}" - } + "doi": "10.1186/1471-2105-12-385", + "identifier": "biotools:krona" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "report": { + "type": "file", + "description": "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored.", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "taxonomy": { + "type": "file", + "description": "Path to a Krona taxonomy .tab file normally downloaded and generated by\nkrona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but\nmust end in `.tab`.\n", + "pattern": "*tab" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "file", + "description": "A html file containing an interactive krona plot.", + "pattern": "*.{html}" + } + }, + { + "*.html": { + "type": "file", + "description": "A html file containing an interactive krona plot.", + "pattern": "*.{html}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76110,45 +95614,56 @@ "doi": "10.1186/1471-2105-12-385", "licence": [ "https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt" - ] + ], + "identifier": "biotools:krona" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "report": { - "type": "file", - "description": "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored.", - "pattern": "*.{txt}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "report": { + "type": "file", + "description": "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored.", + "pattern": "*.{txt}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "A html file containing an interactive krona plot.", + "pattern": "*.{html}" + } + } + ] }, { - "html": { - "type": "file", - "description": "A html file containing an interactive krona plot.", - "pattern": "*.{html}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76184,24 +95699,33 @@ "description": "Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.", "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", "documentation": "https://github.com/marbl/Krona/wiki/Installing", - "doi": "10.1186/1471-2105-12-385" + "doi": "10.1186/1471-2105-12-385", + "identifier": "biotools:krona" } } ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "taxonomy/taxonomy.tab": { + "type": "file", + "description": "A TAB separated file that contains a taxonomy database.", + "pattern": "*.{tab}" + } + } + ] }, { - "db": { - "type": "file", - "description": "A TAB separated file that contains a taxonomy database.", - "pattern": "*.{tab}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76241,76 +95765,107 @@ "tool_dev_url": "https://gitlab.com/mcfrith/last", "licence": [ "GPL v3-or-later" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "maf": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, compressed with gzip", + "pattern": "*.{maf.gz}" + } + }, + { + "annot_b": { + "type": "file", + "description": "Annotation file in BED, Repeamasker, genePred or AGP format for the second (vertical) sequence", + "pattern": "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample2', single_end:false ]`\n" + } + }, + { + "annot_a": { + "type": "file", + "description": "Annotation file in BED, Repeamasker, genePred or AGP format for the first (horizontal) sequence", + "pattern": "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Output format (PNG or GIF)." + } + } + ] + ], + "output": [ + { + "gif": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gif": { + "type": "file", + "description": "Pairwise alignment dot plot image, in GIF format.", + "pattern": "*.gif" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Pairwise alignment dot plot image, in PNG format.", + "pattern": "*.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}" - } - }, - { - "format": { - "type": "string", - "description": "Output format (PNG or GIF)." - } - }, - { - "annot_a": { - "type": "file", - "description": "Annotation file in BED, Repeamasker, genePred or AGP format for the first (horizontal) sequence", - "pattern": "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" - } - }, - { - "annot_b": { - "type": "file", - "description": "Annotation file in BED, Repeamasker, genePred or AGP format for the second (vertical) sequence", - "pattern": "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "png": { - "type": "file", - "description": "Pairwise alignment dot plot image, in PNG format.", - "pattern": "*.png" - } - }, - { - "gif": { - "type": "file", - "description": "Pairwise alignment dot plot image, in GIF format.", - "pattern": "*.gif" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@charles-plessy" + "authors": [ + "@charles-plessy" ], "maintainers": [ "@charles-plessy" @@ -76345,66 +95900,89 @@ "tool_dev_url": "https://gitlab.com/mcfrith/last", "licence": [ "GPL v3-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "FASTA/FASTQ file", - "pattern": "*.{fasta,fastq}" - } - }, - { - "param_file": { - "type": "file", - "description": "Trained parameter file", - "pattern": "*.train" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing the files of the LAST index", - "pattern": "lastdb/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "maf": { - "type": "file", - "description": "Gzipped MAF (Multiple Alignment Format) file", - "pattern": "*.{maf.gz}" - } - }, - { - "multiqc": { - "type": "file", - "description": "Alignment summary for MultiQC", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "FASTA/FASTQ file", + "pattern": "*.{fasta,fastq}" + } + }, + { + "param_file": { + "type": "file", + "description": "Trained parameter file", + "pattern": "*.train" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Directory containing the files of the LAST index", + "pattern": "lastdb/" + } + } + ] + ], + "output": [ + { + "maf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.maf.gz": { + "type": "file", + "description": "Gzipped MAF (Multiple Alignment Format) file", + "pattern": "*.{maf.gz}" + } + } + ] + }, + { + "multiqc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Alignment summary for MultiQC", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76443,45 +96021,56 @@ "tool_dev_url": "https://gitlab.com/mcfrith/last", "licence": [ "GPL v3-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Sequence file in FASTA or FASTQ format. May be compressed with gzip.\n", + "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}" + } } - }, - { - "fastx": { - "type": "file", - "description": "Sequence file in FASTA or FASTQ format. May be compressed with gzip.\n", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "lastdb": { + "type": "directory", + "description": "directory containing the files of the LAST index", + "pattern": "lastdb/" + } + } + ] }, { - "index": { - "type": "directory", - "description": "directory containing the files of the LAST index", - "pattern": "lastdb/" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76520,107 +96109,200 @@ "tool_dev_url": "https://gitlab.com/mcfrith/last", "licence": [ "GPL v3-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, optionally compressed with gzip", - "pattern": "*.{maf.gz,maf}" - } - }, - { - "format": { - "type": "string", - "description": "Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "axt_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in Axt (Blastz) format (optional)", - "pattern": "*.axt.gz" - } - }, - { - "blast_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in blast format (optional)", - "pattern": "*.blast.gz" - } - }, - { - "blasttab_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in blasttab format (optional)", - "pattern": "*.blasttab.gz" - } - }, - { - "chain_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in UCSC chain format (optional)", - "pattern": "*.chain.gz" - } - }, - { - "gff_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in GFF format (optional)", - "pattern": "*.gff.gz" - } - }, - { - "html_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in HTML format (optional)", - "pattern": "*.html.gz" - } - }, - { - "psl_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in PSL (BLAT) format (optional)", - "pattern": "*.psl.gz" - } - }, - { - "sam_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in SAM format (optional)", - "pattern": "*.sam.gz" - } - }, - { - "tab_gz": { - "type": "file", - "description": "Gzipped pairwise alignment in TAB format (optional)", - "pattern": "*.tab.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "maf": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, optionally compressed with gzip", + "pattern": "*.{maf.gz,maf}" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab)" + } + } + ] + ], + "output": [ + { + "axt_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.axt.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in Axt (Blastz) format (optional)", + "pattern": "*.axt.gz" + } + } + ] + }, + { + "blast_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.blast.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in blast format (optional)", + "pattern": "*.blast.gz" + } + } + ] + }, + { + "blasttab_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.blasttab.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in blasttab format (optional)", + "pattern": "*.blasttab.gz" + } + } + ] + }, + { + "chain_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.chain.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in UCSC chain format (optional)", + "pattern": "*.chain.gz" + } + } + ] + }, + { + "gff_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gff.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in GFF format (optional)", + "pattern": "*.gff.gz" + } + } + ] + }, + { + "html_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.html.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in HTML format (optional)", + "pattern": "*.html.gz" + } + } + ] + }, + { + "psl_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.psl.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in PSL (BLAT) format (optional)", + "pattern": "*.psl.gz" + } + } + ] + }, + { + "sam_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.sam.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in SAM format (optional)", + "pattern": "*.sam.gz" + } + } + ] + }, + { + "tab_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tab.gz": { + "type": "file", + "description": "Gzipped pairwise alignment in TAB format (optional)", + "pattern": "*.tab.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76654,45 +96336,56 @@ "tool_dev_url": "https://gitlab.com/mcfrith/last", "licence": [ "GPL v3-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, optionally compressed with gzip", - "pattern": "*.{maf.gz,maf}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "maf": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, optionally compressed with gzip", + "pattern": "*.{maf.gz,maf}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "maf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.maf.gz": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, compressed with gzip", + "pattern": "*.{maf.gz}" + } + } + ] }, { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76732,45 +96425,56 @@ "doi": "10.1371/journal.pone.0028819", "licence": [ "GPL v3-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, optionally compressed with gzip", - "pattern": "*.{maf.gz,maf}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "maf": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, optionally compressed with gzip", + "pattern": "*.{maf.gz,maf}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "maf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.maf.gz": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, compressed with gzip", + "pattern": "*.{maf.gz}" + } + } + ] }, { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76804,52 +96508,73 @@ "tool_dev_url": "https://gitlab.com/mcfrith/last", "licence": [ "GPL v3-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "maf": { - "type": "file", - "description": "Multiple Aligment Format (MAF) file, compressed with gzip", - "pattern": "*.{maf.gz}" - } - }, - { - "multiqc": { - "type": "file", - "description": "Alignment summary for MultiQC", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "maf": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, compressed with gzip", + "pattern": "*.{maf.gz}" + } + } + ] + ], + "output": [ + { + "maf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.maf.gz": { + "type": "file", + "description": "Multiple Aligment Format (MAF) file, compressed with gzip", + "pattern": "*.{maf.gz}" + } + } + ] + }, + { + "multiqc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Alignment summary for MultiQC", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76889,59 +96614,82 @@ "tool_dev_url": "https://gitlab.com/mcfrith/last", "licence": [ "GPL v3-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "FASTA/FASTQ file", - "pattern": "*.{fasta,fastq}" - } - }, - { - "index": { - "type": "directory", - "description": "Directory containing the files of the LAST index", - "pattern": "lastdb/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "param_file": { - "type": "file", - "description": "Trained parameter file", - "pattern": "*.train" - } - }, - { - "multiqc": { - "type": "file", - "description": "Alignment parameter summary for MultiQC", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "FASTA/FASTQ file", + "pattern": "*.{fasta,fastq}" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Directory containing the files of the LAST index", + "pattern": "lastdb/" + } + } + ] + ], + "output": [ + { + "param_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.train": { + "type": "file", + "description": "Trained parameter file", + "pattern": "*.train" + } + } + ] + }, + { + "multiqc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Alignment parameter summary for MultiQC", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -76982,51 +96730,64 @@ "doi": "10.1093/gigascience/giac104", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format. May be gz-compressed or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Alignment file, in FASTA format. May be gzipped or uncompressed.", - "pattern": "*.aln{.gz,}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:learnMSA" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format. May be gz-compressed or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file, in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.aln{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77072,94 +96833,175 @@ "doi": "10.1093/nar/gku699", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Unaligned BAM or one or two gzipped FASTQ file(s)", - "pattern": "*.{bam,fq.gz,fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "fq_pass": { - "type": "file", - "description": "Trimmed and merged FASTQ", - "pattern": "*.fq.gz" - } - }, - { - "fq_fail": { - "type": "file", - "description": "Failed trimmed and merged FASTQs", - "pattern": "*.fail.fq.gz" - } - }, - { - "unmerged_r1_fq_pass": { - "type": "file", - "description": "Passed unmerged R1 FASTQs", - "pattern": "*.r1.fq.gz" - } - }, - { - "unmerged_r1_fq_fail": { - "type": "file", - "description": "Failed unmerged R1 FASTQs", - "pattern": "*.r1.fail.fq.gz" - } - }, - { - "unmerged_r2_fq_pass": { - "type": "file", - "description": "Passed unmerged R2 FASTQs", - "pattern": "*.r2.fq.gz" - } - }, - { - "unmerged_r2_fq_pass": { - "type": "file", - "description": "Failed unmerged R2 FASTQs", - "pattern": "*.r2.fail.fq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log file of command", - "pattern": "*.log" - } + ], + "identifier": "biotools:leehom" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Unaligned BAM or one or two gzipped FASTQ file(s)", + "pattern": "*.{bam,fq.gz,fastq.gz}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "fq_pass": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fq.gz": { + "type": "file", + "description": "Trimmed and merged FASTQ", + "pattern": "*.fq.gz" + } + } + ] + }, + { + "fq_fail": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fail.fq.gz": { + "type": "file", + "description": "Failed trimmed and merged FASTQs", + "pattern": "*.fail.fq.gz" + } + } + ] + }, + { + "unmerged_r1_fq_pass": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_r1.fq.gz": { + "type": "file", + "description": "Passed unmerged R1 FASTQs", + "pattern": "*.r1.fq.gz" + } + } + ] + }, + { + "unmerged_r1_fq_fail": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_r1.fail.fq.gz": { + "type": "file", + "description": "Failed unmerged R1 FASTQs", + "pattern": "*.r1.fail.fq.gz" + } + } + ] + }, + { + "unmerged_r2_fq_pass": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_r2.fq.gz": { + "type": "file", + "description": "Passed unmerged R2 FASTQs", + "pattern": "*.r2.fq.gz" + } + } + ] + }, + { + "unmerged_r2_fq_fail": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_r2.fail.fq.gz": { + "type": "file", + "description": "Failed unmerged R2 FASTQs", + "pattern": "*.r2.fail.fq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of command", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77192,45 +97034,56 @@ "tool_dev_url": "https://github.com/tseemann/legsta", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:legsta" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "FASTA, GenBank or EMBL formatted files", + "pattern": "*.{fasta,gbk,embl}" + } } - }, - { - "seqs": { - "type": "file", - "description": "FASTA, GenBank or EMBL formatted files", - "pattern": "*.{fasta,gbk,embl}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited summary of the results", + "pattern": "*.{tsv}" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited summary of the results", - "pattern": "*.{tsv}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77261,52 +97114,65 @@ "documentation": "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "FAI (FASTA index) file of the target reference", - "pattern": "*.{fai}" - } - }, - { - "chain": { - "type": "file", - "description": "Chain file to index.", - "pattern": "*.{chain}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "clft": { - "type": "file", - "description": "Clft file of indexed chain", - "pattern": "*.{clft}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "FAI (FASTA index) file of the target reference", + "pattern": "*.{fai}" + } + } + ], + [ + { + "chain": { + "type": "file", + "description": "Chain file to index.", + "pattern": "*.{chain}" + } + } + ] + ], + "output": [ + { + "clft": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "*.clft": { + "type": "file", + "description": "Clft file of indexed chain", + "pattern": "*.{clft}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77337,58 +97203,71 @@ "documentation": "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "SAM/BAM/CRAM file to be lifted", - "pattern": "*.{bam}" - } - }, - { - "meta_ref": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "clft": { - "type": "file", - "description": "Clft file of indexed ChainMap.", - "pattern": "*.{clft}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Lifted bam file", - "pattern": "*.{bam}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "SAM/BAM/CRAM file to be lifted", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta_ref": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "clft": { + "type": "file", + "description": "Clft file of indexed ChainMap.", + "pattern": "*.{clft}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'reference' ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Lifted bam file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77423,79 +97302,116 @@ "doi": "10.1093/bioinformatics/bty191", "licence": [ "GPL v3 License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "target_fa": { - "type": "file", - "description": "Target assembly in fasta format", - "pattern": "*.{fsa,fa,fasta}" - } - }, - { - "ref_fa": { - "type": "file", - "description": "Reference assembly in fasta format", - "pattern": "*.{fsa,fa,fasta}" - } - }, - { - "ref_annotation": { - "type": "file", - "description": "Reference assembly annotations in gtf or gff3 format", - "pattern": "*.{gtf,gff3}" - } - }, - { - "ref_db": { - "type": "file", - "description": "Name of feature database; if not specified, the -g argument must\nbe provided and a database will be built automatically\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "gff3": { - "type": "file", - "description": "Lifted annotations for the target assembly in gff3 format", - "pattern": "*.gff3" - } - }, - { - "polished_gff3": { - "type": "file", - "description": "Polished lifted annotations for the target assembly in gff3 format", - "pattern": "*.polished.gff3" - } - }, - { - "unmapped_txt": { - "type": "file", - "description": "List of unmapped reference annotations", - "pattern": "*.unmapped.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:liftoff" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "target_fa": { + "type": "file", + "description": "Target assembly in fasta format", + "pattern": "*.{fsa,fa,fasta}" + } + } + ], + [ + { + "ref_fa": { + "type": "file", + "description": "Reference assembly in fasta format", + "pattern": "*.{fsa,fa,fasta}" + } + } + ], + [ + { + "ref_annotation": { + "type": "file", + "description": "Reference assembly annotations in gtf or gff3 format", + "pattern": "*.{gtf,gff3}" + } + } + ], + [ + { + "ref_db": { + "type": "file", + "description": "Name of feature database; if not specified, the -g argument must\nbe provided and a database will be built automatically\n" + } + } + ] + ], + "output": [ + { + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.gff3": { + "type": "file", + "description": "Lifted annotations for the target assembly in gff3 format", + "pattern": "*.gff3" + } + } + ] + }, + { + "polished_gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.polished.gff3": { + "type": "file", + "description": "Polished lifted annotations for the target assembly in gff3 format", + "pattern": "*.polished.gff3" + } + } + ] + }, + { + "unmapped_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.unmapped.txt": { + "type": "file", + "description": "List of unmapped reference annotations", + "pattern": "*.unmapped.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77529,136 +97445,269 @@ "tool_dev_url": "https://github.com/pacificbiosciences/barcoding/", "licence": [ "BSD-3-Clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "ccs": { - "type": "file", - "description": "A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs", - "pattern": "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" - } - }, - { - "primers": { - "type": "file", - "description": "Fasta file, sequences of primers", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A bam file of ccs purged of primers", - "pattern": "*.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "Pacbio index file of ccs purged of primers", - "pattern": "*.bam" - } - }, - { - "xml": { - "type": "file", - "description": "An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.", - "pattern": "*.xml" - } - }, - { - "json": { - "type": "file", - "description": "A metadata json file", - "pattern": "*.json" - } - }, - { - "clips": { - "type": "file", - "description": "A fasta file of clipped primers", - "pattern": "*.clips" - } - }, - { - "counts": { - "type": "file", - "description": "A tabulated file of describing pairs of primers", - "pattern": "*.counts" - } - }, - { - "guess": { - "type": "file", - "description": "A second tabulated file of describing pairs of primers (no doc available)", - "pattern": "*.guess" - } - }, - { - "report": { - "type": "file", - "description": "A tab-separated file about each ZMW, unfiltered", - "pattern": "*.report" - } - }, - { - "summary": { - "type": "file", - "description": "This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.", - "pattern": "*.summary" - } - }, - { - "fasta": { - "type": "file", - "description": "A fasta file of ccs purged of primers.", - "pattern": "*.fa" - } - }, - { - "fastagz": { - "type": "file", - "description": "A fasta.gz file of ccs purged of primers.", - "pattern": "*.fasta.gz" - } - }, - { - "fastq": { - "type": "file", - "description": "A fastq file of ccs purged of primers.", - "pattern": "*.fastq" - } - }, - { - "fastqgz": { - "type": "file", - "description": "A fastq.gz file of ccs purged of primers.", - "pattern": "*.fastq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "ccs": { + "type": "file", + "description": "A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs", + "pattern": "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" + } + } + ], + [ + { + "primers": { + "type": "file", + "description": "Fasta file, sequences of primers", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.counts": { + "type": "file", + "description": "A tabulated file of describing pairs of primers", + "pattern": "*.counts" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.report": { + "type": "file", + "description": "A tab-separated file about each ZMW, unfiltered", + "pattern": "*.report" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.summary": { + "type": "file", + "description": "This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.", + "pattern": "*.summary" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "A bam file of ccs purged of primers", + "pattern": "*.bam" + } + } + ] + }, + { + "pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam.pbi": { + "type": "file", + "description": "Pacbio index file of ccs purged of primers", + "pattern": "*.bam" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.{fa, fasta}": { + "type": "file", + "description": "A fasta file of ccs purged of primers.", + "pattern": "*.fa" + } + } + ] + }, + { + "fastagz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.{fa.gz, fasta.gz}": { + "type": "file", + "description": "A fasta.gz file of ccs purged of primers.", + "pattern": "*.fasta.gz" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fastq": { + "type": "file", + "description": "A fastq file of ccs purged of primers.", + "pattern": "*.fastq" + } + } + ] + }, + { + "fastqgz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "A fastq.gz file of ccs purged of primers.", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "xml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.", + "pattern": "*.xml" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "A metadata json file", + "pattern": "*.json" + } + } + ] + }, + { + "clips": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.clips": { + "type": "file", + "description": "A fasta file of clipped primers", + "pattern": "*.clips" + } + } + ] + }, + { + "guess": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.guess": { + "type": "file", + "description": "A second tabulated file of describing pairs of primers (no doc available)", + "pattern": "*.guess" + } + } + ] } ], "authors": [ @@ -77698,96 +97747,160 @@ "doi": "10.18129/B9.bioc.limma", "licence": [ "LGPL >=3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" - } - }, - { - "reference": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" - } - }, - { - "target": { - "type": "string", - "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" - } - }, - { - "samplesheeet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata\n" - } - }, - { - "intensities": { - "type": "file", - "description": "Raw TSV or CSV format expression matrix with probes by row and samples\nby column\n" - } - } - ], - "output": [ - { - "results": { - "type": "file", - "description": "TSV-format table of differential expression information as output by Limma", - "pattern": "*.limma.results.tsv" - } - }, - { - "md_plot": { - "type": "file", - "description": "Limma mean difference plot", - "pattern": "*.mean_difference.png" - } - }, - { - "rdata": { - "type": "file", - "description": "Serialised MArrayLM object", - "pattern": "*.MArrayLM.limma.rds" - } - }, - { - "model": { - "type": "file", - "description": "TXT-format limma model", - "pattern": "*.limma.model.tsv" - } - }, - { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:limma" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information. This can be used at the\nworkflow level to pass optional parameters to the module, e.g.\n[ id:'contrast1', blocking:'patient' ] passed in as ext.args like:\n'--blocking_variable $meta.blocking'.\n" + } + }, + { + "contrast_variable": { + "type": "string", + "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n" + } + }, + { + "reference": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n" + } + }, + { + "target": { + "type": "string", + "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "Sample sheet file" + } + }, + { + "intensities": { + "type": "file", + "description": "Raw TSV or CSV format expression matrix with probes by row and samples\nby column\n" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "file", + "description": "TSV-format table of differential expression information as output by Limma", + "pattern": "*.limma.results.tsv" + } + }, + { + "*.limma.results.tsv": { + "type": "file", + "description": "TSV-format table of differential expression information as output by Limma", + "pattern": "*.limma.results.tsv" + } + } + ] + }, + { + "md_plot": [ + { + "meta": { + "type": "file", + "description": "Limma mean difference plot", + "pattern": "*.mean_difference.png" + } + }, + { + "*.limma.mean_difference.png": { + "type": "file", + "description": "Limma mean difference plot", + "pattern": "*.mean_difference.png" + } + } + ] + }, + { + "rdata": [ + { + "meta": { + "type": "file", + "description": "Serialised MArrayLM object", + "pattern": "*.MArrayLM.limma.rds" + } + }, + { + "*.MArrayLM.limma.rds": { + "type": "file", + "description": "Serialised MArrayLM object", + "pattern": "*.MArrayLM.limma.rds" + } + } + ] + }, + { + "model": [ + { + "meta": { + "type": "file", + "description": "TXT-format limma model", + "pattern": "*.limma.model.tsv" + } + }, + { + "*.limma.model.txt": { + "type": "file", + "description": "TXT-format limma model", + "pattern": "*.limma.model.tsv" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77825,45 +97938,56 @@ "tool_dev_url": "https://github.com/MDU-PHL/lissero", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited result file", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited result file", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77896,52 +98020,65 @@ "doi": "10.1093/nar/gks918", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file with base and indel alignment qualities", - "pattern": "*.{bam,cram,sam}" - } + ], + "identifier": "biotools:lofreq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM/CRAM/SAM file with base and indel alignment qualities", + "pattern": "*.{bam,cram,sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -77974,58 +98111,71 @@ "doi": "10.1093/nar/gks918 ", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM input file", - "pattern": "*.{bam}" - } - }, - { - "intervals": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF output file", - "pattern": "*.{vcf}" - } + ], + "identifier": "biotools:lofreq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM input file", + "pattern": "*.{bam}" + } + }, + { + "intervals": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF output file", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78058,92 +98208,117 @@ "doi": "10.1093/nar/gks918", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Tumor sample sorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bam.bai}" - } - }, - { - "intervals": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information about the reference fasta\ne.g. [ id:'reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information about the reference fasta fai\ne.g. [ id:'reference' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome FASTA index file", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Predicted variants file", - "pattern": "*.{vcf}" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of vcf file", - "pattern": "*.{vcf.gz.tbi}" - } + ], + "identifier": "biotools:lofreq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Tumor sample sorted BAM file", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bam.bai}" + } + }, + { + "intervals": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information about the reference fasta\ne.g. [ id:'reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information about the reference fasta fai\ne.g. [ id:'reference' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome FASTA index file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Predicted variants file", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of vcf file", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78181,45 +98356,56 @@ "doi": "10.1093/nar/gks918 ", "licence": [ "MIT" - ] + ], + "identifier": "biotools:lofreq" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF input file", - "pattern": "*.{vcf}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF input file", + "pattern": "*.{vcf}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "VCF filtered output file", + "pattern": "*.{vcf}" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "VCF filtered output file", - "pattern": "*.{vcf}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78252,58 +98438,71 @@ "doi": "10.1093/nar/gks918", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information about the reference fasta\ne.g. [ id:'reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with indel qualities inserted into it", - "pattern": "*.{bam}" - } + ], + "identifier": "biotools:lofreq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information about the reference fasta\ne.g. [ id:'reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with indel qualities inserted into it", + "pattern": "*.{bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78338,99 +98537,114 @@ "doi": "10.1093/nar/gks918", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information" - } - }, - { - "tumor": { - "type": "file", - "description": "tumor sample input BAM file", - "pattern": "*.{bam}" - } - }, - { - "tumor_index": { - "type": "file", - "description": "tumor sample BAM index file", - "pattern": "*.{bam.bai}" - } - }, - { - "normal": { - "type": "file", - "description": "normal sample input BAM file", - "pattern": "*.{bam}" - } - }, - { - "normal_index": { - "type": "file", - "description": "normal sample BAM index file", - "pattern": "*.{bam.bai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome FASTA index file", - "pattern": "*.{fai}" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } + ], + "identifier": "biotools:lofreq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "tumor": { + "type": "file", + "description": "tumor sample input BAM file", + "pattern": "*.{bam}" + } + }, + { + "tumor_index": { + "type": "file", + "description": "tumor sample BAM index file", + "pattern": "*.{bam.bai}" + } + }, + { + "normal": { + "type": "file", + "description": "normal sample input BAM file", + "pattern": "*.{bam}" + } + }, + { + "normal_index": { + "type": "file", + "description": "normal sample BAM index file", + "pattern": "*.{bam.bai}" + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information" + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome FASTA index file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78465,58 +98679,71 @@ "doi": "10.1093/nar/gks918", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information about the reference fasta\ne.g. [ id:'reference' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Realignment and sorted BAM file", - "pattern": "*.{bam}" - } + ], + "identifier": "biotools:lofreq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information about the reference fasta\ne.g. [ id:'reference' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Realignment and sorted BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78550,113 +98777,131 @@ "doi": "10.1093/bioinformatics/btac058", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "Index of sorted BAM/CRAM file", - "pattern": "*.{bai,crai,csi}" - } - }, - { - "snps": { - "type": "file", - "description": "VCF file with SNPs (and INDELs)", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "svs": { - "type": "file", - "description": "VCF file with SVs", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "mods": { - "type": "file", - "description": "modcall-generated VCF with modifications", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fai index", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with haplotagged reads", - "pattern": "*.bam" - } - }, - { - "cram": { - "type": "file", - "description": "CRAM file with haplotagged reads", - "pattern": "*.cram" - } - }, - { - "log": { - "type": "file", - "description": "Log file", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "Index of sorted BAM/CRAM file", + "pattern": "*.{bai,crai,csi}" + } + }, + { + "snps": { + "type": "file", + "description": "VCF file with SNPs (and INDELs)", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "svs": { + "type": "file", + "description": "VCF file with SVs", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "mods": { + "type": "file", + "description": "modcall-generated VCF with modifications", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fai index", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{bam,cram}": { + "type": "file", + "description": "BAM file with haplotagged reads", + "pattern": "*.bam" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78689,99 +98934,114 @@ "doi": "10.1093/bioinformatics/btac058", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file(s)", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "Index of sorted BAM/CRAM file(s)", - "pattern": "*.{bai,crai,csi}" - } - }, - { - "snps": { - "type": "file", - "description": "VCF file with SNPs (and INDELs)", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "svs": { - "type": "file", - "description": "VCF file with SVs", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "mods": { - "type": "file", - "description": "modcall-generated VCF with modifications", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fai index", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file with phased variants", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM file(s)", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "Index of sorted BAM/CRAM file(s)", + "pattern": "*.{bai,crai,csi}" + } + }, + { + "snps": { + "type": "file", + "description": "VCF file with SNPs (and INDELs)", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "svs": { + "type": "file", + "description": "VCF file with SVs", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "mods": { + "type": "file", + "description": "modcall-generated VCF with modifications", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fai index", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file with phased variants", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78817,7 +99077,8 @@ "doi": "10.1186/s13100-019-0193-0", "licence": [ "MIT" - ] + ], + "identifier": "" } }, { @@ -78829,52 +99090,73 @@ "doi": "10.1093/nar/gkm286", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome sequences in fasta format", - "pattern": "*.{fsa,fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "scn": { - "type": "file", - "description": "Annotation in LTRharvest or LTR_FINDER format", - "pattern": "*.scn" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation in gff3 format", - "pattern": "*.gff3" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome sequences in fasta format", + "pattern": "*.{fsa,fa,fasta}" + } + } + ] + ], + "output": [ + { + "scn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.scn": { + "type": "file", + "description": "Annotation in LTRharvest or LTR_FINDER format", + "pattern": "*.scn" + } + } + ] + }, + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "Annotation in gff3 format", + "pattern": "*.gff3" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -78909,7 +99191,8 @@ "tool_dev_url": "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel", "licence": [ "MIT" - ] + ], + "identifier": "" } }, { @@ -78921,52 +99204,73 @@ "doi": "10.1109/TCBB.2013.68", "licence": [ "ISC" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta", - "pattern": "*.{fsa,fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gff3": { - "type": "file", - "description": "Predicted LTR candidates in gff3 format", - "pattern": "*.gff3" - } - }, - { - "scn": { - "type": "file", - "description": "Predicted LTR candidates in scn format", - "pattern": "*.scn" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta", + "pattern": "*.{fsa,fa,fasta}" + } + } + ] + ], + "output": [ + { + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gff3": { + "type": "file", + "description": "Predicted LTR candidates in gff3 format", + "pattern": "*.gff3" + } + } + ] + }, + { + "scn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.scn": { + "type": "file", + "description": "Predicted LTR candidates in scn format", + "pattern": "*.scn" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -79139,73 +99443,100 @@ "doi": "10.1093/nar/gky730", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The genome file that is used to generate everything", - "pattern": "*.{fsa,fa,fasta}" - } - }, - { - "pass_list": { - "type": "file", - "description": "A list of intact LTR-RTs generated by LTR_retriever", - "pattern": "*.pass.list" - } - }, - { - "annotation_out": { - "type": "file", - "description": "RepeatMasker annotation of all LTR sequences in the genome", - "pattern": "*.out" - } - }, - { - "monoploid_seqs": { - "type": "file", - "description": "This parameter is mainly for ployploid genomes. User provides a list of\nsequence names that represent a monoploid (1x). LAI will be calculated only\non these sequences if provided.\n", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "log": { - "type": "file", - "description": "Log from LAI", - "pattern": "*.LAI.log" - } - }, - { - "lai_out": { - "type": "file", - "description": "Output file from LAI if LAI is able to estimate the index from the inputs\n", - "pattern": "*.LAI.out" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The genome file that is used to generate everything", + "pattern": "*.{fsa,fa,fasta}" + } + } + ], + [ + { + "pass_list": { + "type": "file", + "description": "A list of intact LTR-RTs generated by LTR_retriever", + "pattern": "*.pass.list" + } + } + ], + [ + { + "annotation_out": { + "type": "file", + "description": "RepeatMasker annotation of all LTR sequences in the genome", + "pattern": "*.out" + } + } + ], + [ + { + "monoploid_seqs": { + "type": "file", + "description": "This parameter is mainly for ployploid genomes. User provides a list of\nsequence names that represent a monoploid (1x). LAI will be calculated only\non these sequences if provided.\n", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.LAI.log": { + "type": "file", + "description": "Log from LAI", + "pattern": "*.LAI.log" + } + } + ] + }, + { + "lai_out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.LAI.out": { + "type": "file", + "description": "Output file from LAI if LAI is able to estimate the index from the inputs\n", + "pattern": "*.LAI.out" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -79240,209 +99571,329 @@ "doi": "10.1104/pp.17.01310", "licence": [ "GPL v3" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "genome": { + "type": "file", + "description": "Genomic sequences in fasta format", + "pattern": "*.{fsa,fa,fasta}" + } + } + ], + [ + { + "harvest": { + "type": "file", + "description": "LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", + "pattern": "*.tabout" + } + } + ], + [ + { + "finder": { + "type": "file", + "description": "LTR-RT candidates from LTR_FINDER", + "pattern": "*.scn" + } + } + ], + [ + { + "mgescan": { + "type": "file", + "description": "LTR-RT candidates from MGEScan_LTR", + "pattern": "*.out" + } + } + ], + [ + { + "non_tgca": { + "type": "file", + "description": "Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", + "pattern": "*.tabout" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Output log from LTR_retriever", + "pattern": "*.log" + } + } + ] + }, + { + "pass_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.pass.list": { + "type": "file", + "description": "Intact LTR-RTs with coordinate and structural information in summary table format", + "pattern": "*.pass.list" + } + } + ] + }, + { + "pass_list_gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.pass.list.gff3": { + "type": "file", + "description": "Intact LTR-RTs with coordinate and structural information in gff3 format", + "pattern": "*.pass.list.gff3" + } + } + ] + }, + { + "ltrlib": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.LTRlib.fa": { + "type": "file", + "description": "All non-redundant LTR-RTs", + "pattern": "*.LTRlib.fa" + } + } + ] + }, + { + "annotation_out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.out": { + "type": "file", + "description": "Whole-genome LTR-RT annotation by the non-redundant library", + "pattern": "*.out" + } + } + ] + }, + { + "annotation_gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.out.gff3": { + "type": "file", + "description": "Whole-genome LTR-RT annotation by the non-redundant library in gff3 format", + "pattern": "*.out.gff3" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "genome": { - "type": "file", - "description": "Genomic sequences in fasta format", - "pattern": "*.{fsa,fa,fasta}" - } - }, - { - "harvest": { - "type": "file", - "description": "LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", - "pattern": "*.tabout" - } - }, - { - "finder": { - "type": "file", - "description": "LTR-RT candidates from LTR_FINDER", - "pattern": "*.scn" - } - }, - { - "mgescan": { - "type": "file", - "description": "LTR-RT candidates from MGEScan_LTR", - "pattern": "*.out" - } - }, + "authors": [ + "@GallVp" + ], + "maintainers": [ + "@GallVp" + ] + } + }, + { + "name": "macrel_contigs", + "path": "modules/nf-core/macrel/contigs/meta.yml", + "type": "module", + "meta": { + "name": "macrel_contigs", + "description": "A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.", + "keywords": [ + "AMP", + "antimicrobial peptides", + "genome mining", + "metagenomes", + "peptide prediction" + ], + "tools": [ { - "non_tgca": { - "type": "file", - "description": "Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format", - "pattern": "*.tabout" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "log": { - "type": "file", - "description": "Output log from LTR_retriever", - "pattern": "*.log" - } - }, - { - "pass_list": { - "type": "file", - "description": "Intact LTR-RTs with coordinate and structural information in summary table format", - "pattern": "*.pass.list" - } - }, - { - "pass_list_gff": { - "type": "file", - "description": "Intact LTR-RTs with coordinate and structural information in gff3 format", - "pattern": "*.pass.list.gff3" - } - }, - { - "ltrlib": { - "type": "file", - "description": "All non-redundant LTR-RTs", - "pattern": "*.LTRlib.fa" - } - }, - { - "annotation_out": { - "type": "file", - "description": "Whole-genome LTR-RT annotation by the non-redundant library", - "pattern": "*.out" - } - }, - { - "annotation_gff": { - "type": "file", - "description": "Whole-genome LTR-RT annotation by the non-redundant library in gff3 format", - "pattern": "*.out.gff3" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@GallVp" - ], - "maintainers": [ - "@GallVp" - ] - } - }, - { - "name": "macrel_contigs", - "path": "modules/nf-core/macrel/contigs/meta.yml", - "type": "module", - "meta": { - "name": "macrel_contigs", - "description": "A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.", - "keywords": [ - "AMP", - "antimicrobial peptides", - "genome mining", - "metagenomes", - "peptide prediction" - ], - "tools": [ - { - "macrel": { - "description": "A pipeline for AMP (antimicrobial peptide) prediction", - "homepage": "https://macrel.readthedocs.io/en/latest/", - "documentation": "https://macrel.readthedocs.io/en/latest/", - "tool_dev_url": "https://github.com/BigDataBiology/macrel", - "doi": "10.7717/peerj.10555", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A fasta file with nucleotide sequences.", - "pattern": "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "amp_prediction": { - "type": "file", - "description": "A zipped file, with all predicted amps in a table format.", - "pattern": "*.prediction.gz" - } - }, - { - "smorfs": { - "type": "file", - "description": "A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.", - "pattern": "*.smorfs.faa.gz" - } - }, - { - "all_orfs": { - "type": "file", - "description": "A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.", - "pattern": "*.all_orfs.faa.gz" - } - }, - { - "readme_file": { - "type": "file", - "description": "A readme file containing tool specific information (e.g. citations, details about the output, etc.).", - "pattern": "*.md" - } - }, - { - "log_file": { - "type": "file", - "description": "A log file containing the information pertaining to the run.", - "pattern": "*_log.txt" - } + "macrel": { + "description": "A pipeline for AMP (antimicrobial peptide) prediction", + "homepage": "https://macrel.readthedocs.io/en/latest/", + "documentation": "https://macrel.readthedocs.io/en/latest/", + "tool_dev_url": "https://github.com/BigDataBiology/macrel", + "doi": "10.7717/peerj.10555", + "licence": [ + "MIT" + ], + "identifier": "biotools:macrel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A fasta file with nucleotide sequences.", + "pattern": "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}" + } + } + ] + ], + "output": [ + { + "smorfs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.smorfs.faa.gz": { + "type": "file", + "description": "A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.", + "pattern": "*.smorfs.faa.gz" + } + } + ] + }, + { + "all_orfs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.all_orfs.faa.gz": { + "type": "file", + "description": "A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.", + "pattern": "*.all_orfs.faa.gz" + } + } + ] + }, + { + "amp_prediction": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.prediction.gz": { + "type": "file", + "description": "A zipped file, with all predicted amps in a table format.", + "pattern": "*.prediction.gz" + } + } + ] + }, + { + "readme_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.md": { + "type": "file", + "description": "A readme file containing tool specific information (e.g. citations, details about the output, etc.).", + "pattern": "*.md" + } + } + ] + }, + { + "log_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*_log.txt": { + "type": "file", + "description": "A log file containing the information pertaining to the run.", + "pattern": "*_log.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -79481,78 +99932,142 @@ "doi": "10.1101/496521", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ipbam": { - "type": "file", - "description": "The ChIP-seq treatment file" - } - }, - { - "controlbam": { - "type": "file", - "description": "The control file" - } - }, - { - "macs2_gsize": { - "type": "string", - "description": "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "peak": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}" - } - }, - { - "xls": { - "type": "file", - "description": "xls file containing annotated peaks", - "pattern": "*.xls" - } - }, - { - "gapped": { - "type": "file", - "description": "Optional BED file containing gapped peak", - "pattern": "*.gappedPeak" - } - }, - { - "bed": { - "type": "file", - "description": "Optional BED file containing peak summits locations for every peak", - "pattern": "*.bed" - } - }, - { - "bdg": { - "type": "file", - "description": "Optional bedGraph files for input and treatment input samples", - "pattern": "*.bdg" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ipbam": { + "type": "file", + "description": "The ChIP-seq treatment file" + } + }, + { + "controlbam": { + "type": "file", + "description": "The control file" + } + } + ], + [ + { + "macs2_gsize": { + "type": "string", + "description": "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)" + } + } + ] + ], + "output": [ + { + "peak": [ + { + "meta": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}" + } + }, + { + "*.{narrowPeak,broadPeak}": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}" + } + } + ] + }, + { + "xls": [ + { + "meta": { + "type": "file", + "description": "xls file containing annotated peaks", + "pattern": "*.xls" + } + }, + { + "*.xls": { + "type": "file", + "description": "xls file containing annotated peaks", + "pattern": "*.xls" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] + }, + { + "gapped": [ + { + "meta": { + "type": "file", + "description": "Optional BED file containing gapped peak", + "pattern": "*.gappedPeak" + } + }, + { + "*.gappedPeak": { + "type": "file", + "description": "Optional BED file containing gapped peak", + "pattern": "*.gappedPeak" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "file", + "description": "Optional BED file containing peak summits locations for every peak", + "pattern": "*.bed" + } + }, + { + "*.bed": { + "type": "file", + "description": "Optional BED file containing peak summits locations for every peak", + "pattern": "*.bed" + } + } + ] + }, + { + "bdg": [ + { + "meta": { + "type": "file", + "description": "Optional bedGraph files for input and treatment input samples", + "pattern": "*.bdg" + } + }, + { + "*.bdg": { + "type": "file", + "description": "Optional bedGraph files for input and treatment input samples", + "pattern": "*.bdg" + } + } + ] } ], "authors": [ @@ -79608,84 +100123,137 @@ "doi": "10.1101/496521", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample_1', single_end:false ]`\n" - } - }, - { - "ipbam": { - "type": "file", - "description": "The ChIP-seq treatment file" - } - }, - { - "controlbam": { - "type": "file", - "description": "The control file" - } - }, - { - "macs3_gsize": { - "type": "string", - "description": "Effective genome size. It can be 1.0e+9 or 1000000000,\nor shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse\n(2,652,783,500), 'ce' for C. elegans (100,286,401)\nand 'dm' for fruitfly (142,573,017), Default:hs.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "peak": { - "type": "file", - "description": "BED file containing annotated peaks", - "pattern": "*.gappedPeak,*.narrowPeak}" - } - }, - { - "xls": { - "type": "file", - "description": "xls file containing annotated peaks", - "pattern": "*.xls" - } - }, - { - "gapped": { - "type": "file", - "description": "Optional BED file containing gapped peak", - "pattern": "*.gappedPeak" - } - }, - { - "bed": { - "type": "file", - "description": "Optional BED file containing peak summits locations for every peak", - "pattern": "*.bed" - } - }, - { - "bdg": { - "type": "file", - "description": "Optional bedGraph files for input and treatment input samples", - "pattern": "*.bdg" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample_1', single_end:false ]`\n" + } + }, + { + "ipbam": { + "type": "file", + "description": "The ChIP-seq treatment file" + } + }, + { + "controlbam": { + "type": "file", + "description": "The control file" + } + } + ], + [ + { + "macs3_gsize": { + "type": "string", + "description": "Effective genome size. It can be 1.0e+9 or 1000000000,\nor shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse\n(2,652,783,500), 'ce' for C. elegans (100,286,401)\nand 'dm' for fruitfly (142,573,017), Default:hs.\n" + } + } + ] + ], + "output": [ + { + "peak": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{narrowPeak,broadPeak}": { + "type": "file", + "description": "BED file containing annotated peaks", + "pattern": "*.gappedPeak,*.narrowPeak}" + } + } + ] + }, + { + "xls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.xls": { + "type": "file", + "description": "xls file containing annotated peaks", + "pattern": "*.xls" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] + }, + { + "gapped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.gappedPeak": { + "type": "file", + "description": "Optional BED file containing gapped peak", + "pattern": "*.gappedPeak" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Optional BED file containing peak summits locations for every peak", + "pattern": "*.bed" + } + } + ] + }, + { + "bdg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bdg": { + "type": "file", + "description": "Optional bedGraph files for input and treatment input samples", + "pattern": "*.bdg" + } + } + ] } ], "authors": [ @@ -79718,123 +100286,147 @@ "doi": "10.1093/nar/gkf436", "licence": [ "BSD" - ] + ], + "identifier": "biotools:MAFFT" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing the sequences to align. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "add": { - "type": "file", - "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "addfragments": { - "type": "file", - "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "addfull": { - "type": "file", - "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "addprofile": { - "type": "file", - "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "addlong": { - "type": "file", - "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`. May be gzipped or uncompressed.", - "pattern": "*.{fa,fasta}{.gz,}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fas": { - "type": "file", - "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", - "pattern": "*.fas{.gz,}" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "biotools:MAFFT" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing the sequences to align. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "add": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addfragments": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addfull": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addprofile": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "addlong": { + "type": "file", + "description": "FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`. May be gzipped or uncompressed.", + "pattern": "*.{fa,fasta}{.gz,}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "fas": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fas{.gz,}": { + "type": "file", + "description": "Aligned sequences in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.fas{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -79886,59 +100478,82 @@ "doi": "10.1186/s13059-014-0554-4", "licence": [ "BSD License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "library": { - "type": "file", - "description": "library file containing the sgRNA and gene name", - "pattern": "*.{csv,txt,tsv}" - } - }, - { - "inputfile": { - "type": "file", - "description": "library fastq file containing the sgRNA and gene name or count table containing the sgRNA and number of reads to per sample", - "pattern": "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "norm": { - "type": "file", - "description": "File containing normalized read counts", - "pattern": "*.count_normalized.txt" - } - }, - { - "count": { - "type": "file", - "description": "File containing read counts", - "pattern": "*.countsummary.txt" - } + ], + "identifier": "biotools:mageck" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputfile": { + "type": "file", + "description": "library fastq file containing the sgRNA and gene name or count table containing the sgRNA and number of reads to per sample", + "pattern": "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}" + } + } + ], + [ + { + "library": { + "type": "file", + "description": "library file containing the sgRNA and gene name", + "pattern": "*.{csv,txt,tsv}" + } + } + ] + ], + "output": [ + { + "count": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*count.txt": { + "type": "file", + "description": "File containing read counts", + "pattern": "*.countsummary.txt" + } + } + ] + }, + { + "norm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.count_normalized.txt": { + "type": "file", + "description": "File containing normalized read counts", + "pattern": "*.count_normalized.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -79977,59 +100592,82 @@ "doi": "10.1186/s13059-015-0843-6", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "count_table": { - "type": "file", - "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", - "pattern": "*.{txt,tsv}" - } - }, - { - "design_matrix": { - "type": "file", - "description": "Design matrix describing the samples and conditions", - "pattern": "*.{txt,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gene_summary": { - "type": "file", - "description": "Gene summary file describing the fitness score\nand associated p-values.\n", - "pattern": "*.{gene_summary}" - } - }, - { - "sgrna_summary": { - "type": "file", - "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", - "pattern": "*.{gene_summary}" - } + ], + "identifier": "biotools:mageck" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "count_table": { + "type": "file", + "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", + "pattern": "*.{txt,tsv}" + } + } + ], + [ + { + "design_matrix": { + "type": "file", + "description": "Design matrix describing the samples and conditions", + "pattern": "*.{txt,tsv}" + } + } + ] + ], + "output": [ + { + "gene_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gene_summary.txt": { + "type": "file", + "description": "Gene summary file describing the fitness score\nand associated p-values.\n", + "pattern": "*.{gene_summary}" + } + } + ] + }, + { + "sgrna_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sgrna_summary.txt": { + "type": "file", + "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", + "pattern": "*.{gene_summary}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80068,59 +100706,90 @@ "doi": "10.1186/s13059-015-0843-6", "licence": [ "BSD License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "count_table": { - "type": "file", - "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", - "pattern": "*.{txt,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gene_summary": { - "type": "file", - "description": "Gene summary file describing the fitness score\nand associated p-values.\n", - "pattern": "*.{gene_summary.txt}" - } - }, - { - "sgrna_summary": { - "type": "file", - "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", - "pattern": "*.{sgrna_summary.txt}" - } - }, - { - "r_script": { - "type": "file", - "description": "R script allowing to output plots\nfrom main hit genes\n", - "pattern": "*.R" - } + ], + "identifier": "biotools:mageck" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "count_table": { + "type": "file", + "description": "Count table file.\nEach line in the table should include\nsgRNA name (1st column), target gene (2nd column)\nand read counts in each sample.\n", + "pattern": "*.{txt,tsv}" + } + } + ] + ], + "output": [ + { + "gene_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gene_summary.txt": { + "type": "file", + "description": "Gene summary file describing the fitness score\nand associated p-values.\n", + "pattern": "*.{gene_summary.txt}" + } + } + ] + }, + { + "sgrna_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sgrna_summary.txt": { + "type": "file", + "description": "sgRNA summary file describing the sgRNA and\nassociated gene\n", + "pattern": "*.{sgrna_summary.txt}" + } + } + ] + }, + { + "r_script": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.R": { + "type": "file", + "description": "R script allowing to output plots\nfrom main hit genes\n", + "pattern": "*.R" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80160,64 +100829,79 @@ "doi": "10.1093/bioinformatics/btaa992", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing the fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the specified guide tree (if supplied)\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format.", - "pattern": "*.{fa,fna,fasta}" - } - }, - { - "tree": { - "type": "file", - "description": "Optional path to a file containing a guide tree in newick format to use as input. If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, MAGUS will construct its own guide tree. If empty, `fasttree` is used as a default.", - "pattern": "*.{dnd,tree}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample meta information.\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "alignment": { - "type": "file", - "description": "File containing the output alignment, in FASTA format containing gaps. The sequences may be in a different order than in the input FASTA. The output file may or may not be gzipped, depending on the value supplied to `compress`.", - "pattern": "*.aln{.gz,}" - } + ], + "identifier": "biotools:magus" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing the fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format.", + "pattern": "*.{fa,fna,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for the specified guide tree (if supplied)\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Optional path to a file containing a guide tree in newick format to use as input. If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, MAGUS will construct its own guide tree. If empty, `fasttree` is used as a default.", + "pattern": "*.{dnd,tree}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample meta information.\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "File containing the output alignment, in FASTA format containing gaps. The sequences may be in a different order than in the input FASTA. The output file may or may not be gzipped, depending on the value supplied to `compress`.", + "pattern": "*.aln{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80254,45 +100938,56 @@ "doi": "10.1093/bioinformatics/btaa992", "licence": [ "MIT" - ] + ], + "identifier": "biotools:magus" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta meta information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format.", + "pattern": "*.{fa,fna,fasta}" + } } + ] + ], + "output": [ + { + "tree": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tree": { + "type": "file", + "description": "File containing the output guidetree, in newick format.", + "pattern": "*.tree" + } + } + ] }, { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format.", - "pattern": "*.{fa,fna,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tree": { - "type": "file", - "description": "File containing the output guidetree, in newick format.", - "pattern": "*.tree" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80333,54 +101028,73 @@ "doi": "10.1038/s41559-017-0446-6", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "fastas": { - "type": "file", - "description": "Directory of, or list of FASTA reference files for indexing", - "pattern": "*/|*.fasta" + [ + { + "fastas": { + "type": "file", + "description": "Directory of, or list of FASTA reference files for indexing", + "pattern": "*/|*.fasta" + } } - }, - { - "gff": { - "type": "file", - "description": "Directory of, or GFF3 files of input FASTA files", - "pattern": "*/|*.gff|*.gff3" + ], + [ + { + "gff": { + "type": "file", + "description": "Directory of, or GFF3 files of input FASTA files", + "pattern": "*/|*.gff|*.gff3" + } } - }, - { - "mapping_db": { - "type": "file", - "description": "MEGAN .db file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html", - "pattern": "*.db" + ], + [ + { + "mapping_db": { + "type": "file", + "description": "MEGAN .db file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html", + "pattern": "*.db" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "malt_index/": { + "type": "directory", + "description": "Directory containing MALT database index directory", + "pattern": "malt_index/" + } + } + ] }, { - "index": { - "type": "directory", - "description": "Directory containing MALT database index directory", - "pattern": "malt_index/" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] }, { - "log": { - "type": "file", - "description": "Log file from STD out of malt-build", - "pattern": "malt-build.log" - } + "log": [ + { + "malt-build.log": { + "type": "file", + "description": "Log file from STD out of malt-build", + "pattern": "malt-build.log" + } + } + ] } ], "authors": [ @@ -80423,60 +101137,102 @@ "doi": "10.1038/s41559-017-0446-6", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastqs": { - "type": "file", - "description": "Input FASTQ files", - "pattern": "*.{fastq.gz,fq.gz}" - } - }, - { - "index": { - "type": "directory", - "description": "Index/database directory from malt-build", - "pattern": "*/" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "rma6": { - "type": "file", - "description": "MEGAN6 RMA6 file", - "pattern": "*.rma6" - } - }, - { - "alignments": { - "type": "file", - "description": "Alignment files in Tab, Text or MEGAN-compatible SAM format", - "pattern": "*.{tab,txt,sam}" - } - }, - { - "log": { - "type": "file", - "description": "Log of verbose MALT stdout", - "pattern": "*-malt-run.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastqs": { + "type": "file", + "description": "Input FASTQ files", + "pattern": "*.{fastq.gz,fq.gz}" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Index/database directory from malt-build", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "rma6": [ + { + "meta": { + "type": "file", + "description": "MEGAN6 RMA6 file", + "pattern": "*.rma6" + } + }, + { + "*.rma6": { + "type": "file", + "description": "MEGAN6 RMA6 file", + "pattern": "*.rma6" + } + } + ] + }, + { + "alignments": [ + { + "meta": { + "type": "file", + "description": "Alignment files in Tab, Text or MEGAN-compatible SAM format", + "pattern": "*.{tab,txt,sam}" + } + }, + { + "*.{tab,text,sam,tab.gz,text.gz,sam.gz}": { + "type": "file", + "description": "Alignment files in Tab, Text or MEGAN-compatible SAM format", + "pattern": "*.{tab,txt,sam}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log of verbose MALT stdout", + "pattern": "*-malt-run.log" + } + }, + { + "*.log": { + "type": "file", + "description": "Log of verbose MALT stdout", + "pattern": "*-malt-run.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80525,53 +101281,75 @@ "doi": "10.1186/s13059-019-1903-0", "licence": [ "GPL 3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "rma6": { - "type": "file", - "description": "RMA6 files from MALT", - "pattern": "*.rma6" - } - }, - { - "taxon_list": { - "type": "file", - "description": "List of target taxa to evaluate", - "pattern": "*.txt" - } - }, - { - "ncbi_dir": { - "type": "directory", - "description": "Directory containing NCBI taxonomy map and tre files", - "pattern": "${ncbi_dir}/" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "directory", - "description": "Directory containing MaltExtract text results files", - "pattern": "results/" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rma6": { + "type": "file", + "description": "RMA6 files from MALT", + "pattern": "*.rma6" + } + } + ], + [ + { + "taxon_list": { + "type": "file", + "description": "List of target taxa to evaluate", + "pattern": "*.txt" + } + } + ], + [ + { + "ncbi_dir": { + "type": "directory", + "description": "Directory containing NCBI taxonomy map and tre files", + "pattern": "${ncbi_dir}/" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "directory", + "description": "Directory containing MaltExtract text results files", + "pattern": "results/" + } + }, + { + "results": { + "type": "directory", + "description": "Directory containing MaltExtract text results files", + "pattern": "results/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80604,65 +101382,88 @@ "doi": "10.1093/bioinformatics/btv710", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file produces by Manta", - "pattern": "*.vcf.gz" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with reformatted inversions", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "TBI file produces by Manta", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "biotools:manta_sv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file produces by Manta", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fa,fna}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with reformatted inversions", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "TBI file produces by Manta", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80705,134 +101506,201 @@ "doi": "10.1093/bioinformatics/btv710", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file. For joint calling use a list of files.", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM/SAM index file. For joint calling use a list of files.", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - }, - { - "target_bed_tbi": { - "type": "file", - "description": "Index for BED file containing target regions for variant calling", - "pattern": "*.{bed.tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}" - } - }, - { - "config": { - "type": "file", - "description": "Manta configuration file", - "pattern": "*.{ini,conf,config}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "candidate_small_indels_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "candidate_small_indels_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "candidate_sv_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "candidate_sv_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "diploid_sv_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "diploid_sv_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:manta_sv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file. For joint calling use a list of files.", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "index": { + "type": "file", + "description": "BAM/CRAM/SAM index file. For joint calling use a list of files.", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + }, + { + "target_bed_tbi": { + "type": "file", + "description": "Index for BED file containing target regions for variant calling", + "pattern": "*.{bed.tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}" + } + } + ], + [ + { + "config": { + "type": "file", + "description": "Manta configuration file", + "pattern": "*.{ini,conf,config}" + } + } + ] + ], + "output": [ + { + "candidate_small_indels_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_small_indels.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "candidate_small_indels_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_small_indels.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "candidate_sv_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "candidate_sv_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "diploid_sv_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*diploid_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "diploid_sv_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*diploid_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -80883,162 +101751,249 @@ "doi": "10.1093/bioinformatics/btv710", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_normal": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index_normal": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "input_tumor": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index_tumor": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - }, - { - "target_bed_tbi": { - "type": "file", - "description": "Index for BED file containing target regions for variant calling", - "pattern": "*.{bed.tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}" - } - }, - { - "config": { - "type": "file", - "description": "Manta configuration file", - "pattern": "*.{ini,conf,config}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "candidate_small_indels_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "candidate_small_indels_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "candidate_sv_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "candidate_sv_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "diploid_sv_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "diploid_sv_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "somatic_sv_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "somatic_sv_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:manta_sv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_normal": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index_normal": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "input_tumor": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index_tumor": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + }, + { + "target_bed_tbi": { + "type": "file", + "description": "Index for BED file containing target regions for variant calling", + "pattern": "*.{bed.tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}" + } + } + ], + [ + { + "config": { + "type": "file", + "description": "Manta configuration file", + "pattern": "*.{ini,conf,config}" + } + } + ] + ], + "output": [ + { + "candidate_small_indels_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_small_indels.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "candidate_small_indels_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_small_indels.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "candidate_sv_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "candidate_sv_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.candidate_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "diploid_sv_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diploid_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "diploid_sv_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diploid_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "somatic_sv_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "somatic_sv_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81087,134 +102042,201 @@ "doi": "10.1093/bioinformatics/btv710", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - }, - { - "target_bed_tbi": { - "type": "file", - "description": "Index for BED file containing target regions for variant calling", - "pattern": "*.{bed.tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}" - } - }, - { - "config": { - "type": "file", - "description": "Manta configuration file", - "pattern": "*.{ini,conf,config}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "candidate_small_indels_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "candidate_small_indels_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "candidate_sv_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "candidate_sv_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "tumor_sv_vcf": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "tumor_sv_vcf_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:manta_sv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + }, + { + "target_bed_tbi": { + "type": "file", + "description": "Index for BED file containing target regions for variant calling", + "pattern": "*.{bed.tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}" + } + } + ], + [ + { + "config": { + "type": "file", + "description": "Manta configuration file", + "pattern": "*.{ini,conf,config}" + } + } + ] + ], + "output": [ + { + "candidate_small_indels_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_small_indels.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "candidate_small_indels_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_small_indels.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "candidate_sv_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "candidate_sv_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*candidate_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "tumor_sv_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*tumor_sv.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tumor_sv_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*tumor_sv.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81255,45 +102277,56 @@ "tool_dev_url": "https://github.com/mpieva/mapAD", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta,fa,fna}" + } } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta,fa,fna}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mapad/": { + "type": "directory", + "description": "mapAD genome index files", + "pattern": "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + } + } + ] }, { - "index": { - "type": "directory", - "description": "mapAD genome index files", - "pattern": "*.{tbw,tle,toc,tos,tpi,trt,tsa}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81345,100 +102378,127 @@ "tool_dev_url": "https://github.com/mpieva/mapAD", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory)\n", - "pattern": "*.{bam,cram,fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "mapAD genome index files (mandatory)", - "pattern": "*.{tbw,tle,toc,tos,tpi,trt,tsa}" - } - }, - { - "mismatch_parameter": { - "type": "float", - "description": "Minimum probability of the number of mismatches under `-D` base error rate\n" - } - }, - { - "double_stranded_library": { - "type": "boolean", - "description": "Library preparation method - specify if double stranded else it's assumed single stranded" - } - }, - { - "five_prime_overhang": { - "type": "float", - "description": "5'-overhang length parameter" - } - }, - { - "three_prime_overhang": { - "type": "float", - "description": "3'-overhang length parameter" - } - }, - { - "deam_rate_double_stranded": { - "type": "float", - "description": "Deamination rate in double-stranded stem of a read" - } - }, - { - "deam_rate_single_stranded": { - "type": "float", - "description": "Deamination rate in single-stranded ends of a read" - } - }, - { - "indel_rate": { - "type": "float", - "description": "Expected rate of indels between reads and reference" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM/SAM file containing read alignments", - "pattern": "*.bam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory)\n", + "pattern": "*.{bam,cram,fastq,fastq.gz,fq,fq.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "mapAD genome index files (mandatory)", + "pattern": "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + } + } + ], + [ + { + "mismatch_parameter": { + "type": "float", + "description": "Minimum probability of the number of mismatches under `-D` base error rate\n" + } + } + ], + [ + { + "double_stranded_library": { + "type": "boolean", + "description": "Library preparation method - specify if double stranded else it's assumed single stranded" + } + } + ], + [ + { + "five_prime_overhang": { + "type": "float", + "description": "5'-overhang length parameter" + } + } + ], + [ + { + "three_prime_overhang": { + "type": "float", + "description": "3'-overhang length parameter" + } + } + ], + [ + { + "deam_rate_double_stranded": { + "type": "float", + "description": "Deamination rate in double-stranded stem of a read" + } + } + ], + [ + { + "deam_rate_single_stranded": { + "type": "float", + "description": "Deamination rate in single-stranded ends of a read" + } + } + ], + [ + { + "indel_rate": { + "type": "float", + "description": "Expected rate of indels between reads and reference" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM/SAM file containing read alignments", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81473,171 +102533,354 @@ "doi": "10.1093/bioinformatics/btt193", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file, the reference the input BAM was mapped against", - "pattern": "*.{fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "runtime_log": { - "type": "file", - "description": "Log file with a summary of command lines used and timestamps.", - "pattern": "Runtime_log.txt" - } - }, - { - "fragmisincorporation_plot": { - "type": "file", - "description": "A pdf file that displays both fragmentation and misincorporation patterns.", - "pattern": "Fragmisincorporation_plot.pdf" - } - }, - { - "length_plot": { - "type": "file", - "description": "A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand.", - "pattern": "Length_plot.pdf" - } - }, - { - "misincorporation": { - "type": "file", - "description": "Contains a table with occurrences for each type of mutations and relative positions from the reads ends.", - "pattern": "misincorporation.txt" - } - }, - { - "pctot_freq": { - "type": "file", - "description": "Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends.", - "pattern": "5pCtoT_freq.txt" - } - }, - { - "pgtoa_freq": { - "type": "file", - "description": "Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends.", - "pattern": "3pGtoA_freq.txt" - } - }, - { - "dnacomp": { - "type": "file", - "description": "Contains a table of the reference genome base composition per position, inside reads and adjacent regions.", - "pattern": "dnacomp.txt" - } - }, - { - "lgdistribution": { - "type": "file", - "description": "Contains a table with read length distributions per strand.", - "pattern": "lgdistribution.txt" - } - }, - { - "stats_out_mcmc_hist": { - "type": "file", - "description": "A MCMC histogram for the damage parameters and log likelihood.", - "pattern": "Stats_out_MCMC_hist.pdf" - } - }, - { - "stats_out_mcmc_iter": { - "type": "file", - "description": "Values for the damage parameters and log likelihood in each MCMC iteration.", - "pattern": "Stats_out_MCMC_iter.csv" - } - }, - { - "stats_out_mcmc_trace": { - "type": "file", - "description": "A MCMC trace plot for the damage parameters and log likelihood.", - "pattern": "Stats_out_MCMC_trace.pdf" - } - }, - { - "stats_out_mcmc_iter_summ_stat": { - "type": "file", - "description": "Summary statistics for the damage parameters estimated posterior distributions.", - "pattern": "Stats_out_MCMC_iter_summ_stat.csv" - } - }, - { - "stats_out_mcmc_post_pred": { - "type": "file", - "description": "Empirical misincorporation frequency and posterior predictive intervals from the fitted model.", - "pattern": "Stats_out_MCMC_post_pred.pdf" - } - }, - { - "stats_out_mcmc_correct_prob": { - "type": "file", - "description": "Position specific probability of a C->T and G->A misincorporation is due to damage.", - "pattern": "Stats_out_MCMC_correct_prob.csv" - } - }, - { - "dnacomp_genome": { - "type": "file", - "description": "Contains the global reference genome base composition (computed by seqtk).", - "pattern": "dnacomp_genome.csv" - } - }, - { - "rescaled": { - "type": "file", - "description": "Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores.", - "pattern": "*.{bam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Allignments in a FASTA file, only if flagged by -d.", - "pattern": "*.{fasta}" - } - }, - { - "folder": { - "type": "directory", - "description": "Folder created when --plot-only, --rescale and --stats-only flags are passed.", - "pattern": "*/" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Fasta file, the reference the input BAM was mapped against", + "pattern": "*.{fasta}" + } + } + ] + ], + "output": [ + { + "runtime_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Runtime_log.txt": { + "type": "file", + "description": "Log file with a summary of command lines used and timestamps.", + "pattern": "Runtime_log.txt" + } + } + ] + }, + { + "fragmisincorporation_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Fragmisincorporation_plot.pdf": { + "type": "file", + "description": "A pdf file that displays both fragmentation and misincorporation patterns.", + "pattern": "Fragmisincorporation_plot.pdf" + } + } + ] + }, + { + "length_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Length_plot.pdf": { + "type": "file", + "description": "A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand.", + "pattern": "Length_plot.pdf" + } + } + ] + }, + { + "misincorporation": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/misincorporation.txt": { + "type": "file", + "description": "Contains a table with occurrences for each type of mutations and relative positions from the reads ends.", + "pattern": "misincorporation.txt" + } + } + ] + }, + { + "lgdistribution": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/lgdistribution.txt": { + "type": "file", + "description": "Contains a table with read length distributions per strand.", + "pattern": "lgdistribution.txt" + } + } + ] + }, + { + "dnacomp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/dnacomp.txt": { + "type": "file", + "description": "Contains a table of the reference genome base composition per position, inside reads and adjacent regions.", + "pattern": "dnacomp.txt" + } + } + ] + }, + { + "stats_out_mcmc_hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Stats_out_MCMC_hist.pdf": { + "type": "file", + "description": "A MCMC histogram for the damage parameters and log likelihood.", + "pattern": "Stats_out_MCMC_hist.pdf" + } + } + ] + }, + { + "stats_out_mcmc_iter": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Stats_out_MCMC_iter.csv": { + "type": "file", + "description": "Values for the damage parameters and log likelihood in each MCMC iteration.", + "pattern": "Stats_out_MCMC_iter.csv" + } + } + ] + }, + { + "stats_out_mcmc_trace": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Stats_out_MCMC_trace.pdf": { + "type": "file", + "description": "A MCMC trace plot for the damage parameters and log likelihood.", + "pattern": "Stats_out_MCMC_trace.pdf" + } + } + ] + }, + { + "stats_out_mcmc_iter_summ_stat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Stats_out_MCMC_iter_summ_stat.csv": { + "type": "file", + "description": "Summary statistics for the damage parameters estimated posterior distributions.", + "pattern": "Stats_out_MCMC_iter_summ_stat.csv" + } + } + ] + }, + { + "stats_out_mcmc_post_pred": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Stats_out_MCMC_post_pred.pdf": { + "type": "file", + "description": "Empirical misincorporation frequency and posterior predictive intervals from the fitted model.", + "pattern": "Stats_out_MCMC_post_pred.pdf" + } + } + ] + }, + { + "stats_out_mcmc_correct_prob": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/Stats_out_MCMC_correct_prob.csv": { + "type": "file", + "description": "Position specific probability of a C->T and G->A misincorporation is due to damage.", + "pattern": "Stats_out_MCMC_correct_prob.csv" + } + } + ] + }, + { + "dnacomp_genome": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/dnacomp_genome.csv": { + "type": "file", + "description": "Contains the global reference genome base composition (computed by seqtk).", + "pattern": "dnacomp_genome.csv" + } + } + ] + }, + { + "rescaled": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/*rescaled.bam": { + "type": "file", + "description": "Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores.", + "pattern": "*.{bam}" + } + } + ] + }, + { + "pctot_freq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/5pCtoT_freq.txt": { + "type": "file", + "description": "Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends.", + "pattern": "5pCtoT_freq.txt" + } + } + ] + }, + { + "pgtoa_freq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/3pGtoA_freq.txt": { + "type": "file", + "description": "Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends.", + "pattern": "3pGtoA_freq.txt" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "results_*/*.fasta": { + "type": "file", + "description": "Allignments in a FASTA file, only if flagged by -d.", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "folder": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "*/": { + "type": "directory", + "description": "Folder created when --plot-only, --rescale and --stats-only flags are passed.", + "pattern": "*/" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81671,52 +102914,65 @@ "doi": "10.1186/s13059-016-0997-x", "licence": [ "https://github.com/marbl/Mash/blob/master/LICENSE.txt" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reference": { - "type": "file", - "description": "FASTA, FASTQ or Mash sketch", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" - } - }, - { - "query": { - "type": "file", - "description": "FASTA, FASTQ or Mash sketch", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "dist": { - "type": "file", - "description": "The results from mash dist", - "pattern": "*.txt" - } + ], + "identifier": "biotools:mash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query": { + "type": "file", + "description": "FASTA, FASTQ or Mash sketch", + "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" + } + } + ], + [ + { + "reference": { + "type": "file", + "description": "FASTA, FASTQ or Mash sketch", + "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" + } + } + ] + ], + "output": [ + { + "dist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "The results from mash dist", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81750,52 +103006,70 @@ "doi": "10.1186/s13059-016-0997-x", "licence": [ "https://github.com/marbl/Mash/blob/master/LICENSE.txt" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query": { - "type": "file", - "description": "Query sequences", - "pattern": "*.fastq.gz" - } - }, - { - "sequence_sketch": { - "type": "file", - "description": "Sequence files to match against", - "pattern": "*.msh" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "screen": { - "type": "file", - "description": "List of sequences from fastx_db similar to query sequences", - "pattern": "*.screen" - } + ], + "identifier": "biotools:mash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query": { + "type": "file", + "description": "Query sequences", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequences_sketch": { + "type": "file", + "description": "sketch file of sequences" + } + } + ] + ], + "output": [ + { + "screen": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.screen": { + "type": "file", + "description": "List of sequences from fastx_db similar to query sequences", + "pattern": "*.screen" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81842,51 +103116,72 @@ "doi": "10.1186/s13059-016-0997-x", "licence": [ "https://github.com/marbl/Mash/blob/master/LICENSE.txt" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input paired-end FastQ files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mash": { - "type": "file", - "description": "Sketch output", - "pattern": "*.{mash}" - } - }, - { - "stats": { - "type": "file", - "description": "Sketch statistics", - "pattern": "*.{mash_stats}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:mash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired-end FastQ files" + } + } + ] + ], + "output": [ + { + "mash": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.msh": { + "type": "file", + "description": "Sketch output", + "pattern": "*.{mash}" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mash_stats": { + "type": "file", + "description": "Sketch statistics", + "pattern": "*.{mash_stats}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -81930,52 +103225,71 @@ "doi": "10.1007/978-3-319-56970-3_5", "licence": [ "Public Domain" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input fasta file containing query sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "reference": { - "type": "file", - "description": "Input fasta file containing reference sequences", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*.paf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:mashmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input fasta file containing query sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "Input fasta file containing reference sequences", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ] + ], + "output": [ + { + "paf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*.paf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82009,52 +103323,73 @@ "doi": "10.21105/joss.01762", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "FASTA, FASTQ, GenBank, or Mash sketch files", - "pattern": "*.{fna,fna.gz,fasta,fasta.gz,fa,fa.gz,gbk,gbk.gz,fastq.gz,msh}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tree": { - "type": "file", - "description": "A Newick formatted tree file", - "pattern": "*.{dnd}" - } - }, - { - "matrix": { - "type": "file", - "description": "A TSV matrix of pair-wise Mash distances", - "pattern": "*.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "FASTA, FASTQ, GenBank, or Mash sketch files", + "pattern": "*.{fna,fna.gz,fasta,fasta.gz,fa,fa.gz,gbk,gbk.gz,fastq.gz,msh}" + } + } + ] + ], + "output": [ + { + "tree": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dnd": { + "type": "file", + "description": "A Newick formatted tree file", + "pattern": "*.{dnd}" + } + } + ] + }, + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV matrix of pair-wise Mash distances", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82092,100 +103427,184 @@ "doi": "10.1093/bioinformatics/btv638", "licence": [ "BSD 3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs": { - "type": "file", - "description": "Multi FASTA file containing assembled contigs of a given sample", - "pattern": "*.fasta" - } - }, - { - "reads": { - "type": "file", - "description": "Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files.", - "pattern": "*.fasta" - } - }, - { - "abund": { - "type": "file", - "description": "Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "binned_fastas": { - "type": "file", - "description": "Binned contigs, one per bin designated with numeric IDs", - "pattern": "*.fasta.gz" - } - }, - { - "summary": { - "type": "file", - "description": "Summary file describing which contigs are being classified into which bin", - "pattern": "*.summary" - } - }, - { - "log": { - "type": "file", - "description": "Log file recording the core steps of MaxBin algorithm", - "pattern": "*.log.gz" - } - }, - { - "marker": { - "type": "file", - "description": "Marker gene presence numbers for each bin", - "pattern": "*.marker.gz" - } - }, - { - "unbinned_fasta": { - "type": "file", - "description": "All sequences that pass the minimum length threshold but are not classified successfully.", - "pattern": "*.noclass.gz" - } - }, - { - "tooshort_fasta": { - "type": "file", - "description": "All sequences that do not meet the minimum length threshold.", - "pattern": "*.tooshort.gz" - } - }, - { - "marker_genes": { - "type": "file", - "description": "All sequences that do not meet the minimum length threshold.", - "pattern": "*.marker_of_each_gene.tar.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contigs": { + "type": "file", + "description": "Multi FASTA file containing assembled contigs of a given sample", + "pattern": "*.fasta" + } + }, + { + "reads": { + "type": "file", + "description": "Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files.", + "pattern": "*.fasta" + } + }, + { + "abund": { + "type": "file", + "description": "Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files." + } + } + ] + ], + "output": [ + { + "binned_fastas": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "Binned contigs, one per bin designated with numeric IDs", + "pattern": "*.fasta.gz" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary": { + "type": "file", + "description": "Summary file describing which contigs are being classified into which bin", + "pattern": "*.summary" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log.gz": { + "type": "file", + "description": "Log file recording the core steps of MaxBin algorithm", + "pattern": "*.log.gz" + } + } + ] + }, + { + "marker_counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.marker.gz": { + "type": "file", + "description": "Marker counts", + "pattern": "*.marker.gz" + } + } + ] + }, + { + "unbinned_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.noclass.gz": { + "type": "file", + "description": "All sequences that pass the minimum length threshold but are not classified successfully.", + "pattern": "*.noclass.gz" + } + } + ] + }, + { + "tooshort_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tooshort.gz": { + "type": "file", + "description": "All sequences that do not meet the minimum length threshold.", + "pattern": "*.tooshort.gz" + } + } + ] + }, + { + "marker_bins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_bin.tar.gz": null + } + ] + }, + { + "marker_genes": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_gene.tar.gz": { + "type": "file", + "description": "Marker genes", + "pattern": "*_gene.tar.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82222,63 +103641,75 @@ "documentation": "http://coxdocs.org/doku.php?id=maxquant:start", "licence": [ "http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf" - ] - } + ], + "identifier": "biotools:maxquant" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file with protein sequences", + "pattern": "*.{fasta}" + } + }, + { + "paramfile": { + "type": "file", + "description": "MaxQuant parameter file" + } + } + ], + [ + { + "raw": { + "type": "file", + "description": "raw files with mass spectra", + "pattern": "*.{raw,RAW,Raw}" + } + } + ] + ], + "output": [ + { + "maxquant_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "tables with peptides and protein information", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "raw": { - "type": "file", - "description": "raw files with mass spectra", - "pattern": "*.{raw,RAW,Raw}" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file with protein sequences", - "pattern": "*.{fasta}" - } - }, - { - "parfile": { - "type": "file", - "description": "MaxQuant parameter file (XML)", - "pattern": "*.{xml}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "maxquant_txt": { - "type": "file", - "description": "tables with peptides and protein information", - "pattern": "*.{txt}" - } - } - ], - "authors": [ - "@veitveit" + "authors": [ + "@veitveit" ], "maintainers": [ "@veitveit" @@ -82308,71 +103739,86 @@ "doi": "10.1038/s41592-021-01308-y", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "image": { - "type": "file", - "description": "Multi-channel image file", - "pattern": "*.{tiff,tif,h5,hdf5}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mask": { - "type": "file", - "description": "Labeled segmentation mask for image", - "pattern": "*.{tiff,tif,h5,hdf5}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "markerfile": { - "type": "file", - "description": "Marker file with channel names for image to quantify", - "pattern": "*.{csv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "Quantified regionprops_table", - "pattern": "*.{csv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "image": { + "type": "file", + "description": "Multi-channel image file", + "pattern": "*.{tiff,tif,h5,hdf5}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mask": { + "type": "file", + "description": "Labeled segmentation mask for image", + "pattern": "*.{tiff,tif,h5,hdf5}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "markerfile": { + "type": "file", + "description": "Marker file with channel names for image to quantify", + "pattern": "*.{csv}" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Quantified regionprops_table", + "pattern": "*.{csv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82410,52 +103856,73 @@ "tool_dev_url": "https://github.com/liampshaw/mcroni", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A fasta file.", - "pattern": "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "mcroni results in TSV format", - "pattern": "*.tsv" - } - }, - { - "fa": { - "type": "file", - "description": "mcr-1 matching sequences", - "pattern": "*.fa" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A fasta file.", + "pattern": "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "mcroni results in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "mcr-1 matching sequences", + "pattern": "*.fa" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82488,45 +103955,56 @@ "tool_dev_url": "https://github.com/SchapiroLabor/imc2mc", "licence": [ "GPL-3.0 license" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "txtfile": { + "type": "file", + "description": "Acquisition .txt file", + "pattern": "*.{txt}" + } } - }, - { - "txtfile": { - "type": "file", - "description": "Acquisition .txt file", - "pattern": "*.{txt}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tif": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tif": { + "type": "file", + "description": "One output .tif file containing acquisition and metadata", + "pattern": "*.{tif}" + } + } + ] }, { - "tif": { - "type": "file", - "description": "One output .tif file containing acquisition and metadata", - "pattern": "*.{tif}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82560,44 +104038,55 @@ "tool_dev_url": "https://github.com/SchapiroLabor/phenoimager2mc", "licence": [ "GPL-2.0 license" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tiles": { + "type": "list", + "description": "Folder or list with .tif files of one cycle from PhenoImager" + } } - }, - { - "tiles": { - "type": "list", - "description": "Folder or list with .tif files of one cycle from PhenoImager" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tif": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tif": { + "type": "file", + "description": "One output .tif file containing concatenated tiles of the cycle.", + "pattern": "*.{tif,tiff}" + } + } + ] }, { - "tif": { - "type": "file", - "description": "One output .tif file containing concatenated tiles of the cycle.", - "pattern": "*.{tif,tiff}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82628,45 +104117,64 @@ "documentation": "https://man7.org/linux/man-pages/man1/md5sum.1.html", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files": { - "type": "file", - "description": "Any number of files. One md5sum file will be generated for each.", - "pattern": "*.*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "checksum": { - "type": "file", - "description": "File containing checksum", - "pattern": "*.md5" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "files": { + "type": "file", + "description": "Any number of files. One md5sum file will be generated for each.", + "pattern": "*.*" + } + } + ], + [ + { + "as_separate_files": { + "type": "boolean", + "description": "If true, each file will have its own md5sum file. If false, all files will be\nchecksummed into a single md5sum file.\n" + } + } + ] + ], + "output": [ + { + "checksum": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.md5": { + "type": "file", + "description": "File containing checksum", + "pattern": "*.md5" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82704,52 +104212,63 @@ "tool_dev_url": "https://github.com/nanoporetech/medaka", "licence": [ "Mozilla Public License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input nanopore fasta/FastQ files", - "pattern": "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "assembly": { - "type": "file", - "description": "Genome assembly", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "assembly": { - "type": "file", - "description": "Polished genome assembly", - "pattern": "*.fa.gz" - } + ], + "identifier": "biotools:medaka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input nanopore fasta/FastQ files", + "pattern": "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "assembly": { + "type": "file", + "description": "Genome assembly", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "Polished genome assembly", + "pattern": "*.fa.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82791,7 +104310,8 @@ "licence": [ "GPL v3" ], - "args_id": "$args" + "args_id": "$args", + "identifier": "biotools:megahit" } }, { @@ -82799,85 +104319,146 @@ "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", "documentation": "https://zlib.net/pigz/pigz.pdf", - "args_id": "$args2" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed)\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads1": { - "type": "file", - "description": "A single or list of input FastQ files for single-end or R1 of paired-end library(s),\nrespectively in gzipped or uncompressed FASTQ or FASTA format.\n" - } - }, - { - "reads2": { - "type": "file", - "description": "A single or list of input FastQ files for R2 of paired-end library(s),\nrespectively in gzipped or uncompressed FASTQ or FASTA format.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "contigs": { - "type": "file", - "description": "Final final contigs result of the assembly in FASTA format.", - "pattern": "*.contigs.fa.gz" - } - }, - { - "k_contigs": { - "type": "file", - "description": "Contigs assembled from the de Bruijn graph of order-K", - "pattern": "k*.contigs.fa.gz" - } - }, - { - "addi_contigs": { - "type": "file", - "description": "Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K", - "pattern": "k*.addi.fa.gz" - } - }, - { - "local_contigs": { - "type": "file", - "description": "Contigs of the locally assembled contigs for k=K", - "pattern": "k*.local.fa.gz" - } - }, - { - "kfinal_contigs": { - "type": "file", - "description": "Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty", - "pattern": "k*.final.contigs.fa.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing statistics of the assembly output", - "pattern": "*.log" - } + "args_id": "$args2", + "identifier": "biotools:megahit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed)\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads1": { + "type": "file", + "description": "A single or list of input FastQ files for single-end or R1 of paired-end library(s),\nrespectively in gzipped or uncompressed FASTQ or FASTA format.\n" + } + }, + { + "reads2": { + "type": "file", + "description": "A single or list of input FastQ files for R2 of paired-end library(s),\nrespectively in gzipped or uncompressed FASTQ or FASTA format.\n" + } + } + ] + ], + "output": [ + { + "contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.fa.gz": { + "type": "file", + "description": "Final final contigs result of the assembly in FASTA format.", + "pattern": "*.contigs.fa.gz" + } + } + ] + }, + { + "k_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.contigs.fa.gz": { + "type": "file", + "description": "Contigs assembled from the de Bruijn graph of order-K", + "pattern": "k*.contigs.fa.gz" + } + } + ] + }, + { + "addi_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.addi.fa.gz": { + "type": "file", + "description": "Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K", + "pattern": "k*.addi.fa.gz" + } + } + ] + }, + { + "local_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.local.fa.gz": { + "type": "file", + "description": "Contigs of the locally assembled contigs for k=K", + "pattern": "k*.local.fa.gz" + } + } + ] + }, + { + "kfinal_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "intermediate_contigs/k*.final.contigs.fa.gz": { + "type": "file", + "description": "Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty", + "pattern": "k*.final.contigs.fa.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing statistics of the assembly output", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82912,58 +104493,81 @@ "doi": "10.1371/journal.pcbi.1004957", "licence": [ "GPL >=3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "daa": { - "type": "file", - "description": "DAA file from DIAMOND", - "pattern": "*.daa" - } - }, - { - "megan_summary": { - "type": "boolean", - "description": "Specify whether to generate a MEGAN summary file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt_gz": { - "type": "file", - "description": "Compressed text file", - "pattern": "*.txt.gz" - } - }, - { - "megan": { - "type": "file", - "description": "Optionally generated MEGAN summary file", - "pattern": "*.megan" - } + ], + "identifier": "biotools:megan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "daa": { + "type": "file", + "description": "DAA file from DIAMOND", + "pattern": "*.daa" + } + } + ], + [ + { + "megan_summary": { + "type": "boolean", + "description": "Specify whether to generate a MEGAN summary file" + } + } + ] + ], + "output": [ + { + "txt_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Compressed text file", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "megan": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.megan": { + "type": "file", + "description": "Optionally generated MEGAN summary file", + "pattern": "*.megan" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -82997,58 +104601,81 @@ "doi": "10.1371/journal.pcbi.1004957", "licence": [ "GPL >=3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "rma6": { - "type": "file", - "description": "RMA6 file from MEGAN or MALT", - "pattern": "*.rma6" - } - }, - { - "megan_summary": { - "type": "boolean", - "description": "Specify whether to generate an MEGAN summary file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "Compressed text file", - "pattern": "*.txt.gz" - } - }, - { - "megan_summary": { - "type": "file", - "description": "Optionally generated MEGAN summary file", - "pattern": "*.megan" - } + ], + "identifier": "biotools:megan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rma6": { + "type": "file", + "description": "RMA6 file from MEGAN or MALT", + "pattern": "*.rma6" + } + } + ], + [ + { + "megan_summary": { + "type": "boolean", + "description": "Specify whether to generate an MEGAN summary file" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Compressed text file", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "megan_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.megan": { + "type": "file", + "description": "Optionally generated MEGAN summary file", + "pattern": "*.megan" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -83086,45 +104713,56 @@ "tool_dev_url": "https://github.com/MDU-PHL/meningotype", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:meningotype" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited result file", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited result file", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -83157,85 +104795,108 @@ "doi": "10.1038/s41592-022-01445-y", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fasta_assembly": { - "type": "file", - "description": "Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED]", - "pattern": "*.{fasta, fasta.gz}" - } - }, - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample read information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "meryl_db_reads": { - "type": "file", - "description": "K-mer database produced from raw reads using Meryl [REQUIRED]", - "pattern": "*.{meryl_db}" - } - }, - { - "lookup_table": { - "type": "file", - "description": "Input vector of k-mer probabilities (obtained by genomescope2 with parameter --fitted_hist) [OPTIONAL]", - "pattern": "lookup_table.txt" - } - }, - { - "seqmers": { - "type": "file", - "description": "Input for pre-built sequence meryl db. By default, the sequence meryl db will be generated from the input genome assembly [OPTIONAL]", - "pattern": "*.{meryl_db}" - } - }, - { - "peak": { - "type": "float", - "description": "Input to hard set copy 1 and infer multiplicity to copy number. Can be calculated using genomescope2 [REQUIRED]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hist": { - "type": "file", - "description": "The generated 0-centered k* histogram for sequences in . Positive k* values are expected collapsed copies. Negative k* values are expected expanded copies. Closer to 0 means the expected and found k-mers are well balenced, 1:1.", - "pattern": "*.{hist}" - } - }, - { - "log_stderr": { - "type": "file", - "description": "Log (stderr) of hist tool execution. The QV and QV* metrics are reported at the end.", - "pattern": "*.{hist.stderr.log}" - } + ], + "identifier": "biotools:merfin" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta_assembly": { + "type": "file", + "description": "Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED]", + "pattern": "*.{fasta, fasta.gz}" + } + } + ], + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample read information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "meryl_db_reads": { + "type": "file", + "description": "K-mer database produced from raw reads using Meryl [REQUIRED]", + "pattern": "*.{meryl_db}" + } + } + ], + [ + { + "lookup_table": { + "type": "file", + "description": "Input vector of k-mer probabilities (obtained by genomescope2 with parameter --fitted_hist) [OPTIONAL]", + "pattern": "lookup_table.txt" + } + } + ], + [ + { + "seqmers": { + "type": "file", + "description": "Input for pre-built sequence meryl db. By default, the sequence meryl db will be generated from the input genome assembly [OPTIONAL]", + "pattern": "*.{meryl_db}" + } + } + ], + [ + { + "peak": { + "type": "float", + "description": "Input to hard set copy 1 and infer multiplicity to copy number. Can be calculated using genomescope2 [REQUIRED]" + } + } + ] + ], + "output": [ + { + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "The generated 0-centered k* histogram for sequences in . Positive k* values are expected collapsed copies. Negative k* values are expected expanded copies. Closer to 0 means the expected and found k-mers are well balenced, 1:1.", + "pattern": "*.{hist}" + } + } + ] + }, + { + "log_stderr": [ + { + "*.hist.stderr.log": { + "type": "file", + "description": "Log (stderr) of hist tool execution. The QV and QV* metrics are reported at the end.", + "pattern": "*.{hist.stderr.log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -84016,6 +105677,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -84043,87 +105708,142 @@ "doi": "10.1186/s13059-020-02134-9", "licence": [ "United States Government Work" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "child_meryl": { - "type": "directory", - "description": "Childs' k-mers (all, from WGS reads)", - "pattern": "*.meryl" - } - }, - { - "maternal_meryl": { - "type": "directory", - "description": "Haplotype1 k-mers (all, ex. maternal)", - "pattern": "*.meryl" - } - }, - { - "paternal_meryl": { - "type": "directory", - "description": "Haplotype2 k-mers (all, ex. paternal)", - "pattern": "*.meryl" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "mat_hapmer_meryl": { - "type": "directory", - "description": "Inherited maternal hap-mer dbs", - "pattern": "*_mat.hapmer.meryl" - } - }, - { - "pat_hapmer_meryl": { - "type": "directory", - "description": "Inherited paternal hap-mer dbs", - "pattern": "*_pat.hapmer.meryl" - } - }, - { - "inherited_hapmers_fl_png": { - "type": "file", - "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", - "pattern": "*_inherited_hapmers.fl.png" - } - }, - { - "inherited_hapmers_ln_png": { - "type": "file", - "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", - "pattern": "*_inherited_hapmers.ln.png" - } - }, - { - "inherited_hapmers_st_png": { - "type": "file", - "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", - "pattern": "*_inherited_hapmers.st.png" - } + ], + "identifier": "biotools:merqury" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "child_meryl": { + "type": "directory", + "description": "Childs' k-mers (all, from WGS reads)", + "pattern": "*.meryl" + } + } + ], + [ + { + "maternal_meryl": { + "type": "directory", + "description": "Haplotype1 k-mers (all, ex. maternal)", + "pattern": "*.meryl" + } + } + ], + [ + { + "paternal_meryl": { + "type": "directory", + "description": "Haplotype2 k-mers (all, ex. paternal)", + "pattern": "*.meryl" + } + } + ] + ], + "output": [ + { + "mat_hapmer_meryl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_mat.hapmer.meryl": { + "type": "directory", + "description": "Inherited maternal hap-mer dbs", + "pattern": "*_mat.hapmer.meryl" + } + } + ] + }, + { + "pat_hapmer_meryl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_pat.hapmer.meryl": { + "type": "directory", + "description": "Inherited paternal hap-mer dbs", + "pattern": "*_pat.hapmer.meryl" + } + } + ] + }, + { + "inherited_hapmers_fl_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_inherited_hapmers.fl.png": { + "type": "file", + "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", + "pattern": "*_inherited_hapmers.fl.png" + } + } + ] + }, + { + "inherited_hapmers_ln_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_inherited_hapmers.ln.png": { + "type": "file", + "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", + "pattern": "*_inherited_hapmers.ln.png" + } + } + ] + }, + { + "inherited_hapmers_st_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_inherited_hapmers.st.png": { + "type": "file", + "description": "k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs", + "pattern": "*_inherited_hapmers.st.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -84154,155 +105874,316 @@ "doi": "10.1186/s13059-020-02134-9", "licence": [ "PUBLIC DOMAIN" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meryl_db": { - "type": "file", - "description": "Meryl read database" - } - }, - { - "assembly": { - "type": "file", - "description": "FASTA assembly file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "assembly_only_kmers_bed": { - "type": "file", - "description": "The positions of the k-mers found only in an assembly for further investigation in .bed", - "pattern": "*_only.bed" - } - }, - { - "assembly_only_kmers_wig": { - "type": "file", - "description": "The positions of the k-mers found only in an assembly for further investigation in .wig", - "pattern": "*_only.wig" - } - }, - { - "stats": { - "type": "file", - "description": "Assembly statistics file", - "pattern": "*.completeness.stats" - } - }, - { - "dist_hist": { - "type": "file", - "description": "Histogram", - "pattern": "*.dist_only.hist" - } - }, - { - "spectra_cn_fl_png": { - "type": "file", - "description": "Unstacked copy number spectra filled plot in PNG format", - "pattern": "*.spectra-cn.fl.png" - } - }, - { - "spectra_cn_ln_png": { - "type": "file", - "description": "Unstacked copy number spectra line plot in PNG format", - "pattern": "*.spectra-cn.ln.png" - } - }, - { - "spectra_cn_st_png": { - "type": "file", - "description": "Stacked copy number spectra line plot in PNG format", - "pattern": "*.spectra-cn.st.png" - } - }, - { - "spectra_cn_hist": { - "type": "file", - "description": "Copy number spectra histogram", - "pattern": "*.spectra-cn.hist" - } - }, - { - "spectra_asm_fl_png": { - "type": "file", - "description": "Unstacked assembly spectra filled plot in PNG format", - "pattern": "*.spectra-asm.fl.png" - } - }, - { - "spectra_asm_ln_png": { - "type": "file", - "description": "Unstacked assembly spectra line plot in PNG format", - "pattern": "*.spectra-asm.ln.png" - } - }, - { - "spectra_asm_st_png": { - "type": "file", - "description": "Stacked assembly spectra line plot in PNG format", - "pattern": "*.spectra-asm.st.png" - } - }, - { - "spectra_asm_hist": { - "type": "file", - "description": "Assembly spectra histogram", - "pattern": "*.spectra-asm.hist" - } - }, - { - "assembly_qv": { - "type": "file", - "description": "Assembly consensus quality estimation", - "pattern": "*.qv" - } - }, - { - "scaffold_qv": { - "type": "file", - "description": "Scaffold consensus quality estimation", - "pattern": "*.qv" - } - }, - { - "read_ploidy": { - "type": "file", - "description": "Ploidy estimate from read k-mer database", - "pattern": "*.hist.ploidy" - } - }, - { - "hapmers_blob_png": { - "type": "file", - "description": "Hap-mer blob plot", - "pattern": "*.hapmers.blob.png" - } + ], + "identifier": "biotools:merqury" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "meryl_db": { + "type": "file", + "description": "Meryl read database" + } + }, + { + "assembly": { + "type": "file", + "description": "FASTA assembly file" + } + } + ] + ], + "output": [ + { + "assembly_only_kmers_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_only.bed": { + "type": "file", + "description": "The positions of the k-mers found only in an assembly for further investigation in .bed", + "pattern": "*_only.bed" + } + } + ] + }, + { + "assembly_only_kmers_wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ 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"pattern": "*.meryl" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -85000,50 +107242,63 @@ "tool_dev_url": "https://github.com/marbl/meryl", "licence": [ "GPL" - ] + ], + "identifier": "biotools:meryl" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "meryl_db": { + "type": "directory", + "description": "Meryl k-mer database" + } } - }, - { - "meryl_db": { - "type": "directory", - "description": "Meryl k-mer database" - } - }, - { - "kvalue": { - "type": "integer", - "description": "An integer value of k to use as the k-mer value." + ], + [ + { + "kvalue": { + "type": "integer", + "description": "An integer value of k to use as the k-mer value." + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hist": { + "type": "file", + "description": "Histogram of k-mers", + "pattern": "*.hist" + } + } + ] }, { - "hist": { - "type": "file", - "description": "Histogram of k-mers", - "pattern": "*.hist" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -85082,50 +107337,63 @@ "tool_dev_url": "https://github.com/marbl/meryl", "licence": [ "GPL" - ] + ], + "identifier": "biotools:meryl" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meryl_dbs": { - "type": "directory", - "description": "Meryl k-mer databases" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "meryl_dbs": { + "type": "directory", + "description": "Meryl k-mer databases" + } } - }, - { - "kvalue": { - "type": "integer", - "description": "An integer value of k to use as the k-mer value." + ], + [ + { + "kvalue": { + "type": "integer", + "description": "An integer value of k to use as the k-mer value." + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "meryl_db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unionsum.meryl": { + "type": "directory", + "description": "A Meryl k-mer database that is the union sum of the input databases", + "pattern": "*.unionsum.meryl" + } + } + ] }, { - "meryl_db": { - "type": "directory", - "description": "A Meryl k-mer database that is the union sum of the input databases", - "pattern": "*.unionsum.meryl" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -85168,52 +107436,63 @@ "doi": "10.7717/peerj.7359", "licence": [ "BSD-3-clause-LBNL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file of reads aligned on the assembled contigs", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bam.bai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "depth": { - "type": "file", - "description": "Text file listing the coverage per contig", - "pattern": ".txt.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file of reads aligned on the assembled contigs", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bam.bai" + } + } + ] + ], + "output": [ + { + "depth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Text file listing the coverage per contig", + "pattern": ".txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -85255,80 +107534,131 @@ "doi": "10.7717/peerj.7359", "licence": [ "BSD-3-clause-LBNL" - 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] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "profiles": { - "type": "file", - "description": "List of per-sample MetaPhlAn3 taxonomic abundance tables", - "pattern": "*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profiles": { + "type": "file", + "description": "List of per-sample MetaPhlAn3 taxonomic abundance tables", + "pattern": "*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Combined MetaPhlAn3 table", + "pattern": "*.txt" + } + } + ] }, { - 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"input": [ + "authors": [ + "@MGordon09" + ], + "maintainers": [ + "@MGordon09" + ] + } + }, + { + "name": "metaphlan_makedb", + "path": "modules/nf-core/metaphlan/makedb/meta.yml", + "type": "module", + "meta": { + "name": "metaphlan_makedb", + "description": "Build MetaPhlAn database for taxonomic profiling.", + "keywords": [ + "metaphlan", + "index", + "database", + "metagenomics" + ], + "tools": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "metaphlan": { + "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", + "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", + "documentation": "https://github.com/biobakery/MetaPhlAn", + "doi": "10.7554/eLife.65088", + "licence": [ + "MIT License" + ], + "identifier": "biotools:metaphlan" } - }, + } + ], + "output": [ { - "input": { - "type": "file", - "description": "Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)", - "pattern": "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" - } + "db": [ + { + "metaphlan_db_latest": { + "type": "directory", + "description": "Output directory containing the indexed METAPHLAN database", + "pattern": "*/" + } + } + ] }, { - "metaphlan_db": { - "type": "file", - "description": "Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.\nNote that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!\n", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "profile": { - "type": "file", - "description": "Tab-separated output file of the predicted taxon relative abundances", - "pattern": "*.{txt}" - } - }, - { - "biom": { - "type": "file", - "description": "General-use format for representing biological sample by observation contingency tables", - "pattern": "*.{biom}" - } - }, - { - "bowtie2out": { - "type": "file", - "description": "Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )", - "pattern": "*.{bowtie2out.txt}" - } - } - ], - "authors": [ - "@MGordon09" - ], - "maintainers": [ - "@MGordon09" - ] - } - }, - { - "name": "metaphlan_makedb", - "path": "modules/nf-core/metaphlan/makedb/meta.yml", - "type": "module", - "meta": { - "name": "metaphlan_makedb", - "description": "Build MetaPhlAn database for taxonomic profiling.", - "keywords": [ - "metaphlan", - "index", - "database", - "metagenomics" - ], - "tools": [ - { - "metaphlan": { - "description": "Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance", - "homepage": "https://huttenhower.sph.harvard.edu/metaphlan/", - "documentation": "https://github.com/biobakery/MetaPhlAn", - "doi": "10.7554/eLife.65088", - "licence": [ - "MIT License" - ] - } - } - ], - "output": [ - { - "db": { - "type": "directory", - "description": "Output directory containing the indexed METAPHLAN database", - "pattern": "*/" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -85930,45 +108472,56 @@ "doi": "10.1038/s41587-023-01688-w", "licence": [ "MIT License" - ] + ], + "identifier": "biotools:metaphlan" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "profiles": { - "type": "file", - "description": "List of per-sample MetaPhlAn4 taxonomic abundance tables", - "pattern": "*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profiles": { + "type": "file", + "description": "List of per-sample MetaPhlAn4 taxonomic abundance tables", + "pattern": "*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Combined MetaPhlAn4 table", + "pattern": "*.txt" + } + } + ] }, { - "txt": { - "type": "file", - "description": "Combined MetaPhlAn4 table", - "pattern": "*.txt" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86010,66 +108563,99 @@ "doi": "10.1038/s41587-023-01688-w", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Metaphlan can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)", - "pattern": "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" - } - }, - { - "metaphlan_db_latest": { - "type": "file", - "description": "Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/.\nNote that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN!\n", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "profile": { - "type": "file", - "description": "Tab-separated output file of the predicted taxon relative abundances", - "pattern": "*.{txt}" - } - }, - { - "biom": { - "type": "file", - "description": "General-use format for representing biological sample by observation contingency tables", - "pattern": "*.{biom}" - } - }, - { - "bt2out": { - "type": "file", - "description": "Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )", - "pattern": "*.{bowtie2out.txt}" - } + ], + "identifier": "biotools:metaphlan" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Metaphlan can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)", + "pattern": "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" + } + } + ], + [ + { + "metaphlan_db_latest": { + "type": "file", + "description": "Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/.\nNote that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN!\n", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_profile.txt": { + "type": "file", + "description": "Tab-separated output file of the predicted taxon relative abundances", + "pattern": "*.{txt}" + } + } + ] + }, + { + "biom": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.biom": { + "type": "file", + "description": "General-use format for representing biological sample by observation contingency tables", + "pattern": "*.{biom}" + } + } + ] + }, + { + "bt2out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bowtie2out.txt": { + "type": "file", + "description": "Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )", + "pattern": "*.{bowtie2out.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86114,73 +108700,98 @@ "documentation": "https://github.com/dpryan79/MethylDackel/blob/master/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.fai" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedgraph": { - "type": "file", - "description": "bedGraph file, containing per-base methylation metrics", - "pattern": "*.bedGraph" - } - }, - { - "methylkit": { - "type": "file", - "description": "methylKit file, containing per-base methylation metrics", - "pattern": "*.methylKit" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:methyldackel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedGraph": { + "type": "file", + "description": "bedGraph file, containing per-base methylation metrics", + "pattern": "*.bedGraph" + } + } + ] + }, + { + "methylkit": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.methylKit": { + "type": "file", + "description": "methylKit file, containing per-base methylation metrics", + "pattern": "*.methylKit" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86224,66 +108835,81 @@ "documentation": "https://github.com/dpryan79/MethylDackel/blob/master/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "txt": { - "type": "file", - "description": "Text file containing methylation bias", - "pattern": "*.{txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:methyldackel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Input genome fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mbias.txt": { + "type": "file", + "description": "Text file containing methylation bias", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86322,59 +108948,74 @@ "doi": "10.1101/gr.201863.115", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Reads in FASTQ format", - "pattern": "*.{fastq.gz}" - } - }, - { - "db": { - "type": "file", - "description": "A database formatted for MIDAS", - "pattern": "*.{db}" - } - }, - { - "mode": { - "type": "string", - "description": "The mode to run MIDAS is", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "file", - "description": "A directory of results from MIDAS run", - "pattern": "*" - } + ], + "identifier": "biotools:midashla" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Reads in FASTQ format", + "pattern": "*.{fastq.gz}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "A database formatted for MIDAS", + "pattern": "*.{db}" + } + } + ], + [ + { + "mode": { + "type": "string", + "description": "The mode to run MIDAS is", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*": { + "type": "file", + "description": "A directory of results from MIDAS run", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86406,45 +109047,56 @@ "tool_dev_url": "https://github.com/ViriatoII/MindaGap", "licence": [ "BSD 3-clause License" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "spot_table": { - "type": "file", - "description": "tsv file containing one spot per row with order x,y,z,gene without column header.", - "pattern": "*.{tsv,txt}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "spot_table": { + "type": "file", + "description": "tsv file containing one spot per row with order x,y,z,gene without column header.", + "pattern": "*.{tsv,txt}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "marked_dups_spots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*markedDups.txt": { + "type": "file", + "description": "tsv file containing one spot per row, with duplicated spots labeled with \"Duplicated\" in their gene column.", + "pattern": "*.{markedDups.txt}" + } + } + ] }, { - "marked_dups_spots": { - "type": "file", - "description": "tsv file containing one spot per row, with duplicated spots labeled with \"Duplicated\" in their gene column.", - "pattern": "*.{markedDups.txt}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86482,45 +109134,56 @@ "tool_dev_url": "https://github.com/ViriatoII/MindaGap", "licence": [ "BSD-3-Clause license" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "panorama": { - "type": "file", - "description": "A tiff file containing gridlines as produced by Molecular Cartography imaging.", - "pattern": "*.{tif,tiff}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "panorama": { + "type": "file", + "description": "A tiff file containing gridlines as produced by Molecular Cartography imaging.", + "pattern": "*.{tif,tiff}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tiff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{tif,tiff}": { + "type": "file", + "description": "A tiff file with gridlines filled based on consecutive gaussian blurring.", + "pattern": "*.{tiff}" + } + } + ] }, { - "tiff": { - "type": "file", - "description": "A tiff file with gridlines filled based on consecutive gaussian blurring.", - "pattern": "*.{tiff}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86559,59 +109222,90 @@ "documentation": "https://github.com/GATB/minia", "licence": [ "AGPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input reads in FastQ format", - "pattern": "*.{fastq.gz, fastq}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "contigs": { - "type": "file", - "description": "The assembled contigs", - "pattern": "*.contigs.fa" - } - }, - { - "unitigs": { - "type": "file", - "description": "The assembled unitigs", - "pattern": "*.unitigs.fa" - } - }, - { - "h5": { - "type": "file", - "description": "Minia output h5 file", - "pattern": "*{.h5}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:minia" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input reads in FastQ format", + "pattern": "*.{fastq.gz, fastq}" + } + } + ] + ], + "output": [ + { + "contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contigs.fa": { + "type": "file", + "description": "The assembled contigs", + "pattern": "*.contigs.fa" + } + } + ] + }, + { + "unitigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unitigs.fa": { + "type": "file", + "description": "The assembled unitigs", + "pattern": "*.unitigs.fa" + } + } + ] + }, + { + "h5": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.h5": { + "type": "file", + "description": "Minia output h5 file", + "pattern": "*{.h5}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86652,59 +109346,80 @@ "doi": "10.1093/bioinformatics/btw152", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input PacBio/ONT FastQ files.", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*{.paf,.paf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gfa": { - "type": "file", - "description": "Assembly graph", - "pattern": "*.gfa.gz" - } - }, - { - "assembly": { - "type": "file", - "description": "Genome assembly", - "pattern": "*.fasta.gz" - } + ], + "identifier": "biotools:miniasm" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input PacBio/ONT FastQ files.", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*{.paf,.paf.gz}" + } + } + ] + ], + "output": [ + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gfa.gz": { + "type": "file", + "description": "Assembly graph", + "pattern": "*.gfa.gz" + } + } + ] + }, + { + "assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "Genome assembly", + "pattern": "*.fasta.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86744,102 +109459,143 @@ "documentation": "https://github.com/lh3/minimap2#uguide", "licence": [ "MIT" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FASTA or FASTQ files of size 1 and 2 for single-end\nand paired-end data, respectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test_ref']\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference database in FASTA format.\n" + } + } + ], + [ + { + "bam_format": { + "type": "boolean", + "description": "Specify that output should be in BAM format" + } + } + ], + [ + { + "bam_index_extension": { + "type": "string", + "description": "BAM alignment index extension (e.g. \"bai\")" + } + } + ], + [ + { + "cigar_paf_format": { + "type": "boolean", + "description": "Specify that output CIGAR should be in PAF format" + } + } + ], + [ + { + "cigar_bam": { + "type": "boolean", + "description": "Write CIGAR with >65535 ops at the CG tag. This is recommended when\ndoing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)\n" + } + } + ] + ], + "output": [ + { + "paf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*.paf" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Alignment in BAM format", + "pattern": "*.bam" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam.${bam_index_extension}": { + "type": "file", + "description": "BAM alignment index", + "pattern": "*.bam.*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FASTA or FASTQ files of size 1 and 2 for single-end\nand paired-end data, respectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test_ref']\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference database in FASTA format.\n" - } - }, - { - "bam_format": { - "type": "boolean", - "description": "Specify that output should be in BAM format" - } - }, - { - "bam_index_extension": { - "type": "string", - "description": "BAM alignment index extension (e.g. \"bai\")" - } - }, - { - "cigar_paf_format": { - "type": "boolean", - "description": "Specify that output CIGAR should be in PAF format" - } - }, - { - "cigar_bam": { - "type": "boolean", - "description": "Write CIGAR with >65535 ops at the CG tag. This is recommended when\ndoing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*.paf" - } - }, - { - "bam": { - "type": "file", - "description": "Alignment in BAM format", - "pattern": "*.bam" - } - }, - { - "index": { - "type": "file", - "description": "BAM alignment index", - "pattern": "*.bam.*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@heuermh", - "@sofstam", - "@sateeshperi", - "@jfy133", - "@fellen31" + "authors": [ + "@heuermh", + "@sofstam", + "@sateeshperi", + "@jfy133", + "@fellen31" ], "maintainers": [ "@heuermh", @@ -86900,44 +109656,55 @@ "documentation": "https://github.com/lh3/minimap2#uguide", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format.\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format.\n" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "Minimap2 fasta index.", - "pattern": "*.mmi" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mmi": { + "type": "file", + "description": "Minimap2 fasta index.", + "pattern": "*.mmi" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -86991,63 +109758,86 @@ "documentation": "https://github.com/lh3/miniprot", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pep": { - "type": "file", - "description": "a fasta file contains one or multiple protein sequences" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\n" - } - }, - { - "ref": { - "type": "file", - "description": "Reference database in FASTA format or miniprot index format." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*.paf" - } - }, - { - "gff": { - "type": "file", - "description": "Alignment in gff format", - "pattern": "*.gff" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:miniprot" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pep": { + "type": "file", + "description": "a fasta file contains one or multiple protein sequences" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\n" + } + }, + { + "ref": { + "type": "file", + "description": "Reference database in FASTA format or miniprot index format." + } + } + ] + ], + "output": [ + { + "paf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*.paf" + } + } + ] + }, + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gff": { + "type": "file", + "description": "Alignment in gff format", + "pattern": "*.gff" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87081,44 +109871,55 @@ "documentation": "https://github.com/lh3/miniprot", "licence": [ "MIT" - ] + ], + "identifier": "biotools:miniprot" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format.\n" + } } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format.\n" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "miniprot fasta index.", - "pattern": "*.mpi" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpi": { + "type": "file", + "description": "miniprot fasta index.", + "pattern": "*.mpi" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87152,52 +109953,65 @@ "doi": "10.1186/gb-2003-5-1-r1", "licence": [ "GNU Public License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "query": { - "type": "file", - "description": "FASTA file containing the microRNA query sequences", - "pattern": "*.{fa,fasta}" - } - }, - { - "mirbase": { - "type": "file", - "description": "FASTA file containing the sequence(s) to be scanned", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "txt": { - "type": "file", - "description": "Reformatted TXT file containing microRNA targets", - "pattern": "*.{txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "query": { + "type": "file", + "description": "FASTA file containing the microRNA query sequences", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "mirbase": { + "type": "file", + "description": "FASTA file containing the sequence(s) to be scanned", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Reformatted TXT file containing microRNA targets", + "pattern": "*.{txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87235,65 +110049,92 @@ "tool_dev_url": "https://github.com/miRTop/mirtop", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "mirtop_gff": { - "type": "file", - "description": "GFF file", - "pattern": "*.{gff}" - } - }, - { - "hairpin": { - "type": "file", - "description": "Hairpin file", - "pattern": "*.{fa,fasta}" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}" - } - }, - { - "species": { - "type": "string", - "description": "Species name of the GTF file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file", - "pattern": "*.{tsv}" - } + ], + "identifier": "biotools:miRTop" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mirtop_gff": { + "type": "file", + "description": "GFF file", + "pattern": "*.{gff}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "hairpin": { + "type": "file", + "description": "Hairpin file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.{gtf}" + } + }, + { + "species": { + "type": "string", + "description": "Species name of the GTF file" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "counts/*.tsv": { + "type": "file", + "description": "TSV file", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87325,79 +110166,126 @@ "tool_dev_url": "https://github.com/miRTop/mirtop", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "mirtop_gff": { - "type": "file", - "description": "GFF file", - "pattern": "*.{gff}" - } - }, - { - "hairpin": { - "type": "file", - "description": "Hairpin file", - "pattern": "*.{fa,fasta}" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}" - } - }, - { - "species": { - "type": "string", - "description": "Species name of the GTF file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file", - "pattern": "*.{tsv}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" - } + ], + "identifier": "biotools:miRTop" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mirtop_gff": { + "type": "file", + "description": "GFF file", + "pattern": "*.{gff}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "hairpin": { + "type": "file", + "description": "Hairpin file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.{gtf}" + } + }, + { + "species": { + "type": "string", + "description": "Species name of the GTF file" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "export/*_rawData.tsv": { + "type": "file", + "description": "TSV file", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "export/*.fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "export/*.vcf*": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87429,65 +110317,92 @@ "tool_dev_url": "https://github.com/miRTop/mirtop", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "hairpin": { - "type": "file", - "description": "Hairpin file", - "pattern": "*.{fa,fasta}" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}" - } - }, - { - "species": { - "type": "string", - "description": "Species name of the GTF file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gff": { - "type": "file", - "description": "GFF file", - "pattern": "*.{gff}" - } + ], + "identifier": "biotools:miRTop" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "hairpin": { + "type": "file", + "description": "Hairpin file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.{gtf}" + } + }, + { + "species": { + "type": "string", + "description": "Species name of the GTF file" + } + } + ] + ], + "output": [ + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mirtop/*mirtop.gff": { + "type": "file", + "description": "GFF file", + "pattern": "*.{gff}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87519,52 +110434,73 @@ "tool_dev_url": "https://github.com/miRTop/mirtop", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "mirtop_gff": { - "type": "file", - "description": "Mirtop GFF file obtained with mirtop_gff", - "pattern": "*.{gff}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "TXT file with stats", - "pattern": "*.{txt}" - } - }, - { - "log": { - "type": "file", - "description": "log file with stats", - "pattern": "*.{log}" - } + ], + "identifier": "biotools:miRTop" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mirtop_gff": { + "type": "file", + "description": "Mirtop GFF file obtained with mirtop_gff", + "pattern": "*.{gff}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "stats/*.txt": { + "type": "file", + "description": "TXT file with stats", + "pattern": "*.{txt}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "stats/*_stats.log": { + "type": "file", + "description": "log file with stats", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87597,85 +110533,138 @@ "doi": "10.1186/s13059-018-1588-9", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "microRNA sequencing data", - "pattern": "*.{fastq,fastq.gz}" - } - }, - { - "mirtrace_config": { - "type": "file", - "description": "(Optional) CSV with list of FASTQ files to process with one entry per row. No headers. Each row consists of the following columns \"FASTQ file path, id, adapter, PHRED-ASCII-offset\"." - } - }, - { - "mirtrace_species": { - "type": "string", - "description": "Target species in microRNA sequencing data (miRbase encoding, e.g. “hsa” for Homo sapiens)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "html": { - "type": "file", - "description": "HTML file", - "pattern": "*.{html}" - } - }, - { - "json": { - "type": "file", - "description": "JSON file", - "pattern": "*.{json}" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file", - "pattern": "*.{tsv}" - } - }, - { - "all_fa": { - "type": "file", - "description": "QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance.", - "pattern": "*.{fa,fasta}" - } - }, - { - "rnatype_unknown_fa": { - "type": "file", - "description": "Unknown RNA type QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance.", - "pattern": "*.{fa,fasta}" - } + ], + "identifier": "biotools:miRTrace" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "microRNA sequencing data", + "pattern": "*.{fastq,fastq.gz}" + } + }, + { + "mirtrace_config": { + "type": "file", + "description": "(Optional) CSV with list of FASTQ files to process with one entry per row. No headers. Each row consists of the following columns \"FASTQ file path, id, adapter, PHRED-ASCII-offset\"." + } + } + ], + [ + { + "mirtrace_species": { + "type": "string", + "description": "Target species in microRNA sequencing data (miRbase encoding, e.g. “hsa” for Homo sapiens)" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML file", + "pattern": "*.{html}" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file", + "pattern": "*.{json}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "all_fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "qc_passed_reads.all.collapsed/*.{fa,fasta}": { + "type": "file", + "description": "QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance.", + "pattern": "*.{fa,fasta}" + } + } + ] + }, + { + "rnatype_unknown_fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}": { + "type": "file", + "description": "Unknown RNA type QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance.", + "pattern": "*.{fa,fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87708,40 +110697,75 @@ "doi": "10.1101/2022.12.23.521667", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "species": { - "type": "string", - "description": "Latin name of the species for which a mitochondrial genome should be fetched", - "pattern": "[A-Z]?[a-z]* [a-z]*" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Downloaded mitochondrial genome in Fasta format", - "pattern": "*.{fasta,fa}" - } - }, - { - "gb": { - "type": "file", - "description": "Downloaded mitochondrial genome in Genbank format", - "pattern": "*.gb" - } + ], + "identifier": "biotools:mitohifi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "species": { + "type": "string", + "description": "Latin name of the species for which a mitochondrial genome should be fetched", + "pattern": "[A-Z]?[a-z]* [a-z]*" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "file", + "description": "Downloaded mitochondrial genome in Fasta format", + "pattern": "*.{fasta,fa}" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Downloaded mitochondrial genome in Fasta format", + "pattern": "*.{fasta,fa}" + } + } + ] + }, + { + "gb": [ + { + "meta": { + "type": "file", + "description": "Downloaded mitochondrial genome in Genbank format", + "pattern": "*.gb" + } + }, + { + "*.gb": { + "type": "file", + "description": "Downloaded mitochondrial genome in Genbank format", + "pattern": "*.gb" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -87774,235 +110798,441 @@ "doi": "10.1101/2022.12.23.521667", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:mitohifi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Path to PacBio HiFi reads or contigs. Type (-r/-c) is specified in ext.args2", + "pattern": "*.{fa,fa.gz,fasta,fasta.gz}" + } + } + ], + [ + { + "ref_fa": { + "type": "file", + "description": "Reference sequence", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "ref_gb": { + "type": "file", + "description": "Reference annotation", + "pattern": "*.{gb}" + } + } + ], + [ + { + "input_mode": { + "type": "string", + "description": "Specifies type of input - reads or contigs", + "pattern": "{r,c}" + } + } + ], + [ + { + "mito_code": { + "type": "string", + "description": "Mitochondrial genetic code" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "file", + "description": "Mitochondrial sequence", + "pattern": "*.{fasta,fa}" + } + }, + { + "*fasta": { + "type": "file", + "description": "Mitochondrial sequence", + "pattern": "*.{fasta,fa}" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*contigs_stats.tsv": { + "type": "file", + "description": "Contigs statistics", + "pattern": "*contigs_stats.tsv" + } + } + ] + }, + { + "gb": [ + { + "meta": { + "type": "file", + "description": "Genome annotation in case mitofinder was used", + "pattern": "*.gb" + } + }, + { + "*gb": { + "type": "file", + "description": "Genome annotation in case mitofinder was used", + "pattern": "*.gb" + } + } + ] + }, + { + "gff": [ + { + "meta": { + "type": "file", + "description": "Genome annotation in case mitos was used", + "pattern": "*.gff" + } + }, + { + "*gff": { + "type": "file", + "description": "Genome annotation in case mitos was used", + "pattern": "*.gff" + } + } + ] + }, + { + "all_potential_contigs": [ + { + "meta": { + "type": "file", + "description": "Contains sequences of all potential contigs", + "pattern": "*all_potential_contigs.fa" + } + }, + { + "*all_potential_contigs.fa": { + "type": "file", + "description": "Contains sequences of all potential contigs", + "pattern": "*all_potential_contigs.fa" + } + } + ] + }, + { + "contigs_annotations": [ + { + "meta": { + "type": "file", + "description": "Graphical representation of annotated genes and tRNAs", + "pattern": "*contigs_annotations.png" + } + }, + { + "*contigs_annotations.png": { + "type": "file", + "description": "Graphical representation of annotated genes and tRNAs", + "pattern": "*contigs_annotations.png" + } + } + ] + }, + { + "contigs_circularization": [ + { + "meta": { + "type": "directory", + "description": "Contains circularization reports", + "pattern": "*contigs_circularization" + } + }, + { + "*contigs_circularization": { + "type": "directory", + "description": "Contains circularization reports", + "pattern": "*contigs_circularization" + } + } + ] + }, + { + "contigs_filtering": [ + { + "meta": { + "type": "directory", + "description": "Contains files with initial blast matches", + "pattern": "*contigs_filtering" + } + }, + { + "*contigs_filtering": { + "type": "directory", + "description": "Contains files with initial blast matches", + "pattern": "*contigs_filtering" + } + } + ] + }, + { + "coverage_mapping": [ + { + "meta": { + "type": "directory", + "description": "Contains statistics on coverage mapping", + "pattern": "*coverage_mapping" + } + }, + { + "*coverage_mapping": { + "type": "directory", + "description": "Contains statistics on coverage mapping", + "pattern": "*coverage_mapping" + } + } + ] + }, + { + "coverage_plot": [ + { + "meta": { + "type": "file", + "description": "Read coverage plot for mitochondrial contigs", + "pattern": "*coverage_plot.png" + } + }, + { + "*coverage_plot.png": { + "type": "file", + "description": "Read coverage plot for mitochondrial contigs", + "pattern": "*coverage_plot.png" + } + } + ] + }, + { + "final_mitogenome_annotation": [ + { + "meta": { + "type": "file", + "description": "Graphical representation of annotated genes for the final mito contig", + "pattern": "*final_mitogenome.annotation.png" + } + }, + { + "*final_mitogenome.annotation.png": { + "type": "file", + "description": "Graphical representation of annotated genes for the final mito contig", + "pattern": "*final_mitogenome.annotation.png" + } + } + ] + }, + { + "final_mitogenome_choice": [ + { + "meta": { + "type": "directory", + "description": "Files with potential contigs clusterings and alignments", + "pattern": "*final_mitogenome_choice" + } + }, + { + "*final_mitogenome_choice": { + "type": "directory", + "description": "Files with potential contigs clusterings and alignments", + "pattern": "*final_mitogenome_choice" + } + } + ] + }, + { + "final_mitogenome_coverage": [ + { + "meta": { + "type": "file", + "description": "Graphical representation of reads coverage plot for the final mito contig", + "pattern": "*final_mitogenome.coverage.png" + } + }, + { + "*final_mitogenome.coverage.png": { + "type": "file", + "description": "Graphical representation of reads coverage plot for the final mito contig", + "pattern": "*final_mitogenome.coverage.png" + } + } + ] + }, + { + "potential_contigs": [ + { + "meta": { + "type": "directory", + "description": "Files with sequences and annotations of the potential contigs", + "pattern": "*potential_contigs" + } + }, + { + "*potential_contigs": { + "type": "directory", + "description": "Files with sequences and annotations of the potential contigs", + "pattern": "*potential_contigs" + } + } + ] + }, + { + "reads_mapping_and_assembly": [ + { + "meta": { + "type": "directory", + "description": "Read mapping files for run from the raw reads", + "pattern": "*reads_mapping_and_assembly" + } + }, + { + "*reads_mapping_and_assembly": { + "type": "directory", + "description": "Read mapping files for run from the raw reads", + "pattern": "*reads_mapping_and_assembly" + } + } + ] + }, + { + "shared_genes": [ + { + "meta": { + "type": "directory", + "description": "Report on genes shared with the reference genome", + "pattern": "*shared_genes.tsv" + } + }, + { + "*shared_genes.tsv": { + "type": "directory", + "description": "Report on genes shared with the reference genome", + "pattern": "*shared_genes.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "input": { - "type": "file", - "description": "Path to PacBio HiFi reads or contigs. Type (-r/-c) is specified in ext.args2", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz}" - } - }, + "authors": [ + "@ksenia-krasheninnikova" + ], + "maintainers": [ + "@ksenia-krasheninnikova" + ] + } + }, + { + "name": "mlst", + "path": "modules/nf-core/mlst/meta.yml", + "type": "module", + "meta": { + "name": "mlst", + "description": "Run Torsten Seemann's classic MLST on a genome assembly", + "keywords": [ + "mlst", + "typing", + "bacteria", + "assembly" + ], + "tools": [ { - "ref_fa": { - "type": "file", - "description": "Reference sequence", - "pattern": "*.{fa,fasta}" + "mlst": { + "description": "Scan contig files against PubMLST typing schemes", + "homepage": "https://github.com/tseemann/mlst", + "licence": [ + "GPL v2" + ], + "identifier": "biotools:mlst" } - }, - { - "ref_gb": { - "type": "file", - "description": "Reference annotation", - "pattern": "*.{gb}" + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembly fasta file", + "pattern": "*.{fasta,fa,fna}" + } } - }, + ] + ], + "output": [ { - "input_mode": { - "type": "string", - "description": "Specifies type of input - reads or contigs", - "pattern": "{r,c}" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "MLST calls in tsv format", + "pattern": "*.{tsv}" + } + } + ] }, { - "code": { - "type": "integer", - "description": "Mitochndrial code for annotation", - "pattern": "[0-9]*" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Mitochondrial sequence", - "pattern": "*.{fasta,fa}" - } - }, - { - "gb": { - "type": "file", - "description": "Genome annotation in case mitofinder was used", - "pattern": "*.gb" - } - }, - { - "gff": { - "type": "file", - "description": "Genome annotation in case mitos was used", - "pattern": "*.gff" - } - }, - { - "all_potential_contigs": { - "type": "file", - "description": "Contains sequences of all potential contigs", - "pattern": "*all_potential_contigs.fa" - } - }, - { - "contigs_annotations": { - "type": "file", - "description": "Graphical representation of annotated genes and tRNAs", - "pattern": "*contigs_annotations.png" - } - }, - { - "contigs_circularization": { - "type": "directory", - "description": "Contains circularization reports", - "pattern": "*contigs_circularization" - } - }, - { - "contigs_filtering": { - "type": "directory", - "description": "Contains files with initial blast matches", - "pattern": "*contigs_filtering" - } - }, - { - "coverage_mapping": { - "type": "directory", - "description": "Contains statistics on coverage mapping", - "pattern": "*coverage_mapping" - } - }, - { - "coverage_plot": { - "type": "file", - "description": "Read coverage plot for mitochondrial contigs", - "pattern": "*coverage_plot.png" - } - }, - { - "final_mitogenome_annotation": { - "type": "file", - "description": "Graphical representation of annotated genes for the final mito contig", - "pattern": "*final_mitogenome.annotation.png" - } - }, - { - "final_mitogenome_choice": { - "type": "directory", - "description": "Files with potential contigs clusterings and alignments", - "pattern": "*final_mitogenome_choice" - } - }, - { - "final_mitogenome_coverage": { - "type": "file", - "description": "Graphical representation of reads coverage plot for the final mito contig", - "pattern": "*final_mitogenome.coverage.png" - } - }, - { - "potential_contigs": { - "type": "directory", - "description": "Files with sequences and annotations of the potential contigs", - "pattern": "*potential_contigs" - } - }, - { - "reads_mapping_and_assembly": { - "type": "directory", - "description": "Read mapping files for run from the raw reads", - "pattern": "*reads_mapping_and_assembly" - } - }, - { - "shared_genes": { - "type": "directory", - "description": "Report on genes shared with the reference genome", - "pattern": "*shared_genes.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "Software versions used in the run", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@ksenia-krasheninnikova" - ], - "maintainers": [ - "@ksenia-krasheninnikova" - ] - } - }, - { - "name": "mlst", - "path": "modules/nf-core/mlst/meta.yml", - "type": "module", - "meta": { - "name": "mlst", - "description": "Run Torsten Seemann's classic MLST on a genome assembly", - "keywords": [ - "mlst", - "typing", - "bacteria", - "assembly" - ], - "tools": [ - { - "mlst": { - "description": "Scan contig files against PubMLST typing schemes", - "homepage": "https://github.com/tseemann/mlst", - "licence": [ - "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly fasta file", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "MLST calls in tsv format", - "pattern": "*.{tsv}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88040,43 +111270,54 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:mmseqs" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "input_db": { - "type": "directory", - "description": "a MMseqs2 database used for clustering" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_input": { + "type": "file", + "description": "Input database" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_cluster": { - "type": "file", - "description": "a clustered MMseqs2 database used for clustering" - } + "db_cluster": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "file", + "description": "a clustered MMseqs2 database used for clustering" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88112,44 +111353,55 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:mmseqs" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "sequence": { - "type": "file", - "description": "Input sequences in FASTA/Q (zipped or unzipped) format to parse into an mmseqs database", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "sequence": { + "type": "file", + "description": "Input sequences in FASTA/Q (zipped or unzipped) format to parse into an mmseqs database", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "The created MMseqs2 database" - } + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "The created MMseqs2 database" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88191,39 +111443,57 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:mmseqs" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db": { - "type": "directory", - "description": "Directory containing the DB to be indexed\n", - "pattern": "*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the DB to be indexed\n", + "pattern": "*" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions\n", - "pattern": "versions.yml" - } + "db_indexed": [ + { + "meta": { + "type": "directory", + "description": "Directory containing the DB and the generated indexes\n", + "pattern": "*" + } + }, + { + "db": { + "type": "directory", + "description": "Directory containing the DB and the generated indexes\n", + "pattern": "*" + } + } + ] }, { - "db_indexed": { - "type": "directory", - "description": "Directory containing the DB and the generated indexes\n", - "pattern": "*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions\n", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88266,68 +111536,83 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_result": { - "type": "directory", - "description": "an MMseqs2 database with result data" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_query": { - "type": "directory", - "description": "an MMseqs2 database with query data" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_target": { - "type": "directory", - "description": "an MMseqs2 database with target data" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "The resulting tsv file created using the query, target and result MMseqs databases", - "pattern": "*.{tsv}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_result": { + "type": "directory", + "description": "an MMseqs2 database with result data" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_query": { + "type": "directory", + "description": "an MMseqs2 database with query data" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_target": { + "type": "directory", + "description": "an MMseqs2 database with target data" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The resulting tsv file created using the query, target and result MMseqs databases", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88367,31 +111652,42 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:mmseqs" } } ], "input": [ - { - "database": { - "type": "string", - "description": "Database available through the mmseqs2 databases interface - see https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details" + [ + { + "database": { + "type": "string", + "description": "Database available through the mmseqs2 databases interface - see https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "database": [ + { + "${prefix}/": { + "type": "directory", + "description": "Directory containing processed mmseqs database" + } + } + ] }, { - "database": { - "type": "directory", - "description": "Directory containing processed mmseqs database" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88435,57 +111731,70 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing database information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "db_target": { - "type": "directory", - "description": "an MMseqs2 database with target data, e.g. uniref90" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test']`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "tsv file with the results of the search", - "pattern": "*.{tsv}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing database information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "db_target": { + "type": "directory", + "description": "an MMseqs2 database with target data, e.g. uniref90" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing input fasta file information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "tsv file with the results of the search", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88521,43 +111830,54 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:mmseqs" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "input_db": { - "type": "directory", - "description": "a MMseqs2 database used for clustering" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_input": { + "type": "file", + "description": "Input database" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_cluster": { - "type": "directory", - "description": "a clustered MMseqs2 database" - } + "db_cluster": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "a clustered MMseqs2 database" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88593,55 +111913,68 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "query_db": { - "type": "directory", - "description": "an MMseqs2 database with query data" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "target_db": { - "type": "directory", - "description": "an MMseqs2 database with target data, e.g. uniref90" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "db_search": { - "type": "directory", - "description": "an MMseqs2 database with search results" - } + ], + "identifier": "biotools:mmseqs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_query": { + "type": "file", + "description": "Query database" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_target": { + "type": "file", + "description": "Target database" + } + } + ] + ], + "output": [ + { + "db_search": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "an MMseqs2 database with search results" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88677,49 +112010,62 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:mmseqs" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_query": { - "type": "directory", - "description": "An MMseqs2 database with query data" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "db_query": { + "type": "directory", + "description": "An MMseqs2 database with query data" + } } - }, - { - "db_target": { - "type": "directory", - "description": "an MMseqs2 database with target data including the taxonomy classification" + ], + [ + { + "db_target": { + "type": "directory", + "description": "an MMseqs2 database with target data including the taxonomy classification" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "db_taxonomy": { - "type": "directory", - "description": "An MMseqs2 database with target data including the taxonomy classification" - } + "db_taxonomy": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}_taxonomy": { + "type": "directory", + "description": "An MMseqs2 database with target data including the taxonomy classification" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88760,33 +112106,44 @@ "doi": "10.1093/bioinformatics/btw006", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:mmseqs" } } ], "input": [ - { - "db": { - "type": "directory", - "description": "Directory containing the DB to be indexed\n", - "pattern": "*" + [ + { + "db": { + "type": "directory", + "description": "Directory containing the DB to be indexed\n", + "pattern": "*" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions\n", - "pattern": "versions.yml" - } + "db_exprofile": [ + { + "db": { + "type": "directory", + "description": "Directory containing the expandable profile DB\n", + "pattern": "*" + } + } + ] }, { - "db_exprofile": { - "type": "directory", - "description": "Directory containing the expandable profile DB\n", - "pattern": "*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions\n", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88825,66 +112182,107 @@ "doi": "10.1099/mgen.0.000435", "licence": [ "Apache License, Version 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A bacterial genome assembly in FASTA format", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "chromosome": { - "type": "file", - "description": "FASTA file of all contigs found to belong to the chromosome", - "pattern": "chromosome.fasta" - } - }, - { - "contig_report": { - "type": "file", - "description": "Assignment of the contig to chromosome or a particular plasmid grouping", - "pattern": "contig_report.txt" - } - }, - { - "plasmids": { - "type": "file", - "description": "Each plasmid group is written to an individual FASTA", - "pattern": "plasmid_*.fasta" - } - }, - { - "mobtyper_results": { - "type": "file", - "description": "Aggregate MOB-typer report files for all identified plasmid", - "pattern": "mobtyper_results.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A bacterial genome assembly in FASTA format", + "pattern": "*.{fasta,fa,fna}" + } + } + ] + ], + "output": [ + { + "chromosome": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/chromosome.fasta": { + "type": "file", + "description": "FASTA file of all contigs found to belong to the chromosome", + "pattern": "chromosome.fasta" + } + } + ] + }, + { + "contig_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/contig_report.txt": { + "type": "file", + "description": "Assignment of the contig to chromosome or a particular plasmid grouping", + "pattern": "contig_report.txt" + } + } + ] + }, + { + "plasmids": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/plasmid_*.fasta": { + "type": "file", + "description": "Each plasmid group is written to an individual FASTA", + "pattern": "plasmid_*.fasta" + } + } + ] + }, + { + "mobtyper_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/mobtyper_results.txt": { + "type": "file", + "description": "Aggregate MOB-typer report files for all identified plasmid", + "pattern": "mobtyper_results.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -88916,117 +112314,152 @@ "tool_dev_url": "https://github.com/nanoporetech/modkit", "licence": [ "Oxford Nanopore Technologies PLC. Public License Version 1.0" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "Associated index file for BAM", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing BED file information\ne.g. `[ id:'regions' ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the file", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "bedMethyl output file(s)", + "pattern": "*.bed" + } + } + ] + }, + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bedgraph": { + "type": "file", + "description": "bedgraph output files", + "pattern": "*.bedgraph" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File for debug logs to be written to", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "Associated index file for BAM", - "pattern": "*.bai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'hg38' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing BED file information\ne.g. `[ id:'regions' ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the file", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "bedMethyl output file(s)", - "pattern": "*.bed" - } - }, - { - "bedgraph": { - "type": "file", - "description": "bedgraph output files", - "pattern": "*.bedgraph" - } - }, - { - "log": { - "type": "file", - "description": "File for debug logs to be written to", - "pattern": "*.log" - } - } - ], - "authors": [ - "@Michal-Babins", - "@fellen31" - ], - "maintainers": [ - "@fellen31" - ] - } - }, - { - "name": "molkartgarage_clahe", - "path": "modules/nf-core/molkartgarage/clahe/meta.yml", - "type": "module", - "meta": { - "name": "molkartgarage_clahe", - "description": "Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.", - "keywords": [ - "clahe", - "image_processing", - "imaging", - "correction" - ], - "tools": [ + "authors": [ + "@Michal-Babins", + "@fellen31" + ], + "maintainers": [ + "@fellen31" + ] + } + }, + { + "name": "molkartgarage_clahe", + "path": "modules/nf-core/molkartgarage/clahe/meta.yml", + "type": "module", + "meta": { + "name": "molkartgarage_clahe", + "description": "Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.", + "keywords": [ + "clahe", + "image_processing", + "imaging", + "correction" + ], + "tools": [ { "molkartgarage": { "description": "One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines.", @@ -89035,45 +112468,56 @@ "tool_dev_url": "https://github.com/SchapiroLabor/molkart-local/blob/main/scripts/molkart_clahe.py", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "image": { - "type": "file", - "description": "Single-channel tiff file to be corrected.", - "pattern": "*.{tif,tiff}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "image": { + "type": "file", + "description": "Single-channel tiff file to be corrected.", + "pattern": "*.{tif,tiff}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "img_clahe": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.tiff": { + "type": "file", + "description": "CLAHE corrected tiff file.", + "pattern": "*.{tiff}" + } + } + ] }, { - "img_clahe": { - "type": "file", - "description": "CLAHE corrected tiff file.", - "pattern": "*.{tiff}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89105,149 +112549,272 @@ "doi": "10.1093/bioinformatics/btx699", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "Index for BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file with intersected intervals", - "pattern": "*.{bed}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing bed information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "global_txt": { - "type": "file", - "description": "Text file with global cumulative coverage distribution", - "pattern": "*.{global.dist.txt}" - } - }, - { - "regions_txt": { - "type": "file", - "description": "Text file with region cumulative coverage distribution", - "pattern": "*.{region.dist.txt}" - } - }, - { - "summary_txt": { - "type": "file", - "description": "Text file with summary mean depths per chromosome and regions", - "pattern": "*.{summary.txt}" - } - }, - { - "per_base_bed": { - "type": "file", - "description": "BED file with per-base coverage", - "pattern": "*.{per-base.bed.gz}" - } - }, - { - "per_base_csi": { - "type": "file", - "description": "Index file for BED file with per-base coverage", - "pattern": "*.{per-base.bed.gz.csi}" - } - }, - { - "per_base_d4": { - "type": "file", - "description": "D4 file with per-base coverage", - "pattern": "*.{per-base.d4}" - } - }, - { - "regions_bed": { - "type": "file", - "description": "BED file with per-region coverage", - "pattern": "*.{regions.bed.gz}" - } - }, - { - "regions_csi": { - "type": "file", - "description": "Index file for BED file with per-region coverage", - "pattern": "*.{regions.bed.gz.csi}" - } - }, - { - "quantized_bed": { - "type": "file", - "description": "BED file with binned coverage", - "pattern": "*.{quantized.bed.gz}" - } - }, - { - "quantized_csi": { - "type": "file", - "description": "Index file for BED file with binned coverage", - "pattern": "*.{quantized.bed.gz.csi}" - } - }, - { - "thresholds_bed": { - "type": "file", - "description": "BED file with the number of bases in each region that are covered at or above each threshold", - "pattern": "*.{thresholds.bed.gz}" - } - }, - { - "thresholds_csi": { - "type": "file", - "description": "Index file for BED file with threshold coverage", - "pattern": "*.{thresholds.bed.gz.csi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:mosdepth" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + }, + { + "bed": { + "type": "file", + "description": "BED file with intersected intervals", + "pattern": "*.{bed}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing bed information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "global_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.global.dist.txt": { + "type": "file", + "description": "Text file with global cumulative coverage distribution", + "pattern": "*.{global.dist.txt}" + } + } + ] + }, + { + "summary_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary.txt": { + "type": "file", + "description": "Text file with summary mean depths per chromosome and regions", + "pattern": "*.{summary.txt}" + } + } + ] + }, + { + "regions_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.region.dist.txt": { + "type": "file", + "description": "Text file with region cumulative coverage distribution", + "pattern": "*.{region.dist.txt}" + } + } + ] + }, + { + "per_base_d4": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.per-base.d4": { + "type": "file", + "description": "D4 file with per-base coverage", + "pattern": "*.{per-base.d4}" + } + } + ] + }, + { + "per_base_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.per-base.bed.gz": { + "type": "file", + "description": "BED file with per-base coverage", + "pattern": "*.{per-base.bed.gz}" + } + } + ] + }, + { + "per_base_csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.per-base.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with per-base coverage", + "pattern": "*.{per-base.bed.gz.csi}" + } + } + ] + }, + { + "regions_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.regions.bed.gz": { + "type": "file", + "description": "BED file with per-region coverage", + "pattern": "*.{regions.bed.gz}" + } + } + ] + }, + { + "regions_csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.regions.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with per-region coverage", + "pattern": "*.{regions.bed.gz.csi}" + } + } + ] + }, + { + "quantized_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.quantized.bed.gz": { + "type": "file", + "description": "BED file with binned coverage", + "pattern": "*.{quantized.bed.gz}" + } + } + ] + }, + { + "quantized_csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.quantized.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with binned coverage", + "pattern": "*.{quantized.bed.gz.csi}" + } + } + ] + }, + { + "thresholds_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.thresholds.bed.gz": { + "type": "file", + "description": "BED file with the number of bases in each region that are covered at or above each threshold", + "pattern": "*.{thresholds.bed.gz}" + } + } + ] + }, + { + "thresholds_csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.thresholds.bed.gz.csi": { + "type": "file", + "description": "Index file for BED file with threshold coverage", + "pattern": "*.{thresholds.bed.gz.csi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89310,33 +112877,43 @@ "doi": "10.1186/s40168-022-01410-z", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "motus_downloaddb": { - "type": "directory", - "description": "The mOTUs downloadDB script source file.\nIt is the source file installed or\nremote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py\n", - "pattern": "downloadDB.py" + [ + { + "motus_downloaddb_script": { + "type": "file", + "description": "The script to download the mOTUs database" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "db_mOTU/": { + "type": "directory", + "description": "The mOTUs database directory", + "pattern": "db_mOTU" + } + } + ] }, { - "db": { - "type": "directory", - "description": "The mOTUs database directory", - "pattern": "db_mOTU" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89373,52 +112950,91 @@ "doi": "10.1186/s40168-022-01410-z", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "input": { - "type": "file", - "description": "List of output files (more than one) from motus profile,\nor a single directory containing motus output files.\n" - } - }, - { - "db": { - "type": "directory", - "description": "mOTUs database downloaded by `motus downloadDB`\npattern: \"db_mOTU/\"\n" - } - }, - { - "profile_version_yml": { - "type": "file", - "description": "A single versions.yml file output from motus/profile. motus/merge cannot reconstruct\nthis itself without having the motus database present and configured with the tool\nso here we take it from what is already reported by the upstream module.\n", - "pattern": "versions.yml" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "OTU table in txt format, if BIOM format not requested", - "pattern": "*.txt" - } - }, - { - "biom": { - "type": "file", - "description": "OTU table in biom format, if BIOM format requested", - "pattern": "*.biom" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "List of output files (more than one) from motus profile,\nor a single directory containing motus output files.\n" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "mOTUs database downloaded by `motus downloadDB`\npattern: \"db_mOTU/\"\n" + } + } + ], + [ + { + "profile_version_yml": { + "type": "file", + "description": "A single versions.yml file output from motus/profile. motus/merge cannot reconstruct\nthis itself without having the motus database present and configured with the tool\nso here we take it from what is already reported by the upstream module.\n", + "pattern": "versions.yml" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "file", + "description": "OTU table in txt format, if BIOM format not requested", + "pattern": "*.txt" + } + }, + { + "*.txt": { + "type": "file", + "description": "OTU table in txt format, if BIOM format not requested", + "pattern": "*.txt" + } + } + ] + }, + { + "biom": [ + { + "meta": { + "type": "file", + "description": "OTU table in biom format, if BIOM format requested", + "pattern": "*.biom" + } + }, + { + "*.biom": { + "type": "file", + "description": "OTU table in biom format, if BIOM format requested", + "pattern": "*.biom" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89458,72 +113074,115 @@ "doi": "10.1186/s40168-022-01410-z", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nOr the intermediate bam file mapped by bwa to the mOTUs database or\nthe output bam file from motus profile.\nOr the intermediate mgc read counts table.\n", - "pattern": "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}" - } - }, - { - "db": { - "type": "directory", - "description": "mOTUs database downloaded by `motus downloadDB`\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "out": { - "type": "file", - "description": "Results with taxonomic classification of each read", - "pattern": "*.out" - } - }, - { - "bam": { - "type": "file", - "description": "Optional intermediate sorted BAM file from BWA", - "pattern": "*.{bam}" - } - }, - { - "mgc": { - "type": "file", - "description": "Optional intermediate mgc read count table file saved with `-M`.", - "pattern": "*.{mgc}" - } - }, - { - "log": { - "type": "file", - "description": "Standard error logging file containing summary statistics", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,\nrespectively.\nOr the intermediate bam file mapped by bwa to the mOTUs database or\nthe output bam file from motus profile.\nOr the intermediate mgc read counts table.\n", + "pattern": "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}" + } + } + ], + [ + { + "db": { + "type": "directory", + "description": "mOTUs database downloaded by `motus downloadDB`\n" + } + } + ] + ], + "output": [ + { + "out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out": { + "type": "file", + "description": "Results with taxonomic classification of each read", + "pattern": "*.out" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Optional intermediate sorted BAM file from BWA", + "pattern": "*.{bam}" + } + } + ] + }, + { + "mgc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mgc": { + "type": "file", + "description": "Optional intermediate mgc read count table file saved with `-M`.", + "pattern": "*.{mgc}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Standard error logging file containing summary statistics", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89563,77 +113222,132 @@ "tool_dev_url": "https://github.com/niu-lab/msisensor2", "license": [ "GPL-3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tumor_bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "normal_bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "intervals": { - "type": "file", - "description": "BED", - "pattern": "*.bed" - } - }, - { - "models": { - "type": "file", - "description": "Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)", - "pattern": "*/*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "msi": { - "type": "file", - "description": "MSI classifications as a text file" - } - }, - { - "distribution": { - "type": "file", - "description": "Read count distributions of MSI regions" - } - }, - { - "somatic": { - "type": "file", - "description": "Somatic MSI regions detected." - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "tumor_bam_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai}" + } + }, + { + "normal_bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "normal_bam_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "BED", + "pattern": "*.bed" + } + } + ], + [ + { + "scan": { + "type": "file", + "description": "Input scan file from MSIsensor2 scan module" + } + } + ], + [ + { + "models": { + "type": "file", + "description": "Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)", + "pattern": "*/*" + } + } + ] + ], + "output": [ + { + "msi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "MSI classifications as a text file" + } + } + ] + }, + { + "distribution": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_dis": { + "type": "file", + "description": "Read count distributions of MSI regions" + } + } + ] + }, + { + "somatic": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_somatic": { + "type": "file", + "description": "Somatic MSI regions detected." + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89666,39 +113380,51 @@ "tool_dev_url": "https://github.com/niu-lab/msisensor2", "licence": [ "GPL-3.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Path to reference genome.", - "pattern": "*.fasta" + [ + { + "fasta": { + "type": "file", + "description": "Path to reference genome.", + "pattern": "*.fasta" + } } - }, - { - "output": { - "type": "string", - "description": "Name of output MSI scan to write." + ], + [ + { + "output": { + "type": "string", + "description": "Name of output MSI scan to write." + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "scan": [ + { + "output_path": { + "type": "file", + "description": "Path to output MSI scan file." + } + } + ] }, { - "output": { - "type": "file", - "description": "Output scan of MSI regions in FASTA file.", - "pattern": "*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89730,94 +113456,137 @@ "doi": "10.1093/bioinformatics/btt755", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal_bam": { - "type": "file", - "description": "Coordinate sorted BAM/CRAM/SAM file from normal tissue", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "normal_bai": { - "type": "file", - "description": "Index for coordinate sorted BAM/CRAM/SAM file from normal tissue", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "tumor_bam": { - "type": "file", - "description": "Coordinate sorted BAM/CRAM/SAM file from tumor tissue", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "tumor_bai": { - "type": "file", - "description": "Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "homopolymers": { - "type": "file", - "description": "Output file from MSIsensor scan module", - "pattern": "*.msisensor_scan.tab" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "MSIsensor MSI final report file", - "pattern": "*.output" - } - }, - { - "txt": { - "type": "file", - "description": "MSIsensor MSI DIS report file", - "pattern": "*.output_dis" - } - }, - { - "txt": { - "type": "file", - "description": "MSIsensor MSI germline report file", - "pattern": "*.output_germline" - } - }, - { - "txt": { - "type": "file", - "description": "MSIsensor MSI somatic report file", - "pattern": "*.output_somatic" - } + ], + "identifier": "biotools:msisensor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normal_bam": { + "type": "file", + "description": "Coordinate sorted BAM/CRAM/SAM file from normal tissue", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "normal_bai": { + "type": "file", + "description": "Index for coordinate sorted BAM/CRAM/SAM file from normal tissue", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "Coordinate sorted BAM/CRAM/SAM file from tumor tissue", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "tumor_bai": { + "type": "file", + "description": "Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "metascan": { + "type": "file", + "description": "metascan file" + } + }, + { + "homopolymers": { + "type": "file", + "description": "Output file from MSIsensor scan module", + "pattern": "*.msisensor_scan.tab" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "Output file from MSIsensor msi module" + } + } + ] + }, + { + "output_dis": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_dis": { + "type": "file", + "description": "Output file from MSIsensor module" + } + } + ] + }, + { + "output_germline": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_germline": { + "type": "file", + "description": "Output file from MSIsensor module" + } + } + ] + }, + { + "output_somatic": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_somatic": { + "type": "file", + "description": "Output file from MSIsensor module" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89848,45 +113617,56 @@ "doi": "10.1093/bioinformatics/btt755", "licence": [ "MIT" - ] + ], + "identifier": "biotools:msisensor" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "MSIsensor scan output file of homopolymers & minisatellites", + "pattern": "*.msisensor_scan.txt" + } + } + ] }, { - "txt": { - "type": "file", - "description": "MSIsensor scan output file of homopolymers & minisatellites", - "pattern": "*.msisensor_scan.txt" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -89920,104 +113700,149 @@ "doi": "10.1016/j.gpb.2020.02.001", "licence": [ "Custom Licence" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "normal_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "tumor": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "tumor_index": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "intervals": { - "type": "file", - "description": "bed file containing interval information, optional", - "pattern": "*.{bed}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fasta}" - } - }, - { - "msisensor_scan": { - "type": "file", - "description": "Output from msisensor-pro/scan, containing list of msi regions", - "pattern": "*.list" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output_report": { - "type": "file", - "description": "File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score" - } - }, - { - "output_dis": { - "type": "file", - "description": "File containing distribution results" - } - }, - { - "output_germline": { - "type": "file", - "description": "File containing germline results" - } - }, - { - "output_somatic": { - "type": "file", - "description": "File containing somatic results" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normal": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "normal_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "tumor": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "tumor_index": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "intervals": { + "type": "file", + "description": "bed file containing interval information, optional", + "pattern": "*.{bed}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference genome", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "msisensor_scan": { + "type": "file", + "description": "Output from msisensor-pro/scan, containing list of msi regions", + "pattern": "*.list" + } + } + ] + ], + "output": [ + { + "output_report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score" + } + } + ] + }, + { + "output_dis": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_dis": { + "type": "file", + "description": "File containing distribution results" + } + } + ] + }, + { + "output_germline": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_germline": { + "type": "file", + "description": "File containing germline results" + } + } + ] + }, + { + "output_somatic": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_somatic": { + "type": "file", + "description": "File containing somatic results" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -90056,45 +113881,56 @@ "doi": "10.1016/j.gpb.2020.02.001", "licence": [ "Custom Licence" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome", - "pattern": "*.{fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome", + "pattern": "*.{fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list": { + "type": "file", + "description": "File containing microsatellite list", + "pattern": "*.{list}" + } + } + ] }, { - "list": { - "type": "file", - "description": "File containing microsatellite list", - "pattern": "*.{list}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -90134,65 +113970,89 @@ "doi": "10.1093/bioinformatics/btx828", "licence": [ "None" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "pdbs": { - "type": "file", - "description": "Input protein structures in PDB format. Files may be gzipped or uncompressed. They should contain exactly one chain!", - "pattern": "*.{pdb}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Alignment in FASTA format. May be gzipped or uncompressed.", - "pattern": "*.aln{.gz,}" - } - }, - { - "structure": { - "type": "file", - "description": "Overlaid structures in PDB format. May be gzipped or uncompressed.", - "pattern": "${prefix}.pdb{.gz,}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "pdbs": { + "type": "file", + "description": "Input protein structures in PDB format. Files may be gzipped or uncompressed. They should contain exactly one chain!", + "pattern": "*.{pdb}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}.aln${compress ? '.gz' : ''}": { + "type": "file", + "description": "Alignment in FASTA format. May be gzipped or uncompressed.", + "pattern": "*.aln{.gz,}" + } + } + ] + }, + { + "structure": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${prefix}.pdb${compress ? '.gz' : ''}": { + "type": "file", + "description": "Overlaid structures in PDB format. May be gzipped or uncompressed.", + "pattern": "${prefix}.pdb{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -90235,58 +114095,81 @@ "doi": "10.1186/s13059-016-0918-z", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "(coordinate) sorted BAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "mt_id": { - "type": "string", - "description": "Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "mtnucratio": { - "type": "file", - "description": "Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)", - "pattern": "*.mtnucratio" - } - }, - { - "json": { - "type": "file", - "description": "JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file", - "pattern": "*.json" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "(coordinate) sorted BAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "mt_id": { + "type": "string", + "description": "Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria" + } + } + ] + ], + "output": [ + { + "mtnucratio": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mtnucratio": { + "type": "file", + "description": "Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)", + "pattern": "*.mtnucratio" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -90321,71 +114204,98 @@ "tool_dev_url": "https://github.com/OceanGenomics/mudskipper", "licence": [ "BSD 3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Name-Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "gtf": { - "type": "file", - "description": "Annotation file", - "pattern": "*.{gtf,gff,gff3}" - } - }, - { - "index": { - "type": "directory", - "description": "Annotation index created by mudskipper/index" - } - }, - { - "rad": { - "type": "string", - "description": "File type" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam" - } - }, - { - "rad": { - "type": "file", - "description": "RAD file", - "pattern": "*.rad" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Name-Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Annotation index created by mudskipper/index" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "Annotation file", + "pattern": "*.{gtf,gff,gff3}" + } + } + ], + [ + { + "rad": { + "type": "string", + "description": "File type" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "rad": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${prefix}.rad": { + "type": "file", + "description": "RAD file", + "pattern": "*.rad" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -90417,33 +114327,44 @@ "tool_dev_url": "https://github.com/OceanGenomics/mudskipper", "licence": [ "BSD 3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "gtf": { - "type": "file", - "description": "Transcript annotation file.", - "pattern": "*.{gtf,gff,gff3}" + [ + { + "gtf": { + "type": "file", + "description": "Transcript annotation file.", + "pattern": "*.{gtf,gff,gff3}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "index/": { + "type": "directory", + "description": "Mudskipper index for running mudskipper conversion tools", + "pattern": "*/" + } + } + ] }, { - "index": { - "type": "directory", - "description": "Mudskipper index for running mudskipper conversion tools", - "pattern": "*/" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -90471,81 +114392,110 @@ "documentation": "https://multiqc.info/docs/", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "multiqc_files": { - "type": "file", - "description": "List of reports / files recognised by MultiQC, for example the html and zip output of FastQC\n" - } - }, - { - "multiqc_config": { - "type": "file", - "description": "Optional config yml for MultiQC", - "pattern": "*.{yml,yaml}" - } - }, - { - "extra_multiqc_config": { - "type": "file", - "description": "Second optional config yml for MultiQC. Will override common sections in multiqc_config.", - "pattern": "*.{yml,yaml}" - } - }, - { - "multiqc_logo": { - "type": "file", - "description": "Optional logo file for MultiQC", - "pattern": "*.{png}" - } - }, - { - "replace_names": { - "type": "file", - "description": "Optional two-column sample renaming file. First column a set of\npatterns, second column a set of corresponding replacements. Passed via\nMultiQC's `--replace-names` option.\n", - "pattern": "*.{tsv}" - } - }, - { - "sample_names": { - "type": "file", - "description": "Optional TSV file with headers, passed to the MultiQC --sample_names\nargument.\n", - "pattern": "*.{tsv}" - } - } - ], - "output": [ - { - "report": { - "type": "file", - "description": "MultiQC report file", - "pattern": "multiqc_report.html" - } - }, - { - "data": { - "type": "directory", - "description": "MultiQC data dir", - "pattern": "multiqc_data" - } - }, - { - "plots": { - "type": "file", - "description": "Plots created by MultiQC", - "pattern": "*_data" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:multiqc" + } + } + ], + "input": [ + [ + { + "multiqc_files": { + "type": "file", + "description": "List of reports / files recognised by MultiQC, for example the html and zip output of FastQC\n" + } + } + ], + [ + { + "multiqc_config": { + "type": "file", + "description": "Optional config yml for MultiQC", + "pattern": "*.{yml,yaml}" + } + } + ], + [ + { + "extra_multiqc_config": { + "type": "file", + "description": "Second optional config yml for MultiQC. Will override common sections in multiqc_config.", + "pattern": "*.{yml,yaml}" + } + } + ], + [ + { + "multiqc_logo": { + "type": "file", + "description": "Optional logo file for MultiQC", + "pattern": "*.{png}" + } + } + ], + [ + { + "replace_names": { + "type": "file", + "description": "Optional two-column sample renaming file. First column a set of\npatterns, second column a set of corresponding replacements. Passed via\nMultiQC's `--replace-names` option.\n", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "sample_names": { + "type": "file", + "description": "Optional TSV file with headers, passed to the MultiQC --sample_names\nargument.\n", + "pattern": "*.{tsv}" + } + } + ] + ], + "output": [ + { + "report": [ + { + "*multiqc_report.html": { + "type": "file", + "description": "MultiQC report file", + "pattern": "multiqc_report.html" + } + } + ] + }, + { + "data": [ + { + "*_data": { + "type": "directory", + "description": "MultiQC data dir", + "pattern": "multiqc_data" + } + } + ] + }, + { + "plots": [ + { + "*_plots": { + "type": "file", + "description": "Plots created by MultiQC", + "pattern": "*_data" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -90889,168 +114839,337 @@ "doi": "10.1038/nature13591", "licence": [ "GPL >=3" - ] - } - } - ], - "input": [ - { - "vcfs": { - "type": "file", - "description": "One or a list of uncompressed VCF file", - "pattern": "*.vcf" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome VCF was generated against", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "snpeff_results": { - "type": "file", - "description": "Results from snpEff in txt format (Optional)", - "pattern": "*.txt" - } - }, - { - "gff": { - "type": "file", - "description": "GFF file corresponding to reference genome fasta (Optional)", - "pattern": "*.gff" - } - }, - { - "allele_freqs": { - "type": "boolean", - "description": "Whether to include the percentage of reads a given allele is\npresent in in the SNP table.\n" - } - }, - { - "genotype_quality": { - "type": "integer", - "description": "Minimum GATK genotyping threshold threshold of which a SNP call\nfalling under is 'discarded'\n" - } - }, - { - "coverage": { - "type": "integer", - "description": "Minimum number of a reads that a position must be covered by to be\nreported\n" - } - }, - { - "homozygous_freq": { - "type": "integer", - "description": "Fraction of reads a base must have to be called 'homozygous'" - } - }, - { - "heterozygous_freq": { - "type": "integer", - "description": "Fraction of which whereby if a call falls above this value, and lower\nthan the homozygous threshold, a base will be called 'heterozygous'.\n" - } - }, - { - "gff_exclude": { - "type": "file", - "description": "file listing positions that will be 'filtered' (i.e. ignored)\n(Optional)\n", - "pattern": "*.vcf" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "full_alignment": { - "type": "file", - "description": "Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls", - "pattern": ".fasta.gz" - } - }, - { - "info_txt": { - "type": "file", - "description": "Information about the run", - "pattern": ".txt" - } - }, - { - "snp_alignment": { - "type": "file", - "description": "A fasta file of just SNP positions with samples only", - "pattern": ".fasta.gz" - } - }, - { - "snp_genome_alignment": { - "type": "file", - "description": "A fasta file of just SNP positions with reference genome", - "pattern": ".fasta.gz" - } - }, - { - "snpstatistics": { - "type": "file", - "description": "Some basic statistics about the SNP calls of each sample", - "pattern": ".tsv" - } - }, - { - "snptable": { - "type": "file", - "description": "Basic SNP table of combined positions taken from each VCF file", - "pattern": ".tsv" - } - }, - { - "snptable_snpeff": { - "type": "file", - "description": "Input file for SnpEff", - "pattern": ".tsv" - } - }, - { - "snptable_uncertainty": { - "type": "file", - "description": "Same as above, but with lower case characters indicating uncertain calls", - "pattern": ".tsv" - } - }, - { - "structure_genotypes": { - "type": "file", - "description": "Input file for STRUCTURE", - "pattern": ".tsv" - } - }, - { - "structure_genotypes_nomissing": { - "type": "file", - "description": "Alternate input file for STRUCTURE", - "pattern": ".tsv" - } - }, - { - "json": { - "type": "file", - "description": "Summary statistics in MultiQC JSON format", - "pattern": ".json" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "One or a list of uncompressed VCF file", + "pattern": "*.vcf" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome VCF was generated against", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "snpeff_results": { + "type": "file", + "description": "Results from snpEff in txt format (Optional)", + "pattern": "*.txt" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gff": { + "type": "file", + "description": "GFF file corresponding to reference genome fasta (Optional)", + "pattern": "*.gff" + } + } + ], + [ + { + "allele_freqs": { + "type": "boolean", + "description": "Whether to include the percentage of reads a given allele is\npresent in in the SNP table.\n" + } + } + ], + [ + { + "genotype_quality": { + "type": "integer", + "description": "Minimum GATK genotyping threshold threshold of which a SNP call\nfalling under is 'discarded'\n" + } + } + ], + [ + { + "coverage": { + "type": "integer", + "description": "Minimum number of a reads that a position must be covered by to be\nreported\n" + } + } + ], + [ + { + "homozygous_freq": { + "type": "integer", + "description": "Fraction of reads a base must have to be called 'homozygous'" + } + } + ], + [ + { + "heterozygous_freq": { + "type": "integer", + "description": "Fraction of which whereby if a call falls above this value, and lower\nthan the homozygous threshold, a base will be called 'heterozygous'.\n" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "gff_exclude": { + "type": "file", + "description": "file listing positions that will be 'filtered' (i.e. ignored)\n(Optional)\n", + "pattern": "*.vcf" + } + } + ] + ], + "output": [ + { + "full_alignment": [ + { + "meta": { + "type": "file", + "description": "Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls", + "pattern": ".fasta.gz" + } + }, + { + "fullAlignment.fasta.gz": { + "type": "file", + "description": "Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls", + "pattern": ".fasta.gz" + } + } + ] + }, + { + "info_txt": [ + { + "meta": { + "type": "file", + "description": "Information about the run", + "pattern": ".txt" + } + }, + { + "info.txt": { + "type": "file", + "description": "Information about the run", + "pattern": ".txt" + } + } + ] + }, + { + "snp_alignment": [ + { + "meta": { + "type": "file", + "description": "A fasta file of just SNP positions with samples only", + "pattern": ".fasta.gz" + } + }, + { + "snpAlignment.fasta.gz": { + "type": "file", + "description": "A fasta file of just SNP positions with samples only", + "pattern": ".fasta.gz" + } + } + ] + }, + { + "snp_genome_alignment": [ + { + "meta": { + "type": "file", + "description": "A fasta file of just SNP positions with reference genome", + "pattern": ".fasta.gz" + } + }, + { + "snpAlignmentIncludingRefGenome.fasta.gz": { + "type": "file", + "description": "A fasta file of just SNP positions with reference genome", + "pattern": ".fasta.gz" + } + } + ] + }, + { + "snpstatistics": [ + { + "meta": { + "type": "file", + "description": "Some basic statistics about the SNP calls of each sample", + "pattern": ".tsv" + } + }, + { + "snpStatistics.tsv": { + "type": "file", + "description": "Some basic statistics about the SNP calls of each sample", + "pattern": ".tsv" + } + } + ] + }, + { + "snptable": [ + { + "meta": { + "type": "file", + "description": "Basic SNP table of combined positions taken from each VCF file", + "pattern": ".tsv" + } + }, + { + "snpTable.tsv": { + "type": "file", + "description": "Basic SNP table of combined positions taken from each VCF file", + "pattern": ".tsv" + } + } + ] + }, + { + "snptable_snpeff": [ + { + "meta": { + "type": "file", + "description": "Input file for SnpEff", + "pattern": ".tsv" + } + }, + { + "snpTableForSnpEff.tsv": { + "type": "file", + "description": "Input file for SnpEff", + "pattern": ".tsv" + } + } + ] + }, + { + "snptable_uncertainty": [ + { + "meta": { + "type": "file", + "description": "Same as above, but with lower case characters indicating uncertain calls", + "pattern": ".tsv" + } + }, + { + "snpTableWithUncertaintyCalls.tsv": { + "type": "file", + "description": "Same as above, but with lower case characters indicating uncertain calls", + "pattern": ".tsv" + } + } + ] + }, + { + "structure_genotypes": [ + { + "meta": { + "type": "file", + "description": "Input file for STRUCTURE", + "pattern": ".tsv" + } + }, + { + "structureGenotypes.tsv": { + "type": "file", + "description": "Input file for STRUCTURE", + "pattern": ".tsv" + } + } + ] + }, + { + "structure_genotypes_nomissing": [ + { + "meta": { + "type": "file", + "description": "Alternate input file for STRUCTURE", + "pattern": ".tsv" + } + }, + { + "structureGenotypes_noMissingData-Columns.tsv": { + "type": "file", + "description": "Alternate input file for STRUCTURE", + "pattern": ".tsv" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "file", + "description": "Summary statistics in MultiQC JSON format", + "pattern": ".json" + } + }, + { + "MultiVCFAnalyzer.json": { + "type": "file", + "description": "Summary statistics in MultiQC JSON format", + "pattern": ".json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91083,52 +115202,63 @@ "doi": "10.1186/gb-2004-5-2-r12", "licence": [ "The Artistic License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "FASTA file of the reference sequence", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - }, - { - "query": { - "type": "file", - "description": "FASTA file of the query sequence", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "coords": { - "type": "file", - "description": "File containing coordinates of matches between reference and query sequence", - "pattern": "*.coords" - } + ], + "identifier": "biotools:mummer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "FASTA file of the reference sequence", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + }, + { + "query": { + "type": "file", + "description": "FASTA file of the query sequence", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + } + ] + ], + "output": [ + { + "coords": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.coords": { + "type": "file", + "description": "File containing coordinates of matches between reference and query sequence", + "pattern": "*.coords" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91162,82 +115292,176 @@ "doi": "10.1093/nar/gkh340", "licence": [ "http://www.drive5.com/muscle/manual/license.html" - ] - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "Input sequences for alignment must be in FASTA format", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "aligned_fasta": { - "type": "file", - "description": "Multiple sequence alignment produced in FASTA format", - "pattern": "*.{afa}" - } - }, - { - "msf": { - "type": "file", - "description": "GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)", - "pattern": "*.{msf}" - } - }, - { - "clustalw": { - "type": "file", - "description": "Multiple sequence alignment produced in ClustalW format without base/residue numbering", - "pattern": "*.{clw}" - } - }, - { - "phyi": { - "type": "file", - "description": "Multiple sequence alignment produced in PHYLIP interleaved format", - "pattern": "*.{phyi}" - } - }, - { - "phys": { - "type": "file", - "description": "Multiple sequence alignment produced in PHYLIP sequential format", - "pattern": "*.{phys}" - } - }, - { - "html": { - "type": "file", - "description": "Multiple sequence alignment produced in HTML format", - "pattern": "*.{html}" - } - }, - { - "tree": { - "type": "file", - "description": "NJ or UPGMA tree in Newick format produced from a multiple sequence alignment", - "pattern": "*.{tree}" - } - }, - { - "log": { - "type": "file", - "description": "Log file of MUSCLE run", - "pattern": "*{.log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:muscle" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences for alignment must be in FASTA format", + "pattern": "*.{fasta,fa,fna}" + } + } + ] + ], + "output": [ + { + "aligned_fasta": [ + { + "meta": { + "type": "file", + "description": "Multiple sequence alignment produced in FASTA format", + "pattern": "*.{afa}" + } + }, + { + "*.afa": { + "type": "file", + "description": "Multiple sequence alignment produced in FASTA format", + "pattern": "*.{afa}" + } + } + ] + }, + { + "phyi": [ + { + "meta": { + "type": "file", + "description": "Multiple sequence alignment produced in PHYLIP interleaved format", + "pattern": "*.{phyi}" + } + }, + { + "*.phyi": { + "type": "file", + "description": "Multiple sequence alignment produced in PHYLIP interleaved format", + "pattern": "*.{phyi}" + } + } + ] + }, + { + "phys": [ + { + "meta": { + "type": "file", + "description": "Multiple sequence alignment produced in PHYLIP sequential format", + "pattern": "*.{phys}" + } + }, + { + "*.phys": { + "type": "file", + "description": "Multiple sequence alignment produced in PHYLIP sequential format", + "pattern": "*.{phys}" + } + } + ] + }, + { + "clustalw": [ + { + "meta": { + "type": "file", + "description": "Multiple sequence alignment produced in ClustalW format without base/residue numbering", + "pattern": "*.{clw}" + } + }, + { + "*.clw": { + "type": "file", + "description": "Multiple sequence alignment produced in ClustalW format without base/residue numbering", + "pattern": "*.{clw}" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "file", + "description": "Multiple sequence alignment produced in HTML format", + "pattern": "*.{html}" + } + }, + { + "*.html": { + "type": "file", + "description": "Multiple sequence alignment produced in HTML format", + "pattern": "*.{html}" + } + } + ] + }, + { + "msf": [ + { + "meta": { + "type": "file", + "description": "GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)", + "pattern": "*.{msf}" + } + }, + { + "*.msf": { + "type": "file", + "description": "GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)", + "pattern": "*.{msf}" + } + } + ] + }, + { + "tree": [ + { + "meta": { + "type": "file", + "description": "NJ or UPGMA tree in Newick format produced from a multiple sequence alignment", + "pattern": "*.{tree}" + } + }, + { + "*.tree": { + "type": "file", + "description": "NJ or UPGMA tree in Newick format produced from a multiple sequence alignment", + "pattern": "*.{tree}" + } + } + ] + }, + { + "log": [ + { + "*.log": { + "type": "file", + "description": "Log file of MUSCLE run", + "pattern": "*{.log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91269,58 +115493,72 @@ "doi": "10.1101/2021.06.20.449169", "licence": [ "Public Domain" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences for alignment must be in FASTA format", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "alignment": { - "type": "file", - "description": "Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input!", - "pattern": "*.{aln.gz}" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences for alignment must be in FASTA format", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input!", + "pattern": "*.{aln.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91362,52 +115600,73 @@ "doi": "10.1093/nar/gks1114", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gene_list": { - "type": "file", - "description": "A tsv/csv file that contains a list of gene ids in one of the columns. By default, the column name should be \"gene_id\", but this can be changed by using \"--columname gene_id\" in ext.args.", - "pattern": "*.{csv,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gmt": { - "type": "file", - "description": "Each row contains the GO id, a description, and a list of gene ids.\n", - "pattern": "*.gmt" - } - }, - { - "tsv": { - "type": "file", - "description": "(optional) A tsv file with the following columns:\nquery, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid\n", - "pattern": "*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:mygene" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gene_list": { + "type": "file", + "description": "A tsv/csv file that contains a list of gene ids in one of the columns. By default, the column name should be \"gene_id\", but this can be changed by using \"--columname gene_id\" in ext.args.", + "pattern": "*.{csv,tsv}" + } + } + ] + ], + "output": [ + { + "gmt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gmt": { + "type": "file", + "description": "Each row contains the GO id, a description, and a list of gene ids.\n", + "pattern": "*.gmt" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "(optional) A tsv file with the following columns:\nquery, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid\n", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91440,59 +115699,82 @@ "doi": "10.1038/ncomms10063", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "BAM or FASTQ file", - "pattern": "*.{bam,fastq.gz,fq.gz}" - } - }, - { - "species": { - "type": "string", - "description": "Species to make AMR prediction against", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "AMR predictions in CSV format", - "pattern": "*.csv" - } - }, - { - "json": { - "type": "file", - "description": "AMR predictions in JSON format", - "pattern": "*.json" - } + ], + "identifier": "biotools:Mykrobe" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "BAM or FASTQ file", + "pattern": "*.{bam,fastq.gz,fq.gz}" + } + } + ], + [ + { + "species": { + "type": "string", + "description": "Species to make AMR prediction against", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.csv": { + "type": "file", + "description": "AMR predictions in CSV format", + "pattern": "*.csv" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.json": { + "type": "file", + "description": "AMR predictions in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91525,164 +115807,345 @@ "documentation": "https://github.com/wdecoster/nanocomp", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "filelist": { - "type": "file", - "description": "List of all the files you want to compare, they have to be all the same filetype (either fastq, fasta, bam or Nanopore sequencing summary)", - "pattern": "*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - 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only for sequencing summary input", + "pattern": "*NanoComp_CumulativeYieldPlot_Gigabases.html" + } + } + ] + }, + { + "sequencing_speed_over_time_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "*NanoComp_sequencing_speed_over_time.html": { + "type": "file", + "description": "Scatter plot of sequencing speed over time, only for sequencing summary input", + "pattern": "*NanoComp_sequencing_speed_over_time.html" + } + } + ] + }, + { + "stats_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "*NanoStats.txt": { + "type": "file", + "description": "txt file with basic statistics", + "pattern": "*NanoStats.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91721,58 +116184,75 @@ "doi": "10.1093/bioinformatics/bty149", "licence": [ "GLP-3.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Gunziped fastq files from Oxford Nanopore sequencing.", - "pattern": "*.fastq.gz" - } - }, - { - "summary_file": { - "type": "file", - "description": "Optional - Albacore or guppy summary file for quality scores" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "filtreads": { - "type": "file", - "description": "Gunziped fastq files after filtering.", - "pattern": "*.fastq.gz" - } - }, - { - "log_file": { - "type": "file", - "description": "Log file generated by --logfile option in NanoFilt, the file must end with .log extension.", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Gunziped fastq files from Oxford Nanopore sequencing.", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "summary_file": { + "type": "file", + "description": "Optional - Albacore or guppy summary file for quality scores" + } + } + ] + ], + "output": [ + { + "filtreads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Gunziped fastq files after filtering.", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "log_file": [ + { + "*.log": { + "type": "file", + "description": "Log file generated by --logfile option in NanoFilt, the file must end with .log extension.", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91803,59 +116283,76 @@ "documentation": "https://github.com/wdecoster/nanolyse#nanolyse", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Basecalled reads in FASTQ.GZ format\n", - "pattern": "*.fastq.gz" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference fasta file against which to filter.\n", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Reads with contaminants removed in FASTQ format", - "pattern": "*.fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log of the Nanolyse run.", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Basecalled reads in FASTQ.GZ format\n", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "A reference fasta file against which to filter.\n", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Reads with contaminants removed in FASTQ format", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "log": [ + { + "*.log": { + "type": "file", + "description": "Log of the Nanolyse run.", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -91901,101 +116398,182 @@ "doi": "10.1101/2020.07.22.214262 ", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Aligned BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "insertions": { - "type": "file", - "description": "Gzipped BED file containing reads supporting insertions", - "pattern": "*.{bed.gz}" - } - }, - { - "insertions_index": { - "type": "file", - "description": "Index for gzipped BED file containing reads supporting insertions", - "pattern": "*.{bed.gz.tbi}" - } - }, - { - "deletions": { - "type": "file", - "description": "Gzipped BED file containing reads supporting deletions", - "pattern": "*.{bed.gz}" - } - }, - { - "deletions_index": { - "type": "file", - "description": "Index for gzipped BED file containing reads supporting deletions", - "pattern": "*.{bed.gz.tbi}" - } - }, - { - "rearrangements": { - "type": "file", - "description": "Gzipped BED file containing reads supporting rearrangements", - "pattern": "*.{bed.gz}" - } - }, - { - "rearrangements_index": { - "type": "file", - "description": "Index for gzipped BED file containing reads supporting rearrangements", - "pattern": "*.{bed.gz.tbi}" - } - }, - { - "bp_info": { - "type": "file", - "description": "Gzipped BED file containing breakpoint info", - "pattern": "*.{bed.gz}" - } - }, - { - "bp_info_index": { - "type": "file", - "description": "Index for gzipped BED file containing breakpoint info", - "pattern": "*.{bed.gz.tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Aligned BAM file", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}" + } + } + ] + ], + "output": [ + { + "insertions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.insertion.sorted.bed.gz": { + "type": "file", + "description": "Gzipped BED file containing reads supporting insertions", + "pattern": "*.{bed.gz}" + } + } + ] + }, + { + "insertions_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.insertion.sorted.bed.gz.tbi": { + "type": "file", + "description": "Index for gzipped BED file containing reads supporting insertions", + "pattern": "*.{bed.gz.tbi}" + } + } + ] + }, + { + "deletions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.deletion.sorted.bed.gz": { + "type": "file", + "description": "Gzipped BED file containing reads supporting deletions", + "pattern": "*.{bed.gz}" + } + } + ] + }, + { + "deletions_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.deletion.sorted.bed.gz.tbi": { + "type": "file", + "description": "Index for gzipped BED file containing reads supporting deletions", + "pattern": "*.{bed.gz.tbi}" + } + } + ] + }, + { + "rearrangements": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.rearrangement.sorted.bedpe.gz": { + "type": "file", + "description": "Gzipped BED file containing reads supporting rearrangements", + "pattern": "*.{bed.gz}" + } + } + ] + }, + { + "rearrangements_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.rearrangement.sorted.bedpe.gz.tbi": { + "type": "file", + "description": "Index for gzipped BED file containing reads supporting rearrangements", + "pattern": "*.{bed.gz.tbi}" + } + } + ] + }, + { + "bp_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bp_info.sorted.bed.gz": { + "type": "file", + "description": "Gzipped BED file containing breakpoint info", + "pattern": "*.{bed.gz}" + } + } + ] + }, + { + "bp_info_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bp_info.sorted.bed.gz.tbi": { + "type": "file", + "description": "Index for gzipped BED file containing breakpoint info", + "pattern": "*.{bed.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92028,71 +116606,106 @@ "documentation": "https://github.com/wdecoster/NanoPlot", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "List of input basecalled-FastQ files.\n" - } - }, - { - "summary_txt": { - "type": "file", - "description": "List of sequencing_summary.txt files from running basecalling.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "html": { - "type": "file", - "description": "NanoPlot report", - "pattern": "*{.html}" - } - }, - { - "png": { - "type": "file", - "description": "Plots generated by NanoPlot", - "pattern": "*{.png}" - } - }, - { - "txt": { - "type": "file", - "description": "Stats from NanoPlot", - "pattern": "*{.txt}" - } - }, - { - "log": { - "type": "file", - "description": "log file of NanoPlot run", - "pattern": "*{.log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:nanoplot" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ontfile": { + "type": "file", + "description": "ONT file" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "NanoPlot report", + "pattern": "*{.html}" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Plots generated by NanoPlot", + "pattern": "*{.png}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Stats from NanoPlot", + "pattern": "*{.txt}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file of NanoPlot run", + "pattern": "*{.log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92158,58 +116771,81 @@ "doi": "10.21105/joss.02991", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "ontreads": { - "type": "file", - "description": "Compressed or uncompressed nanopore reads in fasta or fastq formats.", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}" - } - }, - { - "output_format": { - "type": "string", - "description": "Specifies the output format. One of these formats: fasta, fastq; fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "stats": { - "type": "file", - "description": "Summary report of reads statistics.", - "pattern": "*.{stats,json}" - } - }, - { - "reads": { - "type": "file", - "description": "Filtered reads.", - "pattern": "*.{fasta,fastq}{,.gz,.bz2,.lzma}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ontreads": { + "type": "file", + "description": "Compressed or uncompressed nanopore reads in fasta or fastq formats.", + "pattern": "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}" + } + } + ], + [ + { + "output_format": { + "type": "string", + "description": "Specifies the output format. One of these formats: fasta, fastq; fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." + } + } + ] + ], + "output": [ + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{stats,json}": { + "type": "file", + "description": "Summary report of reads statistics.", + "pattern": "*.{stats,json}" + } + } + ] + }, + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_filtered.${output_format}": { + "type": "file", + "description": "Filtered reads.", + "pattern": "*.{fasta,fastq}{,.gz,.bz2,.lzma}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92243,51 +116879,111 @@ "tool_dev_url": "https://github.com/edmundmiller/narfmap", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hashmap": { - "type": "file", - "description": "NARFMAP hash table", - "pattern": "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "hashmap": { + "type": "file", + "description": "NARFMAP hash table", + "pattern": "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + [ + { + "sort_bam": { + "type": "boolean", + "description": "Sort the BAM file after alignment" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of NARFMAP run", + "pattern": "*{.log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92320,44 +117016,55 @@ "tool_dev_url": "https://github.com/edmundmiller/narfmap", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "hashmap": { - "type": "file", - "description": "NARFMAP hash table", - "pattern": "*.{cmp,.bin,.txt}" - } + "hashmap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "narfmap": { + "type": "file", + "description": "NARFMAP hash table", + "pattern": "*.{cmp,.bin,.txt}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92389,142 +117096,279 @@ "tool_dev_url": "https://github.com/kblin/ncbi-genome-download", "licence": [ "Apache Software License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "accessions": { - "type": "file", - "description": "List of accessions (one per line) to download", - "pattern": "*.txt" - } - }, - { - "taxids": { - "type": "file", - "description": "List of taxids (one per line) to download", - "pattern": "*.txt" - } - }, - { - "groups": { - "type": "string", - "description": "NCBI taxonomic groups to download. Can be a comma-separated list. Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral']" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gbk": { - "type": "file", - "description": "GenBank format of the genomic sequence(s) in the assembly", - "pattern": "*_genomic.gbff.gz" - } - }, - { - "fna": { - "type": "file", - "description": "FASTA format of the genomic sequence(s) in the assembly.", - "pattern": "*_genomic.fna.gz" - } - }, - { - "rm": { - "type": "file", - "description": "RepeatMasker output for eukaryotes.", - "pattern": "*_rm.out.gz" - } - }, - { - "features": { - "type": "file", - "description": "Tab-delimited text file reporting locations and attributes for a subset of annotated features", - "pattern": "*_feature_table.txt.gz" - } - }, - { - "gff": { - "type": "file", - "description": "Annotation of the genomic sequence(s) in GFF3 format", - "pattern": "*_genomic.gff.gz" - } - }, - { - "faa": { - "type": "file", - "description": "FASTA format of the accessioned protein products annotated on the genome assembly.", - "pattern": "*_protein.faa.gz" - } - }, - { - "gpff": { - "type": "file", - "description": "GenPept format of the accessioned protein products annotated on the genome assembly.", - "pattern": "*_protein.gpff.gz" - } - }, - { - "wgs_gbk": { - "type": "file", - "description": "GenBank flat file format of the WGS master for the assembly", - "pattern": "*_wgsmaster.gbff.gz" - } - }, - { - "cds": { - "type": "file", - "description": "FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly", - "pattern": "*_cds_from_genomic.fna.gz" - } - }, - { - "rna": { - "type": "file", - "description": "FASTA format of accessioned RNA products annotated on the genome assembly", - "pattern": "*_rna.fna.gz" - } - }, - { - "rna_fna": { - "type": "file", - "description": "FASTA format of the nucleotide sequences corresponding to all RNA features annotated on the assembly", - "pattern": "*_rna_from_genomic.fna.gz" - } - }, - { - "report": { - "type": "file", - "description": "Tab-delimited text file reporting the name, role and sequence accession.version for objects in the assembly", - "pattern": "*_assembly_report.txt" - } - }, - { - "stats": { - "type": "file", - "description": "Tab-delimited text file reporting statistics for the assembly", - "pattern": "*_assembly_stats.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ], + [ + { + "accessions": { + "type": "file", + "description": "List of accessions (one per line) to download", + "pattern": "*.txt" + } + } + ], + [ + { + "taxids": { + "type": "file", + "description": "List of taxids (one per line) to download", + "pattern": "*.txt" + } + } + ], + [ + { + "groups": { + "type": "string", + "description": "NCBI taxonomic groups to download. Can be a comma-separated list. Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral']" + } + } + ] + ], + "output": [ + { + "gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genomic.gbff.gz": { + "type": "file", + "description": "GenBank format of the genomic sequence(s) in the assembly", + "pattern": "*_genomic.gbff.gz" + } + } + ] + }, + { + "fna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genomic.fna.gz": { + "type": "file", + "description": "FASTA format of the genomic sequence(s) in the assembly.", + "pattern": "*_genomic.fna.gz" + } + } + ] + }, + { + "rm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_rm.out.gz": { + "type": "file", + "description": "RepeatMasker output for eukaryotes.", + "pattern": "*_rm.out.gz" + } + } + ] + }, + { + "features": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_feature_table.txt.gz": { + "type": "file", + "description": "Tab-delimited text file reporting locations and attributes for a subset of annotated features", + "pattern": "*_feature_table.txt.gz" + } + } + ] + }, + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_genomic.gff.gz": { + "type": "file", + "description": "Annotation of the genomic sequence(s) in GFF3 format", + "pattern": "*_genomic.gff.gz" + } + } + ] + }, + { + "faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_protein.faa.gz": { + "type": "file", + "description": "FASTA format of the accessioned protein products annotated on the genome assembly.", + "pattern": "*_protein.faa.gz" + } + } + ] + }, + { + "gpff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_protein.gpff.gz": { + "type": "file", + "description": "GenPept format of the accessioned protein products annotated on the genome assembly.", + "pattern": "*_protein.gpff.gz" + } + } + ] + }, + { + "wgs_gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_wgsmaster.gbff.gz": { + "type": "file", + "description": "GenBank flat file format of the WGS master for the assembly", + "pattern": "*_wgsmaster.gbff.gz" + } + } + ] + }, + { + "cds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_cds_from_genomic.fna.gz": { + "type": "file", + "description": "FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly", + "pattern": "*_cds_from_genomic.fna.gz" + } + } + ] + }, + { + "rna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_rna.fna.gz": { + "type": "file", + "description": "FASTA format of accessioned RNA products annotated on the genome assembly", + "pattern": "*_rna.fna.gz" + } + } + ] + }, + { + "rna_fna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_rna_from_genomic.fna.gz": { + "type": "file", + "description": "FASTA format of the nucleotide sequences corresponding to all RNA features annotated on the assembly", + "pattern": "*_rna_from_genomic.fna.gz" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_assembly_report.txt": { + "type": "file", + "description": "Tab-delimited text file reporting the name, role and sequence accession.version for objects in the assembly", + "pattern": "*_assembly_report.txt" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_assembly_stats.txt": { + "type": "file", + "description": "Tab-delimited text file reporting statistics for the assembly", + "pattern": "*_assembly_stats.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92565,50 +117409,69 @@ "tool_dev_url": "https://www.ncbi.nlm.nih.gov/tools/vecscreen/", "licence": [ "The Open Database License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'6973' ]\n" - } - }, - { - "fasta_file": { - "type": "file", - "description": "FASTA file that will be screened for contaminants" - } - }, - { - "adapters_database_file": { - "type": "file", - "description": "Path to a nucleotide BLAST database file with vector sequences" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'9606' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vecscreen_output": { - "type": "file", - "description": "VecScreen report file. This can be in different formats depending on the value of the optional -f parameter. 0 = HTML format, with alignments. 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, no alignments. default = 0", - "pattern": "*.vecscreen.out" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'6973' ]\n" + } + }, + { + "fasta_file": { + "type": "file", + "description": "FASTA file that will be screened for contaminants" + } + } + ], + [ + { + "adapters_database_meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "adapters_database_directory": { + "type": "directory", + "description": "Directory containing the adapters database" + } + } + ] + ], + "output": [ + { + "vecscreen_output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', taxid:'9606' ]\n" + } + }, + { + "${meta.id}.vecscreen.out": { + "type": "file", + "description": "VecScreen report file. This can be in different formats depending on the value of the optional -f parameter. 0 = HTML format, with alignments. 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, no alignments. default = 0", + "pattern": "*.vecscreen.out" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92637,40 +117500,52 @@ "tool_dev_url": "https://github.com/nextstrain/nextclade", "licence": [ "MIT" - ] + ], + "identifier": "biotools:nextclade" } } ], "input": [ - { - "dataset": { - "type": "string", - "description": "Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command.", - "pattern": ".+" + [ + { + "dataset": { + "type": "string", + "description": "Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command.", + "pattern": ".+" + } } - }, - { - "tag": { - "type": "string", - "description": "Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command.", - "pattern": ".+" + ], + [ + { + "tag": { + "type": "string", + "description": "Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command.", + "pattern": ".+" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "dataset": [ + { + "$prefix": { + "type": "directory", + "description": "Directory containing the dataset" + } + } + ] }, { - "prefix": { - "type": "directory", - "description": "A directory containing the dataset files needed for nextclade run", - "pattern": "prefix" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92713,115 +117588,218 @@ "tool_dev_url": "https://github.com/nextstrain/nextclade", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dataset": { - "type": "directory", - "description": "Path containing the dataset files obtained by running nextclade dataset get", - "pattern": "*" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing one or more consensus sequences", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "CSV file containing nextclade results", - "pattern": "*.{csv}" - } - }, - { - "csv_errors": { - "type": "file", - "description": "CSV file containing errors from nextclade results", - "pattern": "*.{errors.csv}" - } - }, - { - "csv_insertions": { - "type": "file", - "description": "CSV file containing insertions from nextclade results", - "pattern": "*.{insertions.csv}" - } - }, - { - "fasta_aligned": { - "type": "file", - "description": "FASTA file containing aligned sequences from nextclade results", - "pattern": "*.{aligned.fasta}" - } - }, - { - "fasta_translation": { - "type": "file", - "description": "FASTA file containing aligned peptides from nextclade results", - "pattern": "*.{_translation.}*.{fasta}" - } - }, - { - "ndjson": { - "type": "file", - "description": "newline-delimited JSON file containing nextclade results", - "pattern": "*.{ndjson}" - } - }, - { - "json": { - "type": "file", - "description": "JSON file containing nextclade results", - "pattern": "*.{json}" - } - }, - { - "json_auspice": { - "type": "file", - "description": "Auspice JSON V2 containing nextclade results", - "pattern": "*.{tree.json}" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file containing nextclade results", - "pattern": "*.{tsv}" - } - }, - { - "nwk": { - "type": "file", - "description": "NWK file containing nextclade results", - "pattern": "*.{nwk}" - } + ], + "identifier": "biotools:nextclade" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing one or more consensus sequences", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "dataset": { + "type": "directory", + "description": "Path containing the dataset files obtained by running nextclade dataset get", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.csv": { + "type": "file", + "description": "CSV file containing nextclade results", + "pattern": "*.{csv}" + } + } + ] + }, + { + "csv_errors": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.errors.csv": { + "type": "file", + "description": "CSV file containing errors from nextclade results", + "pattern": "*.{errors.csv}" + } + } + ] + }, + { + "csv_insertions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.insertions.csv": { + "type": "file", + "description": "CSV file containing insertions from nextclade results", + "pattern": "*.{insertions.csv}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "TSV file containing nextclade results", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.json": { + "type": "file", + "description": "JSON file containing nextclade results", + "pattern": "*.{json}" + } + } + ] + }, + { + "json_auspice": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.auspice.json": { + "type": "file", + "description": "Auspice JSON V2 containing nextclade results", + "pattern": "*.{tree.json}" + } + } + ] + }, + { + "ndjson": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.ndjson": { + "type": "file", + "description": "newline-delimited JSON file containing nextclade results", + "pattern": "*.{ndjson}" + } + } + ] + }, + { + "fasta_aligned": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.aligned.fasta": { + "type": "file", + "description": "FASTA file containing aligned sequences from nextclade results", + "pattern": "*.{aligned.fasta}" + } + } + ] + }, + { + "fasta_translation": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_translation.*.fasta": { + "type": "file", + "description": "FASTA file containing aligned peptides from nextclade results", + "pattern": "*.{_translation.}*.{fasta}" + } + } + ] + }, + { + "nwk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.nwk": { + "type": "file", + "description": "NWK file containing nextclade results", + "pattern": "*.{nwk}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92869,51 +117847,64 @@ "doi": "10.1093/bioinformatics/btt468", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1, if meta.single_end is true, and 2\nif meta.single_end is false.\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genomic reference fasta file\n", - "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information. First item of tuple with\nbam, below.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments. Second item of tuple with\nmeta, above\n", - "pattern": "*.{bam}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:nextgenmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1, if meta.single_end is true, and 2\nif meta.single_end is false.\n" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Genomic reference fasta file\n", + "pattern": "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information. First item of tuple with\nbam, below.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file containing read alignments. Second item of tuple with\nmeta, above\n", + "pattern": "*.{bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -92946,45 +117937,56 @@ "doi": "10.1099/mgen.0.000076", "licence": [ "GPL v3 only" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited result file", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited result file", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93017,59 +118019,90 @@ "doi": "10.1186/s12859-018-2579-2", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 2; i.e., paired-end data.\n", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "merged_reads": { - "type": "file", - "description": "fastq file merged reads", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - } - }, - { - "unstitched_read1": { - "type": "file", - "description": "fastq file unstitched read 1", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - } - }, - { - "unstitched_read2": { - "type": "file", - "description": "fastq file unstitched read 2", - "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 2; i.e., paired-end data.\n", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + } + } + ] + ], + "output": [ + { + "merged_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.merged.fq.gz": { + "type": "file", + "description": "fastq file merged reads", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + } + } + ] + }, + { + "unstitched_read1": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_1.fastq.gz": { + "type": "file", + "description": "fastq file unstitched read 1", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + } + } + ] + }, + { + "unstitched_read2": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_2.fastq.gz": { + "type": "file", + "description": "fastq file unstitched read 2", + "pattern": "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93104,85 +118137,102 @@ "tool_dev_url": "https://github.com/imgag/ngs-bits", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "One or more BAM/CRAM files to determine the gender of", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "The index file(s) from the input BAM/CRAM file(s)", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference fasta information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA to use (mandatory when CRAM files are used)", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fasta index information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The index of the reference FASTA to use (mandatory when CRAM files are used)", - "pattern": "*.fai" - } - }, - { - "method": { - "type": "string", - "description": "The method to use to define the gender (posibilities are 'xy', 'hetx' and 'sry')", - "pattern": "(xy|hetx|sry)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "An output TSV file containing the results of the gender prediction", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "One or more BAM/CRAM files to determine the gender of", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "The index file(s) from the input BAM/CRAM file(s)", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA to use (mandatory when CRAM files are used)", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference fasta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index file from the reference FASTA", + "pattern": "*.fai" + } + } + ], + [ + { + "method": { + "type": "string", + "description": "The method to use to define the gender (posibilities are 'xy', 'hetx' and 'sry')", + "pattern": "(xy|hetx|sry)" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "An output TSV file containing the results of the gender prediction", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93222,58 +118272,71 @@ "doi": "10.1093/nar/gkx193", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the fastq files\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Raw fastq files for one sample, single or paired end.", - "pattern": "*.{fastq.gz}" - } - }, - { - "meta2": { - "type": "file", - "description": "Groovy Map containing sample information about the NGSCheckMate SNP pt file\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "snp_pt": { - "type": "file", - "description": "PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate's github repository.", - "pattern": "*.{pt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vaf": { - "type": "file", - "description": "Text file containing reference/alt allele depth for each SNP position contained in the PT file.", - "pattern": "*.{vaf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the fastq files\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Raw fastq files for one sample, single or paired end.", + "pattern": "*.{fastq.gz}" + } + } + ], + [ + { + "meta2": { + "type": "file", + "description": "Groovy Map containing sample information about the NGSCheckMate SNP pt file\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "snp_pt": { + "type": "file", + "description": "PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate's github repository.", + "pattern": "*.{pt}" + } + } + ] + ], + "output": [ + { + "vaf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vaf": { + "type": "file", + "description": "Text file containing reference/alt allele depth for each SNP position contained in the PT file.", + "pattern": "*.{vaf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93306,93 +118369,159 @@ "doi": "10.1093/nar/gkx193", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "files": { - "type": "file", - "description": "VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too.", - "pattern": "*.{vcf,vcf.gz,bam,bai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing SNP information\ne.g. [ id:'test' ]\n" - } - }, - { - "snp_bed": { - "type": "file", - "description": "BED file containing the SNPs to analyse", - "pattern": "*.{bed}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fasta index information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file for the genome, only used in the bam mode", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pdf": { - "type": "file", - "description": "A pdf containing a dendrogram showing how the samples match up", - "pattern": "*.{pdf}" - } - }, - { - "corr_matrix": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt" - } - }, - { - "matched": { - "type": "file", - "description": "A txt file containing only the samples that match with each other", - "pattern": "*matched.txt" - } - }, - { - "all": { - "type": "file", - "description": "A txt file containing all the sample comparisons, whether they match or not", - "pattern": "*all.txt" - } - }, - { - "vcf": { - "type": "file", - "description": "If ran in bam mode, vcf files for each sample giving the SNP calls used", - "pattern": "*.vcf" - } + ], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "files": { + "type": "file", + "description": "VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too.", + "pattern": "*.{vcf,vcf.gz,bam,bai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing SNP information\ne.g. [ id:'test' ]\n" + } + }, + { + "snp_bed": { + "type": "file", + "description": "BED file containing the SNPs to analyse", + "pattern": "*.{bed}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fasta index information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file for the genome, only used in the bam mode", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "corr_matrix": [ + { + "meta": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt" + } + }, + { + "*_corr_matrix.txt": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt" + } + } + ] + }, + { + "matched": [ + { + "meta": { + "type": "file", + "description": "A txt file containing only the samples that match with each other", + "pattern": "*matched.txt" + } + }, + { + "*_matched.txt": { + "type": "file", + "description": "A txt file containing only the samples that match with each other", + "pattern": "*matched.txt" + } + } + ] + }, + { + "all": [ + { + "meta": { + "type": "file", + "description": "A txt file containing all the sample comparisons, whether they match or not", + "pattern": "*all.txt" + } + }, + { + "*_all.txt": { + "type": "file", + "description": "A txt file containing all the sample comparisons, whether they match or not", + "pattern": "*all.txt" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "A pdf containing a dendrogram showing how the samples match up", + "pattern": "*.{pdf}" + } + }, + { + "*.pdf": { + "type": "file", + "description": "A pdf containing a dendrogram showing how the samples match up", + "pattern": "*.{pdf}" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "If ran in bam mode, vcf files for each sample giving the SNP calls used", + "pattern": "*.vcf" + } + }, + { + "*.vcf": { + "type": "file", + "description": "If ran in bam mode, vcf files for each sample giving the SNP calls used", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93432,64 +118561,85 @@ "doi": "10.1093/nar/gkx193", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the bed file\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file containing population-level SNPs to use", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information about the fasta genome\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.fasta" - } - }, - { - "bowtie_index": { - "type": "directory", - "description": "Folder of Bowtie genome index files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pt": { - "type": "file", - "description": "Generated binary pattern file, containing FASTQ strings to match from within raw data", - "pattern": "*.pt" - } + ], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the bed file\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file containing population-level SNPs to use", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information about the fasta genome\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bowtie_index": { + "type": "directory", + "description": "Folder of Bowtie genome index files" + } + } + ] + ], + "output": [ + { + "pt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.pt": { + "type": "file", + "description": "Generated binary pattern file, containing FASTQ strings to match from within raw data", + "pattern": "*.pt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93523,66 +118673,107 @@ "doi": "10.1093/nar/gkx193", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" - } - }, - { - "vafs": { - "type": "file", - "description": "Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq", - "pattern": "*.{vaf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" - } - }, - { - "pdf": { - "type": "file", - "description": "A pdf containing a dendrogram showing how the samples match up. | Note due to a bug in the R script used by the tool this is not produced when only two samples are given.", - "pattern": "*.{pdf}" - } - }, - { - "corr_matrix": { - "type": "file", - "description": "A text file containing the correlation matrix between each sample", - "pattern": "*corr_matrix.txt" - } - }, - { - "matched": { - "type": "file", - "description": "A txt file containing only the samples that match with each other", - "pattern": "*matched.txt" - } - }, - { - "all": { - "type": "file", - "description": "A txt file containing all the sample comparisons, whether they match or not", - "pattern": "*all.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ngscheckmate" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "vafs": { + "type": "file", + "description": "Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq", + "pattern": "*.{vaf}" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "A pdf containing a dendrogram showing how the samples match up. | Note due to a bug in the R script used by the tool this is not produced when only two samples are given.", + "pattern": "*.{pdf}" + } + } + ] + }, + { + "corr_matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*_corr_matrix.txt": { + "type": "file", + "description": "A text file containing the correlation matrix between each sample", + "pattern": "*corr_matrix.txt" + } + } + ] + }, + { + "all": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*_all.txt": { + "type": "file", + "description": "A txt file containing all the sample comparisons, whether they match or not", + "pattern": "*all.txt" + } + } + ] + }, + { + "matched": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information about the combined set of files\ne.g. `[ id:'combined' ]`\n" + } + }, + { + "*_matched.txt": { + "type": "file", + "description": "A txt file containing only the samples that match with each other", + "pattern": "*matched.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93724,45 +118915,56 @@ "doi": "10.1128/msystems.00039-", "licence": [ "Artistic License 2.0" - ] + ], + "identifier": "biotools:nonpareil" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "npo": { - "type": "file", - "description": "Single npo redundancy summary file from nonpareil itself", - "pattern": "*.npo" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "npo": { + "type": "file", + "description": "Single npo redundancy summary file from nonpareil itself", + "pattern": "*.npo" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "PNG file of the Nonpareil curve", + "pattern": "*.png" + } + } + ] }, { - "png": { - "type": "file", - "description": "PNG file of the Nonpareil curve", - "pattern": "*.png" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93798,80 +119000,125 @@ "doi": "10.1128/msystems.00039-", "licence": [ "Artistic License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ or FASTA file (ideally uncompressed, but not required)", - "pattern": "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}" - } - }, - { - "format": { - "type": "string", - "description": "File format of input file", - "pattern": "fasta|fastq" - } - }, - { - "mode": { - "type": "string", - "description": "Mode of redundancy estimation", - "pattern": "kmer|alignment" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "npa": { - "type": "file", - "description": "Raw redundancy values", - "pattern": "*.npa" - } - }, - { - "npc": { - "type": "file", - "description": "Mates distribution file", - "pattern": "*.npc" - } - }, - { - "npl": { - "type": "file", - "description": "Log file", - "pattern": "*.npl" - } - }, - { - "npo": { - "type": "file", - "description": "Redundancy summary file", - "pattern": "*.npo" - } + ], + "identifier": "biotools:nonpareil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ or FASTA file (ideally uncompressed, but not required)", + "pattern": "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "File format of input file", + "pattern": "fasta|fastq" + } + } + ], + [ + { + "mode": { + "type": "string", + "description": "Mode of redundancy estimation", + "pattern": "kmer|alignment" + } + } + ] + ], + "output": [ + { + "npa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npa": { + "type": "file", + "description": "Raw redundancy values", + "pattern": "*.npa" + } + } + ] + }, + { + "npc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npc": { + "type": "file", + "description": "Mates distribution file", + "pattern": "*.npc" + } + } + ] + }, + { + "npl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npl": { + "type": "file", + "description": "Log file", + "pattern": "*.npl" + } + } + ] + }, + { + "npo": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.npo": { + "type": "file", + "description": "Redundancy summary file", + "pattern": "*.npo" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -93908,66 +119155,107 @@ "doi": "10.1128/msystems.00039-", "licence": [ "Artistic License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "npos": { - "type": "file", - "description": "One or a list of Nonpareil NPO files (From nonpareil/nonpareil)", - "pattern": "*.{npo}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "Raw nonpareil data used for generating and plotting curves in JSON format", - "pattern": "*.json" - } - }, - { - "tsv": { - "type": "file", - "description": "Raw nonpareil data used for generating and plotting curves in JSON format", - "pattern": "*.tsv" - } - }, - { - "csv": { - "type": "file", - "description": "Raw nonpareil data used for generating and plotting curves in JSON format", - "pattern": "*.csv" - } - }, - { - "pdf": { - "type": "file", - "description": "Plotted nonpareil curves in PDF format", - "pattern": "*.pdf" - } + ], + "identifier": "biotools:nonpareil" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "npos": { + "type": "file", + "description": "One or a list of Nonpareil NPO files (From nonpareil/nonpareil)", + "pattern": "*.{npo}" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Raw nonpareil data used for generating and plotting curves in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv\" ": { + "type": "file", + "description": "Raw nonpareil data used for generating and plotting curves in JSON format", + "pattern": "*.tsv" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.csv\" ": { + "type": "file", + "description": "Raw nonpareil data used for generating and plotting curves in JSON format", + "pattern": "*.csv" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.pdf\" ": { + "type": "file", + "description": "Plotted nonpareil curves in PDF format", + "pattern": "*.pdf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94004,45 +119292,56 @@ "doi": "10.1128/msystems.00039-", "licence": [ "Artistic License 2.0" - ] + ], + "identifier": "biotools:nonpareil" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "npos": { + "type": "file", + "description": "A list of npo redundancy summary files from nonpareil itself", + "pattern": "*.npo" + } } - }, - { - "npos": { - "type": "file", - "description": "A list of npo redundancy summary files from nonpareil itself", - "pattern": "*.npo" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "PNG file of all the Nonpareil curves of the input npo files", + "pattern": "*.png" + } + } + ] }, { - "png": { - "type": "file", - "description": "PNG file of all the Nonpareil curves of the input npo files", - "pattern": "*.png" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94075,58 +119374,79 @@ "doi": "10.1186/gb-2004-5-2-r12", "licence": [ "The Artistic License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "FASTA file of the reference sequence", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - }, - { - "query": { - "type": "file", - "description": "FASTA file of the query sequence", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "delta": { - "type": "file", - "description": "File containing coordinates of matches between reference and query" - } - }, - { - "coords": { - "type": "file", - "description": "NUCmer1.1 coords output file", - "pattern": "*.{coords}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "FASTA file of the reference sequence", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + }, + { + "query": { + "type": "file", + "description": "FASTA file of the query sequence", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + } + ] + ], + "output": [ + { + "delta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.delta": { + "type": "file", + "description": "File containing coordinates of matches between reference and query" + } + } + ] + }, + { + "coords": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.coords": { + "type": "file", + "description": "NUCmer1.1 coords output file", + "pattern": "*.{coords}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94164,199 +119484,334 @@ "doi": "10.5281/zenodo.10400173", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'Cladonia_norvegica' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "HiFi reads in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz}" - } - }, - { - "mito_hmm": { - "type": "file", - "description": "mitochondria gene annotation HMM profile database", - "pattern": "*.{fa,fam}" - } - }, - { - "mito_hmm_h3f": { - "type": "file", - "description": "mitochondria gene annotation HMM profile binary auxfile", - "pattern": "*.{h3f}" - } - }, - { - "mito_hmm_h3i": { - "type": "file", - "description": "mitochondria gene annotation HMM profile binary auxfile", - "pattern": "*.{h3i}" - } - }, - { - "mito_hmm_h3m": { - "type": "file", - "description": "mitochondria gene annotation HMM profile binary auxfile", - "pattern": "*.{h3m}" - } - }, - { - "mito_hmm_h3p": { - "type": "file", - "description": "mitochondria gene annotation HMM profile binary auxfile", - "pattern": "*.{h3p}" - } - }, - { - "pltd_hmm": { - "type": "file", - "description": "plastid gene annotation HMM profile database", - "pattern": "*.{fa,fam}" - } - }, - { - "pltd_hmm_h3f": { - "type": "file", - "description": "plastid gene annotation HMM profile binary auxfile", - "pattern": "*.{h3f}" - } - }, - { - "pltd_hmm_h3i": { - "type": "file", - "description": "plastid gene annotation HMM profile binary auxfile", - "pattern": "*.{h3i}" - } - }, - { - "pltd_hmm_h3m": { - "type": "file", - "description": "plastid gene annotation HMM profile binary auxfile", - "pattern": "*.{h3m}" - } - }, - { - "pltd_hmm_h3p": { - "type": "file", - "description": "plastid gene annotation HMM profile binary auxfile", - "pattern": "*.{h3p}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "mito_fasta": { - "type": "file", - "description": "the structure-solved MT contigs", - "pattern": "*mito.ctg.fasta" - } - }, - { - "pltd_fasta": { - "type": "file", - "description": "the structure-solved PT contigs", - "pattern": "*pltd.ctg.fasta" - } - }, - { - "mito_bed": { - "type": "file", - "description": "the gene annotation for the MT sequences", - "pattern": "*mito.ctg.bed" - } - }, - { - "pltd_bed": { - "type": "file", - "description": "the gene annotation for the PT sequences", - "pattern": "*pltd.ctg.bed" - } - }, - { - "mito_gfa": { - "type": "file", - "description": "the subgraph for the MT genome", - "pattern": "*mito.gfa" - } - }, - { - "pltd_gfa": { - "type": "file", - "description": "the subgraph for the PT genome", - "pattern": "*pltd.gfa" - } - }, - { - "annot_mito_txt": { - "type": "file", - "description": "the MT gene annotation file over all assembled sequences", - "pattern": "*annot_mito.txt" - } - }, - { - "annot_pltd_txt": { - "type": "file", - "description": "the PT gene annotation file over all assembled sequences", - "pattern": "*annot_pltd.txt" - } - }, - { - "clean_gfa": { - "type": "file", - "description": "the GFA file for the clean genome assembly", - "pattern": "*utg.clean.gfa" - } - }, - { - "final_gfa": { - "type": "file", - "description": "the GFA file for the final genome assembly", - "pattern": "*utg.final.gfa" - } - }, - { - "initial_gfa": { - "type": "file", - "description": "the GFA file for the initial genome assembly", - "pattern": "*utg.gfa" - } - }, - { - "multiplex_gfa": { - "type": "file", - "description": "the mutliplexed GFA file", - "pattern": "*utg.multiplex.gfa" - } - }, - { - "unzip_gfa": { - "type": "file", - "description": "the unzipped GFA file", - "pattern": "*utg.unzip.gfa" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'Cladonia_norvegica' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "HiFi reads in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz}" + } + } + ], + [ + { + "mito_hmm": { + "type": "file", + "description": "mitochondria gene annotation HMM profile database", + "pattern": "*.{fa,fam}" + } + }, + { + "mito_hmm_h3f": { + "type": "file", + "description": "mitochondria gene annotation HMM profile binary auxfile", + "pattern": "*.{h3f}" + } + }, + { + "mito_hmm_h3i": { + "type": "file", + "description": "mitochondria gene annotation HMM profile binary auxfile", + "pattern": "*.{h3i}" + } + }, + { + "mito_hmm_h3m": { + "type": "file", + "description": "mitochondria gene annotation HMM profile binary auxfile", + "pattern": "*.{h3m}" + } + }, + { + "mito_hmm_h3p": { + "type": "file", + "description": "mitochondria gene annotation HMM profile binary auxfile", + "pattern": "*.{h3p}" + } + } + ], + [ + { + "pltd_hmm": { + "type": "file", + "description": "plastid gene annotation HMM profile database", + "pattern": "*.{fa,fam}" + } + }, + { + "pltd_hmm_h3f": { + "type": "file", + "description": "plastid gene annotation HMM profile binary auxfile", + "pattern": "*.{h3f}" + } + }, + { + "pltd_hmm_h3i": { + "type": "file", + "description": "plastid gene annotation HMM profile binary auxfile", + "pattern": "*.{h3i}" + } + }, + { + "pltd_hmm_h3m": { + "type": "file", + "description": "plastid gene annotation HMM profile binary auxfile", + "pattern": "*.{h3m}" + } + }, + { + "pltd_hmm_h3p": { + "type": "file", + "description": "plastid gene annotation HMM profile binary auxfile", + "pattern": "*.{h3p}" + } + } + ] + ], + "output": [ + { + "mito_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*mito.ctg.fasta": { + "type": "file", + "description": "the structure-solved MT contigs", + "pattern": "*mito.ctg.fasta" + } + } + ] + }, + { + "pltd_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*pltd.ctg.fasta": { + "type": "file", + "description": "the structure-solved PT contigs", + "pattern": "*pltd.ctg.fasta" + } + } + ] + }, + { + "mito_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*mito.ctg.bed": { + "type": "file", + "description": "the gene annotation for the MT sequences", + "pattern": "*mito.ctg.bed" + } + } + ] + }, + { + "pltd_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*pltd.ctg.bed": { + "type": "file", + "description": "the gene annotation for the PT sequences", + "pattern": "*pltd.ctg.bed" + } + } + ] + }, + { + "mito_gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*mito.gfa": { + "type": "file", + "description": "the subgraph for the MT genome", + "pattern": "*mito.gfa" + } + } + ] + }, + { + "pltd_gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*pltd.gfa": { + "type": "file", + "description": "the subgraph for the PT genome", + "pattern": "*pltd.gfa" + } + } + ] + }, + { + "annot_mito_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*annot_mito.txt": { + "type": "file", + "description": "the MT gene annotation file over all assembled sequences", + "pattern": "*annot_mito.txt" + } + } + ] + }, + { + "annot_pltd_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*annot_pltd.txt": { + "type": "file", + "description": "the PT gene annotation file over all assembled sequences", + "pattern": "*annot_pltd.txt" + } + } + ] + }, + { + "clean_gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*utg.clean.gfa": { + "type": "file", + "description": "the GFA file for the clean genome assembly", + "pattern": "*utg.clean.gfa" + } + } + ] + }, + { + "final_gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*utg.final.gfa": { + "type": "file", + "description": "the GFA file for the final genome assembly", + "pattern": "*utg.final.gfa" + } + } + ] + }, + { + "initial_gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*utg.gfa": { + "type": "file", + "description": "the GFA file for the initial genome assembly", + "pattern": "*utg.gfa" + } + } + ] + }, + { + "multiplex_gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*utg.multiplex.gfa": { + "type": "file", + "description": "the mutliplexed GFA file", + "pattern": "*utg.multiplex.gfa" + } + } + ] + }, + { + "unzip_gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*utg.unzip.gfa": { + "type": "file", + "description": "the unzipped GFA file", + "pattern": "*utg.unzip.gfa" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94387,45 +119842,56 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] + ], + "identifier": "biotools:odgi" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format", - "pattern": "*.{gfa}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format", + "pattern": "*.{gfa}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "og": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og": { + "type": "file", + "description": "File containing a pangenome graph in ODGI binary format. Usually ends with '.og'", + "pattern": "*.{og}" + } + } + ] }, { - "og": { - "type": "file", - "description": "File containing a pangenome graph in ODGI binary format. Usually ends with '.og'", - "pattern": "*.{og}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94465,52 +119931,63 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or ODGI binary format", - "pattern": "*.{gfa,og}" - } - }, - { - "lay": { - "type": "file", - "description": "2D layout from 'odgi layout' in LAY binary format", - "pattern": "*.{lay}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "png": { - "type": "file", - "description": "File in PNG format containing a 2D drawing of a pangenome graph", - "pattern": "*.{png}" - } + ], + "identifier": "biotools:odgi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or ODGI binary format", + "pattern": "*.{gfa,og}" + } + }, + { + "lay": { + "type": "file", + "description": "2D layout from 'odgi layout' in LAY binary format", + "pattern": "*.{lay}" + } + } + ] + ], + "output": [ + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "File in PNG format containing a 2D drawing of a pangenome graph", + "pattern": "*.{png}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94550,52 +120027,73 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", - "pattern": "*.{gfa,og}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "lay": { - "type": "file", - "description": "File containing a 2D layout of a pangenome graph in a binary format. Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. Either this or the TSV layout output must be specified.", - "pattern": "*.{lay}" - } - }, - { - "tsv": { - "type": "file", - "description": "File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified.", - "pattern": "*.{tsv}" - } + ], + "identifier": "biotools:odgi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", + "pattern": "*.{gfa,og}" + } + } + ] + ], + "output": [ + { + "lay": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lay": { + "type": "file", + "description": "File containing a 2D layout of a pangenome graph in a binary format. Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. Either this or the TSV layout output must be specified.", + "pattern": "*.{lay}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified.", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94635,45 +120133,56 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] + ], + "identifier": "biotools:odgi" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", - "pattern": "*.{gfa,og}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", + "pattern": "*.{gfa,og}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "sorted_graph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og": { + "type": "file", + "description": "1D sorted pangenome graph in ODGI binary format", + "pattern": "*.{og}" + } + } + ] }, { - "sorted_graph": { - "type": "file", - "description": "1D sorted pangenome graph in ODGI binary format", - "pattern": "*.{og}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94713,45 +120222,56 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] + ], + "identifier": "biotools:odgi" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graphs": { - "type": "file", - "description": "Pangenome graph files in ODGI format.", - "pattern": "*.{og}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graphs": { + "type": "file", + "description": "Pangenome graph files in ODGI format.", + "pattern": "*.{og}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Squeezed pangenome graph in ODGI format.", - "pattern": "*.{og}" - } + "graph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og": { + "type": "file", + "description": "Squeezed pangenome graph in ODGI format.", + "pattern": "*.{og}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94791,52 +120311,73 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in binary ODGI or in GFA v1.0 format", - "pattern": "*.{og,gfa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "Optional output file that contains graph statistics in TSV format.", - "pattern": "*.{tsv}" - } - }, - { - "yaml": { - "type": "file", - "description": "Optional output file that contains graph statistics in YAML format.", - "pattern": "*.{yaml}" - } + ], + "identifier": "biotools:odgi" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in binary ODGI or in GFA v1.0 format", + "pattern": "*.{og,gfa}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og.stats.tsv": { + "type": "file", + "description": "Optional output file that contains graph statistics in TSV format.", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "yaml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og.stats.yaml": { + "type": "file", + "description": "Optional output file that contains graph statistics in YAML format.", + "pattern": "*.{yaml}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94876,45 +120417,56 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] + ], + "identifier": "biotools:odgi" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", - "pattern": "*.{gfa,og}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", + "pattern": "*.{gfa,og}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "unchopped_graph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.og": { + "type": "file", + "description": "Unchopped pangenome graph in ODGI binary format", + "pattern": "*.{og}" + } + } + ] }, { - "unchopped_graph": { - "type": "file", - "description": "Unchopped pangenome graph in ODGI binary format", - "pattern": "*.{og}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -94954,45 +120506,56 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] + ], + "identifier": "biotools:odgi" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", - "pattern": "*.{gfa,og}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in GFA v1.0 format or in ODGI binary format", + "pattern": "*.{gfa,og}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gfa": { + "type": "file", + "description": "File containing a pangenome graph in GFA v1.0 format.", + "pattern": "*.{gfa}" + } + } + ] }, { - "gfa": { - "type": "file", - "description": "File containing a pangenome graph in GFA v1.0 format.", - "pattern": "*.{gfa}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95032,45 +120595,56 @@ "doi": "10.1093/bioinformatics/btac308", "licence": [ "MIT" - ] + ], + "identifier": "biotools:odgi" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "graph": { - "type": "file", - "description": "Pangenome graph in binary ODGI or in GFA v1.0 format", - "pattern": "*.{og,gfa}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "graph": { + "type": "file", + "description": "Pangenome graph in binary ODGI or in GFA v1.0 format", + "pattern": "*.{og,gfa}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "A 1D visualization of a pangenome graph.", + "pattern": "*.{png}" + } + } + ] }, { - "png": { - "type": "file", - "description": "A 1D visualization of a pangenome graph.", - "pattern": "*.{png}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95109,88 +120683,132 @@ "doi": "10.1093/bioinformatics/btu436", "license": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal": { - "type": "file", - "description": "BAM files", - "pattern": "*.bam" - } - }, - { - "normal_index": { - "type": "file", - "description": "BAM file indices", - "pattern": "*.bam.bai" - } - }, - { - "tumor": { - "type": "file", - "description": "BAM files", - "pattern": "*.bam" - } - }, - { - "tumor_index": { - "type": "file", - "description": "BAM file indices", - "pattern": "*.bam.bai" - } - }, - { - "bed": { - "type": "file", - "description": "annotated BED file containing target regions", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "genome FASTA file", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "png": { - "type": "file", - "description": "PNG file containing profile plot", - "pattern": "*.profile.png" - } - }, - { - "profile": { - "type": "file", - "description": "TXT file containing profile data", - "pattern": "*.profile.txt" - } - }, - { - "summary": { - "type": "file", - "description": "TXT file containing summarized data", - "pattern": "*.summary.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:oncocnv" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normal": { + "type": "file", + "description": "BAM files", + "pattern": "*.bam" + } + }, + { + "normal_index": { + "type": "file", + "description": "BAM file indices", + "pattern": "*.bam.bai" + } + }, + { + "tumor": { + "type": "file", + "description": "BAM files", + "pattern": "*.bam" + } + }, + { + "tumor_index": { + "type": "file", + "description": "BAM file indices", + "pattern": "*.bam.bai" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "annotated BED file containing target regions", + "pattern": "*.bed" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "genome FASTA file", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "png": [ + { + "meta": { + "type": "file", + "description": "PNG file containing profile plot", + "pattern": "*.profile.png" + } + }, + { + "*.profile.png": { + "type": "file", + "description": "PNG file containing profile plot", + "pattern": "*.profile.png" + } + } + ] + }, + { + "profile": [ + { + "meta": { + "type": "file", + "description": "TXT file containing profile data", + "pattern": "*.profile.txt" + } + }, + { + "*.profile.txt": { + "type": "file", + "description": "TXT file containing profile data", + "pattern": "*.profile.txt" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "file", + "description": "TXT file containing summarized data", + "pattern": "*.summary.txt" + } + }, + { + "*.summary.txt": { + "type": "file", + "description": "TXT file containing summarized data", + "pattern": "*.summary.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95225,45 +120843,56 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file containing protein sequences", - "pattern": "*.{fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file containing protein sequences", + "pattern": "*.{fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "decoy_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Fasta file containing proteins and decoy proteins", + "pattern": "*.{fasta}" + } + } + ] }, { - "decoy_fasta": { - "type": "file", - "description": "Fasta file containing proteins and decoy proteins", - "pattern": "*.{fasta}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95304,52 +120933,63 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "id_file": { - "type": "file", - "description": "Peptide-spectrum matches.", - "pattern": "*.{idXML,consensusXML}" - } - }, - { - "filter_file": { - "type": "file", - "description": "Optional idXML file to filter on/out peptides or proteins", - "patter": "*.{idXML,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "filtered": { - "type": "file", - "description": "Filtered peptide-spectrum matches.", - "pattern": "*.{idXML,consensusXML}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "id_file": { + "type": "file", + "description": "Peptide-spectrum matches.", + "pattern": "*.{idXML,consensusXML}" + } + }, + { + "filter_file": { + "type": "file", + "description": "Optional idXML file to filter on/out peptides or proteins", + "patter": "*.{idXML,fasta}" + } + } + ] + ], + "output": [ + { + "filtered": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.{idXML,consensusXML}": { + "type": "file", + "description": "Filtered peptide-spectrum matches.", + "pattern": "*.{idXML,consensusXML}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95388,59 +121028,80 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "mzmls": { - "type": "file", - "description": "List containing one or more mzML files\ne.g. `[ 'file1.mzML', 'file2.mzML' ]`\n", - "pattern": "*.{mzML}" - } - }, - { - "idxmls": { - "type": "file", - "description": "List containing one or more idXML files\ne.g. `[ 'file1.idXML', 'file2.idXML' ]`\n", - "pattern": "*.{idXML}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "frag_err": { - "type": "file", - "description": "TSV file containing the fragment mass errors", - "pattern": "*frag_mass_err.{tsv}" - } - }, - { - "prec_err": { - "type": "file", - "description": "Optional TSV file containing the precursor mass errors", - "pattern": "*prec_mass_err.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "mzmls": { + "type": "file", + "description": "List containing one or more mzML files\ne.g. `[ 'file1.mzML', 'file2.mzML' ]`\n", + "pattern": "*.{mzML}" + } + }, + { + "idxmls": { + "type": "file", + "description": "List containing one or more idXML files\ne.g. `[ 'file1.idXML', 'file2.idXML' ]`\n", + "pattern": "*.{idXML}" + } + } + ] + ], + "output": [ + { + "frag_err": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*frag_mass_err.tsv": { + "type": "file", + "description": "TSV file containing the fragment mass errors", + "pattern": "*frag_mass_err.{tsv}" + } + } + ] + }, + { + "prec_err": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*prec_mass_err.tsv": { + "type": "file", + "description": "Optional TSV file containing the precursor mass errors", + "pattern": "*prec_mass_err.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95471,45 +121132,56 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "idxmls": { - "type": "file", - "description": "List containing 2 or more idXML files\ne.g. `[ 'file1.idXML', 'file2.idXML' ]`\n", - "pattern": "*.{idXML}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "idxmls": { + "type": "file", + "description": "List containing 2 or more idXML files\ne.g. `[ 'file1.idXML', 'file2.idXML' ]`\n", + "pattern": "*.{idXML}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "idxml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.idXML": { + "type": "file", + "description": "Merged idXML output file", + "pattern": "*.{idXML}" + } + } + ] }, { - "idxml": { - "type": "file", - "description": "Merged idXML output file", - "pattern": "*.{idXML}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95546,45 +121218,56 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "merged_idxml": { - "type": "file", - "description": "Merged idXML file", - "pattern": "*.{idXML}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "merged_idxml": { + "type": "file", + "description": "Merged idXML file", + "pattern": "*.{idXML}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "idxmls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.idXML": { + "type": "file", + "description": "Multiple idXML files", + "pattern": "*.{idXML}" + } + } + ] }, { - "idxmls": { - "type": "file", - "description": "Multiple idXML files", - "pattern": "*.{idXML}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95625,45 +121308,56 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "idxml": { - "type": "file", - "description": "Identification file containing a primary PSM score", - "pattern": "*.{idXML}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "idxml": { + "type": "file", + "description": "Identification file containing a primary PSM score", + "pattern": "*.{idXML}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "idxml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.idXML": { + "type": "file", + "description": "Identification file containing a new primary PSM score\nobtained from a specified meta value\n", + "pattern": "*.{idXML}" + } + } + ] }, { - "idxml": { - "type": "file", - "description": "Identification file containing a new primary PSM score\nobtained from a specified meta value\n", - "pattern": "*.{idXML}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95703,45 +121397,56 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "mzml": { + "type": "file", + "description": "Mass spectrometer output file in mzML format", + "pattern": "*.{mzML}" + } } + ] + ], + "output": [ + { + "mzml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.mzML": { + "type": "file", + "description": "Peak-picked mass spectrometer output file in mzML format", + "pattern": "*.{mzML}" + } + } + ] }, { - "mzml": { - "type": "file", - "description": "Mass spectrometer output file in mzML format", - "pattern": "*.{mzML}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "mzml": { - "type": "file", - "description": "Peak-picked mass spectrometer output file in mzML format", - "pattern": "*.{mzML}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95781,52 +121486,71 @@ "doi": "10.1038/s41592-024-02197-7", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "id_file": { - "type": "file", - "description": "idXML identification file", - "pattern": "*.{idXML}" - } - }, - { - "id_fasta": { - "type": "file", - "description": "Input sequence database in FASTA format", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "id_file_pi": { - "type": "file", - "description": "Refreshed idXML identification file", - "pattern": "*.{idXML}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "id_file": { + "type": "file", + "description": "idXML identification file", + "pattern": "*.{idXML}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "id_fasta": { + "type": "file", + "description": "Input sequence database in FASTA format", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "id_file_pi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.idXML": { + "type": "file", + "description": "Refreshed idXML identification file", + "pattern": "*.{idXML}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95861,59 +121585,80 @@ "doi": "10.1038/nmeth.3959", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "mzml": { - "type": "file", - "description": "File containing mass spectra in mzML format", - "pattern": "*.{mzML}" - } - }, - { - "fasta": { - "type": "file", - "description": "Protein sequence database containing targets and decoys", - "pattern": "*.{fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "idxml": { - "type": "file", - "description": "File containing target and decoy hits in idXML format", - "pattern": "*.{idXML}" - } - }, - { - "pin": { - "type": "file", - "description": "TSV file tailored as Percolator input (pin) file", - "pattern": "*.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mzml": { + "type": "file", + "description": "File containing mass spectra in mzML format", + "pattern": "*.{mzML}" + } + }, + { + "fasta": { + "type": "file", + "description": "Protein sequence database containing targets and decoys", + "pattern": "*.{fasta}" + } + } + ] + ], + "output": [ + { + "idxml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.idXML": { + "type": "file", + "description": "File containing target and decoy hits in idXML format", + "pattern": "*.{idXML}" + } + } + ] + }, + { + "pin": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file tailored as Percolator input (pin) file", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -95945,59 +121690,80 @@ "doi": "10.1093/bioinformatics/btu548", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', seq_type:'DNA' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hla_type": { - "type": "file", - "description": "HLA type", - "pattern": "${prefix}/*.tsv" - } - }, - { - "coverage_plot": { - "type": "file", - "description": "OptiType coverage plot", - "pattern": "${prefix}/*.pdf" - } + ], + "identifier": "biotools:optitype" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}" + } + } + ] + ], + "output": [ + { + "hla_type": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', seq_type:'DNA' ]\n" + } + }, + { + "${prefix}/*.tsv": { + "type": "file", + "description": "HLA type", + "pattern": "${prefix}/*.tsv" + } + } + ] + }, + { + "coverage_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', seq_type:'DNA' ]\n" + } + }, + { + "${prefix}/*.pdf": { + "type": "file", + "description": "OptiType coverage plot", + "pattern": "${prefix}/*.pdf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96041,62 +121807,85 @@ "doi": "10.1186/s13059-019-1832-y", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastas": { - "type": "list", - "description": "Input fasta files", - "pattern": "*.{fa,faa,fasta,fas,pep}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing a name\ne.g. `[ id:'folder1' ]`\n" - } - }, - { - "prior_run": { - "type": "directory", - "description": "A folder container containing a previous WorkingDirectory from Orthofinder.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "orthofinder": { - "type": "directory", - "description": "Orthofinder output directory" - } - }, - { - "working": { - "type": "directory", - "description": "Orthofinder output WorkingDirectory (used for the orthofinder resume function)" - } + ], + "identifier": "biotools:OrthoFinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastas": { + "type": "list", + "description": "Input fasta files", + "pattern": "*.{fa,faa,fasta,fas,pep}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing a name\ne.g. `[ id:'folder1' ]`\n" + } + }, + { + "prior_run": { + "type": "directory", + "description": "A folder container containing a previous WorkingDirectory from Orthofinder.\n" + } + } + ] + ], + "output": [ + { + "orthofinder": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "$prefix": { + "type": "directory", + "description": "Orthofinder output directory" + } + } + ] + }, + { + "working": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "$prefix/WorkingDirectory": { + "type": "directory", + "description": "Orthofinder output WorkingDirectory (used for the orthofinder resume function)" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96127,44 +121916,48 @@ "documentation": "https://github.com/lh3/minimap2/blob/master/README.md", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "An input bam file to be converted into paf." + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "An input bam file to be converted into paf." + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "paf": { - "type": "file", - "description": "An output paf containing detailed data about the sample\n", - "pattern": "${prefix}.paf" - } + "paf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96196,44 +121989,62 @@ "tool_dev_url": "https://github.com/4dn-dcic/pairix", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pair": { - "type": "file", - "description": "pair file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "index": { - "type": "file", - "description": "pair index file", - "pattern": "*.px2" - } + ], + "identifier": "biotools:pairix" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pair": { + "type": "file", + "description": "pair file" + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pair": { + "type": "file", + "description": "pair index file", + "pattern": "*.px2" + } + }, + { + "*.px2": { + "type": "file", + "description": "pair index file", + "pattern": "*.px2" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96272,51 +122083,72 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "pair file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pairs": { - "type": "file", - "description": "Duplicates removed pairs", - "pattern": "*.{pairs.gz}" - } - }, - { - "stat": { - "type": "file", - "description": "stats of the pairs", - "pattern": "*.{pairs.stat}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "pair file" + } + } + ] + ], + "output": [ + { + "pairs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairs.gz": { + "type": "file", + "description": "Duplicates removed pairs", + "pattern": "*.{pairs.gz}" + } + } + ] + }, + { + "stat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairs.stat": { + "type": "file", + "description": "stats of the pairs", + "pattern": "*.{pairs.stat}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96354,50 +122186,63 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sam": { - "type": "file", - "description": "pair file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sam": { + "type": "file", + "description": "pair file" + } } - }, - { - "chromsizes": { - "type": "file", - "description": "chromosome size file" + ], + [ + { + "chromsizes": { + "type": "file", + "description": "chromosome size file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "flip": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.flip.gz": { + "type": "file", + "description": "output file of flip", + "pattern": "*.{flip.gz}" + } + } + ] }, { - "flip": { - "type": "file", - "description": "output file of flip", - "pattern": "*.{flip.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96435,44 +122280,55 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "allpairs": { - "type": "file", - "description": "All pair files to merge" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "allpairs": { + "type": "file", + "description": "All pair files to merge" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "pairs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*pairs.gz": { + "type": "file", + "description": "Merged pairs file", + "pattern": "*.{pairs.gz}" + } + } + ] }, { - "pairs": { - "type": "file", - "description": "Merged pairs file", - "pattern": "*.{pairs.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96504,58 +122360,81 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "chromsizes": { - "type": "file", - "description": "chromosome size file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pairsam": { - "type": "file", - "description": "parsed pair file", - "pattern": "*.{pairsam.gz}" - } - }, - { - "stat": { - "type": "file", - "description": "stats of the pairs", - "pattern": "*.{pairsam.stat}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "chromsizes": { + "type": "file", + "description": "chromosome size file" + } + } + ] + ], + "output": [ + { + "pairsam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairsam.gz": { + "type": "file", + "description": "parsed pair file", + "pattern": "*.{pairsam.gz}" + } + } + ] + }, + { + "stat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairsam.stat": { + "type": "file", + "description": "stats of the pairs", + "pattern": "*.{pairsam.stat}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96593,50 +122472,63 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pairs": { - "type": "file", - "description": "pairs file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pairs": { + "type": "file", + "description": "pairs file" + } } - }, - { - "frag": { - "type": "file", - "description": "a tab-separated BED file with the positions of restriction fragments\n(chrom, start, end).\nCan be generated using cooler digest.\n" + ], + [ + { + "frag": { + "type": "file", + "description": "a tab-separated BED file with the positions of restriction fragments\n(chrom, start, end).\nCan be generated using cooler digest.\n" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "restrict": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairs.gz": { + "type": "file", + "description": "Filtered pairs file", + "pattern": "*.{pairs.gz}" + } + } + ] }, { - "restrict": { - "type": "file", - "description": "Filtered pairs file", - "pattern": "*.{pairs.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96674,51 +122566,72 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "pairs file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "selected": { - "type": "file", - "description": "Selected pairs file", - "pattern": "*.{selected.pairs.gz}" - } - }, - { - "unselected": { - "type": "file", - "description": "Rest pairs file.", - "pattern": "*.{unselected.pairs.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "pairs file" + } + } + ] + ], + "output": [ + { + "selected": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.selected.pairs.gz": { + "type": "file", + "description": "Selected pairs file", + "pattern": "*.{selected.pairs.gz}" + } + } + ] + }, + { + "unselected": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unselected.pairs.gz": { + "type": "file", + "description": "Rest pairs file.", + "pattern": "*.{unselected.pairs.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96756,44 +122669,55 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "A pairs file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "A pairs file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "sorted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairs.gz": { + "type": "file", + "description": "Sorted pairs file", + "pattern": "*.{pairs.gz}" + } + } + ] }, { - "sorted": { - "type": "file", - "description": "Sorted pairs file", - "pattern": "*.{pairs.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96833,71 +122757,92 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pairs": { + "type": "file", + "description": "pairsam file" + } + } + ] + ], + "output": [ + { + "pairs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.split.pairs.gz": { + "type": "file", + "description": "Duplicates removed pairs", + "pattern": "*.{pairs.gz}" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pairs": { - "type": "file", - "description": "pairsam file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pairs": { - "type": "file", - "description": "Duplicates removed pairs", - "pattern": "*.{pairs.gz}" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file", - "pattern": "*.bam" - } - } - ], - "authors": [ - "@nservant" - ] - } - }, - { - "name": "pairtools_stats", - "path": "modules/nf-core/pairtools/stats/meta.yml", - "type": "module", - "meta": { - "name": "pairtools_stats", - "description": "Calculate pairs statistics", - "keywords": [ - "stats", - "pairs", - "pairsam" - ], - "tools": [ + "authors": [ + "@nservant" + ] + } + }, + { + "name": "pairtools_stats", + "path": "modules/nf-core/pairtools/stats/meta.yml", + "type": "module", + "meta": { + "name": "pairtools_stats", + "description": "Calculate pairs statistics", + "keywords": [ + "stats", + "pairs", + "pairsam" + ], + "tools": [ { "pairtools": { "description": "CLI tools to process mapped Hi-C data", @@ -96906,44 +122851,55 @@ "tool_dev_url": "https://github.com/mirnylab/pairtools", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pairs": { - "type": "file", - "description": "pairs file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pairs": { + "type": "file", + "description": "pairs file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pairs.stat": { + "type": "file", + "description": "Pairs statistics", + "pattern": "*{.pairs.stat}" + } + } + ] }, { - "stat": { - "type": "file", - "description": "stats of the pairs", - "pattern": "*.{pairs.stat}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -96976,73 +122932,83 @@ "documentation": "https://github.com/marschall-lab/panacus", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "gfa": { - "type": "file", - "description": "GFA file containing a graph without overlapping nodes", - "pattern": "*.gfa" - } - }, - { - "bed_subset": { - "type": "file", - "description": "Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for getting counts by subsetting the graph", - "pattern": "*.{txt, bed}" - } - }, - { - "bed_exclude": { - "type": "file", - "description": "Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for excluding bp/nodes/edges that intersect these paths", - "pattern": "*.{txt, bed}" - } - }, - { - "tsv_groupby": { - "type": "file", - "description": "Optional 2-column TSV file containing path to group mapping according to which counts from different paths get merged", - "pattern": "*.{txt, bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file containing the statistics. Alternatively, the HTML file can be the output", - "pattern": "*.tsv" - } - }, - { - "html": { - "type": "file", - "description": "HTML file containing a report with the statistics. Alternatively, the TSV file can be the output", - "pattern": "*.html" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "gfa": { + "type": "file", + "description": "GFA file containing a graph without overlapping nodes", + "pattern": "*.gfa" + } + } + ], + [ + { + "bed_subset": { + "type": "file", + "description": "Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for getting counts by subsetting the graph", + "pattern": "*.{txt, bed}" + } + } + ], + [ + { + "bed_exclude": { + "type": "file", + "description": "Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for excluding bp/nodes/edges that intersect these paths", + "pattern": "*.{txt, bed}" + } + } + ], + [ + { + "tsv_groupby": { + "type": "file", + "description": "Optional 2-column TSV file containing path to group mapping according to which counts from different paths get merged", + "pattern": "*.{txt, bed}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.{tsv, html}": { + "type": "file", + "description": "TSV file containing the statistics. Alternatively, the HTML file can be the output", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97077,45 +123043,56 @@ "documentation": "https://github.com/marschall-lab/panacus", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV coverage histogram created with panacus histgrowth", - "pattern": "*.tsv" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "TSV coverage histogram created with panacus histgrowth", + "pattern": "*.tsv" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "image": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}": { + "type": "file", + "description": "Visualizations created from the coverage histogram", + "pattern": "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}" + } + } + ] }, { - "image": { - "type": "file", - "description": "Visualizations created from the coverage histogram", - "pattern": "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97149,52 +123126,73 @@ "doi": "10.1186/s13059-020-02090-4", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "A set of GFF3 formatted files", - "pattern": "*.{gff}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "directory", - "description": "Directory containing Panaroo result files", - "pattern": "*/*" - } - }, - { - "aln": { - "type": "file", - "description": "Core-genome alignment produced by Panaroo (Optional)", - "pattern": "*.{fasta}" - } + ], + "identifier": "biotools:panaroo" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "A set of GFF3 formatted files", + "pattern": "*.{gff}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*": { + "type": "directory", + "description": "Directory containing Panaroo result files", + "pattern": "*/*" + } + } + ] + }, + { + "aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/core_gene_alignment.aln": { + "type": "file", + "description": "Core-genome alignment produced by Panaroo (Optional)", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97225,38 +123223,56 @@ "manual": "https://github.com/cov-lineages/pangolin#pangolearn-description", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:pangolin_cov-lineages" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The genome assembly to be evaluated\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The genome assembly to be evaluated\n" + } } - } + ] ], "output": [ { - "report": { - "type": "file", - "description": "Pangolin lineage report", - "pattern": "*.{csv}" - } + "report": [ + { + "meta": { + "type": "file", + "description": "Pangolin lineage report", + "pattern": "*.{csv}" + } + }, + { + "*.csv": { + "type": "file", + "description": "Pangolin lineage report", + "pattern": "*.{csv}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97296,80 +123312,108 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/", "licence": [ "https://docs.nvidia.com/clara/parabricks/3.8.0/gettingstarted.html#licensing" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "bam file for sample to be variant called.", - "pattern": "*.bam" - } - }, - { - "input_index": { - "type": "file", - "description": "bai index corresponding to input bam file. Only necessary if intervals are provided.", - "pattern": "*.bai" - } - }, - { - "bqsr_table": { - "type": "file", - "description": "Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator.", - "pattern": "*.table" - } - }, - { - "interval_file": { - "type": "file", - "description": "File or files containing genomic intervals for use in base quality score recalibration.", - "pattern": "*.{bed,interval_list,picard,list,intervals}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta - must be unzipped.", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file after applying BQSR.", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "bai index corresponding to output bam file.", - "pattern": "*.bai" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bam_index": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + }, + { + "bqsr_table": { + "type": "file", + "description": "Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator.", + "pattern": "*.table" + } + }, + { + "intervals": { + "type": "file", + "description": "intervals" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta - must be unzipped.", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file after applying BQSR.", + "pattern": "*.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "bai index corresponding to output bam file.", + "pattern": "*.bai" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97401,59 +123445,70 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/4.2.0/index.html", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "vcf_file": { - "type": "file", - "description": "VCF file undergoing annotation.", - "pattern": "*.vcf" - } - }, - { - "dbsnp_file": { - "type": "file", - "description": "dbSNP file required for annotation.", - "pattern": "*.vcf.gz" - } - }, - { - "tabix_file": { - "type": "file", - "description": "dbSNP file index.", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "ann_vcf": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.vcf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "vcf_file": { + "type": "file", + "description": "VCF file undergoing annotation.", + "pattern": "*.vcf" + } + }, + { + "dbsnp_file": { + "type": "file", + "description": "dbSNP file required for annotation.", + "pattern": "*.vcf.gz" + } + }, + { + "tabix_file": { + "type": "file", + "description": "dbSNP file index.", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF file.", + "pattern": "*{.vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97483,72 +123538,85 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/4.0.1/documentation/", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing tumor sample information - id must match read groups for this sample.\n[ id:'test']\n" - } - }, - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information.\n[ id:'test']\n" - } - }, - { - "input": { - "type": "file", - "description": "bam file for sample to be variant called.", - "pattern": "*.bam" - } - }, - { - "input_index": { - "type": "file", - "description": "bai index corresponding to input bam file. Only necessary if intervals are provided.", - "pattern": "*.bai" - } - }, - { - "interval_file": { - "type": "file", - "description": "file or files containing genomic intervals for use in base quality score recalibration.", - "pattern": "*.{bed,interval_list,picard,list,intervals}" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant file.", - "pattern": "*.vcf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing tumor sample information - id must match read groups for this sample.\n[ id:'test']\n" + } + }, + { + "input": { + "type": "file", + "description": "bam file for sample to be variant called.", + "pattern": "*.bam" + } + }, + { + "input_index": { + "type": "file", + "description": "bai index corresponding to input bam file. Only necessary if intervals are provided.", + "pattern": "*.bai" + } + }, + { + "interval_file": { + "type": "file", + "description": "file or files containing genomic intervals for use in base quality score recalibration.", + "pattern": "*.{bed,interval_list,picard,list,intervals}" + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information.\n[ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Variant file.", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97577,113 +123645,152 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/4.0.1/Documentation/", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq.gz files", - "pattern": "*.fastq.gz" - } - }, - { - "interval_file": { - "type": "file", - "description": "(optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR)", - "pattern": "*.{bed,interval_list,picard,list,intervals}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta file - must be unzipped", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing index information\n" - } - }, - { - "index": { - "type": "file", - "description": "reference BWA index", - "pattern": "*.{amb,ann,bwt,pac,sa}" - } - }, - { - "known_sites": { - "type": "file", - "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", - "pattern": "*.vcf.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "index corresponding to sorted BAM file", - "pattern": "*.bai" - } - }, - { - "qc_metrics": { - "type": "directory", - "description": "(optional) optional directory of qc metrics", - "pattern": "qc_metrics" - } - }, - { - "bqsr_table": { - "type": "file", - "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", - "pattern": "*.table" - } - }, - { - "duplicate_metrics": { - "type": "file", - "description": "(optional) metrics calculated from marking duplcates in the bam file", - "pattern": "*-duplicate-metrics.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq.gz files", + "pattern": "*.fastq.gz" + } + }, + { + "interval_file": { + "type": "file", + "description": "(optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR)", + "pattern": "*.{bed,interval_list,picard,list,intervals}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file - must be unzipped", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "index": { + "type": "file", + "description": "reference BWA index", + "pattern": "*.{amb,ann,bwt,pac,sa}" + } + } + ], + [ + { + "known_sites": { + "type": "file", + "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", + "pattern": "*.vcf.gz" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "index corresponding to sorted BAM file", + "pattern": "*.bai" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "qc_metrics": [ + { + "qc_metrics": { + "type": "directory", + "description": "(optional) optional directory of qc metrics", + "pattern": "qc_metrics" + } + } + ] + }, + { + "bqsr_table": [ + { + "*.table": { + "type": "file", + "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", + "pattern": "*.table" + } + } + ] + }, + { + "duplicate_metrics": [ + { + "duplicate-metrics.txt": { + "type": "file", + "description": "(optional) metrics calculated from marking duplcates in the bam file", + "pattern": "*-duplicate-metrics.txt" + } + } + ] } ], "authors": [ @@ -97718,58 +123825,71 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/4.2.0/index.html", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information.\n[ id:'test']\n" - } - }, - { - "input": { - "type": "file", - "description": "gvcf file for samples to be jointly genotyped.", - "pattern": "*.{g.vcf,g.vcf.gz}" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file after gvcf conversion.", - "pattern": "*.vcf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "gvcf file for samples to be jointly genotyped.", + "pattern": "*.{g.vcf,g.vcf.gz}" + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information.\n[ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "vcf file after gvcf conversion.", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97799,72 +123919,85 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/4.2.0/index.html", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\n[ id:'test']\n" - } - }, - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information.\n[ id:'test']\n" - } - }, - { - "input": { - "type": "file", - "description": "bam file for sample to be variant called.", - "pattern": "*.bam" - } - }, - { - "input_index": { - "type": "file", - "description": "(Optional) bai index corresponding to input bam file. Only necessary when using intervals.", - "pattern": "*.bai" - } - }, - { - "interval_file": { - "type": "file", - "description": "file or files containing genomic intervals.", - "pattern": "*.{bed,interval_list,picard,list,intervals}" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "variant file.", - "pattern": "*.vcf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\n[ id:'test']\n" + } + }, + { + "input": { + "type": "file", + "description": "bam file for sample to be variant called.", + "pattern": "*.bam" + } + }, + { + "input_index": { + "type": "file", + "description": "(Optional) bai index corresponding to input bam file. Only necessary when using intervals.", + "pattern": "*.bai" + } + }, + { + "interval_file": { + "type": "file", + "description": "file or files containing genomic intervals.", + "pattern": "*.{bed,interval_list,picard,list,intervals}" + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information.\n[ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "variant file.", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97895,45 +124028,56 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/", "licence": [ "custom" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing gvcf information\n" - } - }, - { - "gvcf": { - "type": "file", - "description": "gvcf file to be indexed", - "pattern": "*.{vcf,vcf.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing gvcf information\n" + } + }, + { + "gvcf": { + "type": "file", + "description": "gvcf file to be indexed", + "pattern": "*.{vcf,vcf.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing output information\n" - } - }, - { - "gvcf_index": { - "type": "file", - "description": "Indexed gvcf file", - "pattern": "*.g.vcf" - } + "gvcf_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing output information\n" + } + }, + { + "*.g.vcf*": { + "type": "file", + "description": "Indexed gvcf file", + "pattern": "*.g.vcf" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -97964,107 +124108,134 @@ "documentation": "https://docs.nvidia.com/clara/parabricks/4.0.1/index.html", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples.\n[ id:'test', tumor_id:'tumor', normal_id:'normal' ]\n" - } - }, - { - "tumor_bam": { - "type": "file", - "description": "bam file for tumor sample.", - "pattern": "*.bam" - } - }, - { - "tumor_bam_index": { - "type": "file", - "description": "(Optional) bai index corresponding to tumor bam file. Only required if intervals are provided.", - "pattern": "*.bam" - } - }, - { - "normal_bam": { - "type": "file", - "description": "(Optional) bam file for normal sample in tumor-vs-normal calling.", - "pattern": "*.bam" - } - }, - { - "normal_bam_index": { - "type": "file", - "description": "(Optional) bai index corresponding to normal bam file. Only required if intervals are provided.", - "pattern": "*.bam" - } - }, - { - "interval_file": { - "type": "file", - "description": "(Optional) file or files containing genomic intervals for use in base quality score recalibration.", - "pattern": "*.{bed,interval_list,picard,list,intervals}" - } - }, - { - "ref_meta": { - "type": "map", - "description": "Groovy Map containing reference information\n[ id:'homo_sapiens' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "reference fasta - must be unzipped.", - "pattern": "*.fasta" - } - }, - { - "panel_of_normals": { - "type": "file", - "description": "(Optional) pannel of normals file.", - "pattern": "*.vcf.gz" - } - }, - { - "panel_of_normals_index": { - "type": "file", - "description": "(Optional) tbi index corresponding to pannel of normals file.", - "pattern": "*.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed variants file. Will include an annoted vcf file if pannel of normals is used.", - "pattern": "*.vcf.gz" - } - }, - { - "stats": { - "type": "file", - "description": "Variant statistics.", - "pattern": "*.vcf.gz.stats" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples.\n[ id:'test', tumor_id:'tumor', normal_id:'normal' ]\n" + } + }, + { + "tumor_bam": { + "type": "file", + "description": "bam file for tumor sample.", + "pattern": "*.bam" + } + }, + { + "tumor_bam_index": { + "type": "file", + "description": "(Optional) bai index corresponding to tumor bam file. Only required if intervals are provided.", + "pattern": "*.bam" + } + }, + { + "normal_bam": { + "type": "file", + "description": "(Optional) bam file for normal sample in tumor-vs-normal calling.", + "pattern": "*.bam" + } + }, + { + "normal_bam_index": { + "type": "file", + "description": "(Optional) bai index corresponding to normal bam file. Only required if intervals are provided.", + "pattern": "*.bam" + } + }, + { + "interval_file": { + "type": "file", + "description": "(Optional) file or files containing genomic intervals for use in base quality score recalibration.", + "pattern": "*.{bed,interval_list,picard,list,intervals}" + } + } + ], + [ + { + "ref_meta": { + "type": "map", + "description": "Groovy Map containing reference information\n[ id:'homo_sapiens' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta - must be unzipped.", + "pattern": "*.fasta" + } + } + ], + [ + { + "panel_of_normals": { + "type": "file", + "description": "(Optional) pannel of normals file.", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "panel_of_normals_index": { + "type": "file", + "description": "(Optional) tbi index corresponding to pannel of normals file.", + "pattern": "*.tbi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed variants file. Will include an annoted vcf file if pannel of normals is used.", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz.stats": { + "type": "file", + "description": "Variant statistics.", + "pattern": "*.vcf.gz.stats" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98093,52 +124264,65 @@ "tool_dev_url": "https://gitlab.com/mcfrith/paraclu", "licence": [ "GPL v3-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.bed" - } - }, - { - "min_cluster": { - "type": "integer", - "description": "Minimum size of cluster", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "clustered BED file", - "pattern": "*.bed" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "BED file", + "pattern": "*.bed" + } + } + ], + [ + { + "min_cluster": { + "type": "integer", + "description": "Minimum size of cluster", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "clustered BED file", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98172,85 +124356,110 @@ "doi": "10.1101/635011", "licence": [ "Apache License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information for the fasta_fai\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference genome FASTA", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "depth": { - "type": "file", - "description": "A JSON file containing depth, depth variance, read length and other parameters", - "pattern": "*.json" - } - }, - { - "binned_depth": { - "type": "file", - "description": "A TSV file containing the binned normalized depth. Can only be calculated for CRAM files", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:Paragraph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information for the fasta\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information for the fasta_fai\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference genome FASTA", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "depth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "A JSON file containing depth, depth variance, read length and other parameters", + "pattern": "*.json" + } + } + ] + }, + { + "binned_depth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV file containing the binned normalized depth. Can only be calculated for CRAM files", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98285,105 +124494,130 @@ "doi": "10.1101/635011", "licence": [ "Apache License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variants": { - "type": "file", - "description": "A VCF or JSON file containing called structural variants", - "pattern": "*.{vcf,json}" - } - }, - { - "variants_index": { - "type": "file", - "description": "The index for the VCF file", - "pattern": "*.tbi" - } - }, - { - "reads": { - "type": "file", - "description": "BAM or CRAM file(s) to genotype against. These should be specified inside the `manifest`", - "pattern": "*.{bam,cram}" - } - }, - { - "reads_index": { - "type": "file", - "description": "The index/indices for the BAM/CRAM file(s)", - "pattern": "*.{bai,crai}" - } - }, - { - "manifest": { - "type": "file", - "description": "A tab separated file containing information on the BAM/CRAM files.\nThis information can be generated using paragraph/idxdepth.\nMore information can be found here: https://github.com/Illumina/paragraph#sample-manifest\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the FASTA file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file used to generate the VCF and BAM/CRAM files", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information for the FASTA index file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The genotyped VCF file in BGZIP format", - "pattern": "*.vcf.gz" - } - }, - { - "json": { - "type": "file", - "description": "The genotyped JSON file in GZIP format", - "pattern": "*.json.gz" - } + ], + "identifier": "biotools:Paragraph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "variants": { + "type": "file", + "description": "A VCF or JSON file containing called structural variants", + "pattern": "*.{vcf,json}" + } + }, + { + "variants_index": { + "type": "file", + "description": "The index for the VCF file", + "pattern": "*.tbi" + } + }, + { + "reads": { + "type": "file", + "description": "BAM or CRAM file(s) to genotype against. These should be specified inside the `manifest`", + "pattern": "*.{bam,cram}" + } + }, + { + "reads_index": { + "type": "file", + "description": "The index/indices for the BAM/CRAM file(s)", + "pattern": "*.{bai,crai}" + } + }, + { + "manifest": { + "type": "file", + "description": "A tab separated file containing information on the BAM/CRAM files.\nThis information can be generated using paragraph/idxdepth.\nMore information can be found here: https://github.com/Illumina/paragraph#sample-manifest\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for the FASTA file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file used to generate the VCF and BAM/CRAM files", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information for the FASTA index file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The genotyped VCF file in BGZIP format", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json.gz": { + "type": "file", + "description": "The genotyped JSON file in GZIP format", + "pattern": "*.json.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98416,45 +124650,71 @@ "doi": "10.1101/635011", "licence": [ "Apache License 2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF/BCF file", - "pattern": "*.{vcf,bcf}(.gz)?" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "graph": { - "type": "file", - "description": "The created graph in BGZIP format", - "pattern": "*.json.gz" - } + ], + "identifier": "biotools:Paragraph" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF/BCF file", + "pattern": "*.{vcf,bcf}(.gz)?" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome VCF was generated against", + "pattern": "*.{fasta,fna,fa}" + } + } + ] + ], + "output": [ + { + "graph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json.gz": { + "type": "file", + "description": "The created graph in BGZIP format", + "pattern": "*.json.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98487,106 +124747,161 @@ "doi": "10.1016/j.ajhg.2023.01.001", "licence": [ "BSD-3-clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Index of BAM file", - "pattern": "*.bai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing config information\ne.g. [ id:'config' ]\n" - } - }, - { - "config": { - "type": "file", - "description": "Config file", - "pattern": "*.yaml" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "(re)aligned BAM file", - "pattern": "*.paraphase.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Index of (re)aligned BAM file", - "pattern": "*.paraphase.bam.bai" - } - }, - { - "json": { - "type": "file", - "description": "Summary of haplotype and variant calls", - "pattern": "*.paraphase.json" - } - }, - { - "vcf": { - "type": "file", - "description": "compressed VCF file(s) per gene", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_index": { - "type": "file", - "description": "compressed VCF file index", - "pattern": "*.vcf.gz.{tbi,csi}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "Index of BAM file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing config information\ne.g. [ id:'config' ]\n" + } + }, + { + "config": { + "type": "file", + "description": "Config file", + "pattern": "*.yaml" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "*.paraphase.json": { + "type": "file", + "description": "Summary of haplotype and variant calls", + "pattern": "*.paraphase.json" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "*.paraphase.bam": { + "type": "file", + "description": "(re)aligned BAM file", + "pattern": "*.paraphase.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "*.paraphase.bam.bai": { + "type": "file", + "description": "Index of (re)aligned BAM file", + "pattern": "*.paraphase.bam.bai" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "${prefix}_paraphase_vcfs/*.vcf.gz": { + "type": "file", + "description": "compressed VCF file(s) per gene", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}": { + "type": "file", + "description": "compressed VCF file index", + "pattern": "*.vcf.gz.{tbi,csi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98619,82 +124934,113 @@ "tool_dev_url": "https://github.com/rpetit3/pasty", "licence": [ "Apache-2.0" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "An assembly in FASTA format", + "pattern": "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "A tab-delimited file with the predicted serogroup", + "pattern": "*.tsv" + } + } + ] + }, + { + "blast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.blastn.tsv": { + "type": "file", + "description": "A tab-delimited file of all blast hits", + "pattern": "*.blastn.tsv" + } + } + ] + }, + { + "details": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.details.tsv": { + "type": "file", + "description": "A tab-delimited file with details for each serogroup", + "pattern": "*.details.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "An assembly in FASTA format", - "pattern": "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" - } - } + "authors": [ + "@rpetit3" ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "A tab-delimited file with the predicted serogroup", - "pattern": "*.tsv" - } - }, - { - "blast": { - "type": "file", - "description": "A tab-delimited file of all blast hits", - "pattern": "*.blastn.tsv" - } - }, - { - "details": { - "type": "file", - "description": "A tab-delimited file with details for each serogroup", - "pattern": "*.details.tsv" - } - } - ], - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "pbbam_pbmerge", - "path": "modules/nf-core/pbbam/pbmerge/meta.yml", - "type": "module", - "meta": { - "name": "pbbam_pbmerge", - "description": "The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.", - "keywords": [ - "pbbam", - "pbmerge", - "bam" - ], - "tools": [ + "maintainers": [ + "@rpetit3" + ] + } + }, + { + "name": "pbbam_pbmerge", + "path": "modules/nf-core/pbbam/pbmerge/meta.yml", + "type": "module", + "meta": { + "name": "pbbam_pbmerge", + "description": "The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.", + "keywords": [ + "pbbam", + "pbmerge", + "bam" + ], + "tools": [ { "pbbam": { "description": "PacBio BAM C++ library", @@ -98703,52 +125049,73 @@ "tool_dev_url": "https://github.com/pacificbiosciences/pbbam/", "licence": [ "BSD-3-Clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM files to merge", - "pattern": "*.bam" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "The merged bam file", - "pattern": "*.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "BAM Pacbio index file", - "pattern": "*.bam.pbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM files to merge", + "pattern": "*.bam" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "The merged bam file", + "pattern": "*.bam" + } + } + ] + }, + { + "pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pbi": { + "type": "file", + "description": "BAM Pacbio index file", + "pattern": "*.bam.pbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98781,92 +125148,147 @@ "tool_dev_url": "https://github.com/PacificBiosciences/ccs", "licence": [ "BSD-3-Clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\nid: id of the split file\n" - } - }, - { - "bam": { - "type": "file", - "description": "Raw subreads bam", - "pattern": "*.subreads.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "Pacbio BAM Index", - "pattern": "*.pbi" - } - }, - { - "chunk_num": { - "type": "integer", - "description": "BAM part to process" - } - }, - { - "chunk_on": { - "type": "integer", - "description": "Total number of bam parts to process" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "CCS sequences in bam format", - "pattern": "*.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "PacBio Index of CCS sequences", - "pattern": "*.pbi" - } - }, - { - "report_txt": { - "type": "file", - "description": "Summary of CCS in txt format", - "pattern": ".txt" - } - }, - { - "report_json": { - "type": "file", - "description": "Summary of CCS in txt json", - "pattern": ".json" - } - }, - { - "metrics": { - "type": "file", - "description": "Metrics about zmws", - "pattern": "*.json.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\nid: id of the split file\n" + } + }, + { + "bam": { + "type": "file", + "description": "Raw subreads bam", + "pattern": "*.subreads.bam" + } + }, + { + "pbi": { + "type": "file", + "description": "Pacbio BAM Index", + "pattern": "*.pbi" + } + } + ], + [ + { + "chunk_num": { + "type": "integer", + "description": "BAM part to process" + } + } + ], + [ + { + "chunk_on": { + "type": "integer", + "description": "Total number of bam parts to process" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.chunk*.bam": { + "type": "file", + "description": "CCS sequences in bam format", + "pattern": "*.bam" + } + } + ] + }, + { + "pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.chunk*.bam.pbi": { + "type": "file", + "description": "PacBio Index of CCS sequences", + "pattern": "*.pbi" + } + } + ] + }, + { + "report_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.report.txt\" ": { + "type": "file", + "description": "Summary of CCS in txt format", + "pattern": ".txt" + } + } + ] + }, + { + "report_json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.report.json\" ": { + "type": "file", + "description": "Summary of CCS in txt json", + "pattern": ".json" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.json.gz": { + "type": "file", + "description": "Metrics about zmws", + "pattern": "*.json.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98905,59 +125327,82 @@ "tool_dev_url": "https://github.com/rpetit3/pbptyper", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "An assembly in FASTA format", - "pattern": "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" - } - }, - { - "db": { - "type": "file", - "description": "A reference PBP database (optional)", - "pattern": "*.{fasta,fna,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "A tab-delimited file with the predicted PBP type", - "pattern": "*.tsv" - } - }, - { - "blast": { - "type": "file", - "description": "A tab-delimited file of all blast hits", - "pattern": "*.tblastn.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "An assembly in FASTA format", + "pattern": "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "A reference PBP database (optional)", + "pattern": "*.{fasta,fna,fa}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "A tab-delimited file with the predicted PBP type", + "pattern": "*.tsv" + } + } + ] + }, + { + "blast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tblastn.tsv": { + "type": "file", + "description": "A tab-delimited file of all blast hits", + "pattern": "*.tblastn.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -98991,52 +125436,63 @@ "doi": "no DOI available", "licence": [ "BSD-3-clause-Clear" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "PacBio BAM file", - "pattern": "*.bam" - } - }, - { - "pbi": { - "type": "file", - "description": "PacBio BAM file index (.pbi)", - "pattern": "*.pbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Gzipped FASTQ file", - "pattern": "*.fastq.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "PacBio BAM file", + "pattern": "*.bam" + } + }, + { + "pbi": { + "type": "file", + "description": "PacBio BAM file index (.pbi)", + "pattern": "*.pbi" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.$extension": { + "type": "file", + "description": "Gzipped FASTQ file", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99071,45 +125527,56 @@ "tool_dev_url": "https://github.com/PacificBiosciences/pbtk", "licence": [ "BSD-3-clause-Clear" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.bam" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.bam" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "pbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.pbi": { + "type": "file", + "description": "Index file", + "pattern": "*.bam.pbi" + } + } + ] }, { - "pbi": { - "type": "file", - "description": "Index file", - "pattern": "*.bam.pbi" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99140,58 +125607,96 @@ "documentation": "https://cme.h-its.org/exelixis/web/software/pear/doc.html", "licence": [ "Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files with paired-end reads forward and reverse.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "assembled": { - "type": "file", - "description": "FastQ file containing Assembled reads.", - "pattern": "*.{fastq.gz}" - } - }, - { - "unassembled": { - "type": "file", - "description": "FastQ files containing Unassembled forward and reverse reads.", - "pattern": "*.{fastq.gz}" - } - }, - { - "discarded": { - "type": "file", - "description": "FastQ file containing discarded reads.", - "pattern": "*.{fastq.gz}" - } + ], + "identifier": "biotools:pear" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files with paired-end reads forward and reverse.\n" + } + } + ] + ], + "output": [ + { + "assembled": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.assembled.fastq.gz": { + "type": "file", + "description": "FastQ file containing Assembled reads.", + "pattern": "*.{fastq.gz}" + } + } + ] + }, + { + "unassembled": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.unassembled.forward.fastq.gz": { + "type": "file", + "description": "FastQ files containing Unassembled forward and reverse reads.", + "pattern": "*.{fastq.gz}" + } + }, + { + "*.unassembled.reverse.fastq.gz": { + "type": "file", + "description": "FastQ files containing Unassembled forward and reverse reads.", + "pattern": "*.{fastq.gz}" + } + } + ] + }, + { + "discarded": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.discarded.fastq.gz": { + "type": "file", + "description": "FastQ file containing discarded reads.", + "pattern": "*.{fastq.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99230,80 +125735,123 @@ "doi": "10.1016/j.ajhg.2017.01.017", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "ped": { - "type": "file", - "description": "PED/FAM file", - "pattern": "*.{ped,fam}" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "TBI file", - "pattern": "*.{vcf.gz.tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ped": { - "type": "file", - "description": "PED/FAM file", - "pattern": "*.peddy.{ped}" - } - }, - { - "html": { - "type": "file", - "description": "HTML file", - "pattern": "*.{html}" - } - }, - { - "csv": { - "type": "file", - "description": "CSV file", - "pattern": "*.{csv}" - } - }, - { - "png": { - "type": "file", - "description": "PNG file", - "pattern": "*.{png}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "TBI file", + "pattern": "*.{vcf.gz.tbi}" + } + } + ], + [ + { + "ped": { + "type": "file", + "description": "PED/FAM file", + "pattern": "*.{ped,fam}" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML file", + "pattern": "*.{html}" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "CSV file", + "pattern": "*.{csv}" + } + } + ] + }, + { + "ped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.peddy.ped": { + "type": "file", + "description": "PED/FAM file", + "pattern": "*.peddy.{ped}" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "PNG file", + "pattern": "*.{png}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99344,81 +125892,203 @@ "doi": "10.1186/s13059-022-02755-2", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "peaks": { - "type": "file", - "description": "BED file of peak regions", - "pattern": "*.{bed,bed.gz}" - } - }, - { - "crosslinks": { - "type": "file", - "description": "BED file of crosslinks", - "pattern": "*.{bed,bed.gz}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference sequence used", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "FAI file corresponding to the reference sequence", - "pattern": "*.{fai}" - } - }, - { - "gtf": { - "type": "file", - "description": "A segmented GTF used to annotate peaks", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "cluster": { - "type": "file", - "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", - "pattern": "*.tsv" - } - }, - { - "distribution": { - "type": "file", - "description": "TSV file with calculated PEKA score and occurrence distribution for all possible k-mers", - "pattern": "*.tsv" - } - }, - { - "pdf": { - "type": "file", - "description": "PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites", - "pattern": "*.pdf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "peaks": { + "type": "file", + "description": "BED file of peak regions", + "pattern": "*.{bed,bed.gz}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "crosslinks": { + "type": "file", + "description": "BED file of crosslinks", + "pattern": "*.{bed,bed.gz}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Genome reference sequence used", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "FAI file corresponding to the reference sequence", + "pattern": "*.{fai}" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "A segmented GTF used to annotate peaks", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "cluster": [ + { + "meta": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv" + } + }, + { + "*mer_cluster_distribution*": { + "type": "file", + "description": "TSV file of summed occurrence distributions of k-mers within defined clusters", + "pattern": "*.tsv" + } + } + ] + }, + { + "distribution": [ + { + "meta": { + "type": "file", + "description": "TSV file with calculated PEKA score and occurrence distribution for all possible k-mers", + "pattern": "*.tsv" + } + }, + { + "*mer_distribution*": { + "type": "file", + "description": "TSV file with calculated PEKA score and occurrence distribution for all possible k-mers", + "pattern": "*.tsv" + } + } + ] + }, + { + "rtxn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*rtxn*": { + "type": "file", + "description": "rtxn file", + "pattern": "*rtxn*" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites", + "pattern": "*.pdf" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites", + "pattern": "*.pdf" + } + } + ] + }, + { + "tsites": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*thresholded_sites*.bed.gz": { + "type": "file", + "description": "BED file of thresholded sites", + "pattern": "*thresholded_sites*.bed.gz" + } + } + ] + }, + { + "oxn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*oxn*.bed.gz": { + "type": "file", + "description": "BED file of oxn sites", + "pattern": "*oxn*.bed.gz" + } + } + ] + }, + { + "clust": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_clusters.csv": { + "type": "file", + "description": "CSV file of clusters", + "pattern": "*_clusters.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99456,59 +126126,90 @@ "doi": "10.1101/gr.136184.111", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "spp": { - "type": "file", - "description": "A ChIP-Seq Processing Pipeline file containing\npeakshift/phantomPeak results\n", - "pattern": "*.{out}" - } - }, - { - "pdf": { - "type": "file", - "description": "A pdf containing save cross-correlation plots", - "pattern": "*.{pdf}" - } - }, - { - "rdata": { - "type": "file", - "description": "Rdata file containing the R session", - "pattern": "*.{Rdata}" - } + ], + "identifier": "biotools:phantompeakqualtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "spp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out": { + "type": "file", + "description": "A ChIP-Seq Processing Pipeline file containing\npeakshift/phantomPeak results\n", + "pattern": "*.{out}" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "A pdf containing save cross-correlation plots", + "pattern": "*.{pdf}" + } + } + ] + }, + { + "rdata": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Rdata": { + "type": "file", + "description": "Rdata file containing the R session", + "pattern": "*.{Rdata}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99555,24 +126256,33 @@ "doi": "10.1093/bioinformatics/btac776", "licence": [ "MIT" - ] + ], + "identifier": "biotools:pharokka" } } ], "output": [ { - "pharokka_db": { - "type": "directory", - "description": "Directory pointing to Pharokka's database", - "pattern": "${prefix}/" - } + "pharokka_db": [ + { + "${prefix}/": { + "type": "directory", + "description": "Directory pointing to Pharokka's database", + "pattern": "${prefix}/" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99613,86 +126323,166 @@ "doi": "10.1093/bioinformatics/btac776", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "phage_fasta": { - "type": "file", - "description": "A FASTA file containing phage sequence(s)", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "pharokka_db": { - "type": "file", - "description": "Directory containing Pharokka's database" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing all logging output", - "pattern": "*.log" - } - }, - { - "cds_functions": { - "type": "file", - "description": "A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs", - "pattern": "*_cds_functions.tsv" - } - }, - { - "card": { - "type": "file", - "description": "OPTIONAL - A file containing any CARD database hits", - "pattern": "*top_hits_card.tsv" - } - }, - { - "vfdb": { - "type": "file", - "description": "OPTIONAL - A file containing any VFDB database hits", - "pattern": "*top_hits_vfdb.tsv" - } - }, - { - "mash": { - "type": "file", - "description": "OPTIONAL - File containing top hits to INPHARED database", - "pattern": "*_top_hits_mash_inphared.tsv" - } - }, - { - "reoriented": { - "type": "file", - "description": "OPTIONAL - FASTA file reoriented to start with the large terminase subunit", - "pattern": "*_genome_terminase_reoriented.fasta" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:pharokka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "phage_fasta": { + "type": "file", + "description": "A FASTA file containing phage sequence(s)", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "pharokka_db": { + "type": "file", + "description": "Directory containing Pharokka's database" + } + } + ] + ], + "output": [ + { + "cds_final_merged_output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv": { + "type": "file", + "description": "A file containing the final merged output of CDSs", + "pattern": "*_cds_final_merged_output.tsv" + } + } + ] + }, + { + "cds_functions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_cds_functions.tsv": { + "type": "file", + "description": "A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs", + "pattern": "*_cds_functions.tsv" + } + } + ] + }, + { + "length_gc_cds_density": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv": { + "type": "file", + "description": "A file containing the length, GC content, and CDS density of the phage genome", + "pattern": "*_length_gc_cds_density.tsv" + } + } + ] + }, + { + "card": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_top_hits_card.tsv": { + "type": "file", + "description": "OPTIONAL - A file containing any CARD database hits", + "pattern": "*top_hits_card.tsv" + } + } + ] + }, + { + "vfdb": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv": { + "type": "file", + "description": "OPTIONAL - A file containing any VFDB database hits", + "pattern": "*top_hits_vfdb.tsv" + } + } + ] + }, + { + "mash": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv": { + "type": "file", + "description": "OPTIONAL - File containing top hits to INPHARED database", + "pattern": "*_top_hits_mash_inphared.tsv" + } + } + ] + }, + { + "reoriented": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta": { + "type": "file", + "description": "OPTIONAL - FASTA file reoriented to start with the large terminase subunit", + "pattern": "*_genome_terminase_reoriented.fasta" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99734,115 +126524,226 @@ "doi": "10.1093/nar/gks406", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gbk": { - "type": "file", - "description": "Genome file in .gbk or .gbff format.", - "pattern": "*.{gbk,gbff}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coordinates": { - "type": "file", - "description": "Coordinates of each prophage identified in the genome,\nand their att sites (if found).\n", - "pattern": "*.{tsv}" - } - }, - { - "gbk": { - "type": "file", - "description": "A duplicate GenBank record that is the same as the input record,\nbut we have inserted the prophage information, including att\nsites into the record.\n", - "pattern": "*.{gbk,gbff}" - } - }, - { - "log": { - "type": "file", - "description": "File containing the PhiSpy execution log", - "pattern": "*.{log}" - } - }, - { - "information": { - "type": "file", - "description": "File containing all the genes of the genome, one per line.\nThe tenth column describes how likely the gene is a phage gene.\n", - "pattern": "*.{tsv}" - } - }, - { - "bacteria_fasta": { - "type": "file", - "description": "Genome with prophage regions masked with N.", - "pattern": "*.{fasta}" - } - }, - { - "bacteria_gbk": { - "type": "file", - "description": "Genome sequences identified as bacterial.", - "pattern": "*.{gbk}" - } - }, - { - "phage_fasta": { - "type": "file", - "description": "Phage sequences extracted from the genome.", - "pattern": "*.{fasta}" - } - }, - { - "phage_gbk": { - "type": "file", - "description": "Phage sequences extracted from the genome.", - "pattern": "*.{gbk}" - } - }, - { - "prophage_gff": { - "type": "file", - "description": "Prophage information in GFF3 format.", - "pattern": "*.{gff3}" - } - }, - { - "prophage_tbl": { - "type": "file", - "description": "File containing prophage number and its location in the genome.\n", - "pattern": "*.{tbl}" - } - }, - { - "prophage_tsv": { - "type": "file", - "description": "A file containing simpler version of the coordinates file,\nwith only prophage number, contig, start and stop.\n", - "pattern": "*.{tsv}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gbk": { + "type": "file", + "description": "Genome file in .gbk or .gbff format.", + "pattern": "*.{gbk,gbff}" + } + } + ] + ], + "output": [ + { + "coordinates": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "Coordinates of each prophage identified in the genome,\nand their att sites (if found).\n", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.gb*": { + "type": "file", + "description": "A duplicate GenBank record that is the same as the input record,\nbut we have inserted the prophage information, including att\nsites into the record.\n", + "pattern": "*.{gbk,gbff}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.log": { + "type": "file", + "description": "File containing the PhiSpy execution log", + "pattern": "*.{log}" + } + } + ] + }, + { + "information": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage_information.tsv": { + "type": "file", + "description": "File containing all the genes of the genome, one per line.\nThe tenth column describes how likely the gene is a phage gene.\n", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "bacteria_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_bacteria.fasta": { + "type": "file", + "description": "Genome with prophage regions masked with N.", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "bacteria_gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_bacteria.gbk": { + "type": "file", + "description": "Genome sequences identified as bacterial.", + "pattern": "*.{gbk}" + } + } + ] + }, + { + "phage_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_phage.fasta": { + "type": "file", + "description": "Phage sequences extracted from the genome.", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "phage_gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_phage.gbk": { + "type": "file", + "description": "Phage sequences extracted from the genome.", + "pattern": "*.{gbk}" + } + } + ] + }, + { + "prophage_gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage.gff3": { + "type": "file", + "description": "Prophage information in GFF3 format.", + "pattern": "*.{gff3}" + } + } + ] + }, + { + "prophage_tbl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage.tbl": { + "type": "file", + "description": "File containing prophage number and its location in the genome.\n", + "pattern": "*.{tbl}" + } + } + ] + }, + { + "prophage_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_prophage.tsv": { + "type": "file", + "description": "A file containing simpler version of the coordinates file,\nwith only prophage number, contig, start and stop.\n", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99875,59 +126776,73 @@ "doi": "10.1128/mSystems.00920-20", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Channel containing single or paired-end reads", - "pattern": "*.{fastq.gz,fq.gz}" - } - }, - { - "sliva_db": { - "type": "directory", - "description": "Folder containing the SILVA database", - "pattern": "ref" - } - }, - { - "univec_db": { - "type": "directory", - "description": "Folder containing UniVec database", - "pattern": "UniVec" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "directory", - "description": "Folder containing the results of phyloFlash analysis", - "pattern": "${prefix}*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:phyloflash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Channel containing single or paired-end reads", + "pattern": "*.{fastq.gz,fq.gz}" + } + } + ], + [ + { + "silva_db": { + "type": "directory", + "description": "Folder containing SILVA database" + } + } + ], + [ + { + "univec_db": { + "type": "directory", + "description": "Folder containing UniVec database", + "pattern": "UniVec" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${meta.id}*/*": { + "type": "directory", + "description": "Folder containing the results of phyloFlash analysis", + "pattern": "${prefix}*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -99960,85 +126875,120 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Sequence reads file, can be SAM/BAM/CRAM format", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Output BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "An optional BAM index file", - "pattern": "*.{bai}" - } - }, - { - "cram": { - "type": "file", - "description": "Output CRAM file", - "pattern": "*.{cram}" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Sequence reads file, can be SAM/BAM/CRAM format", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_index": { + "type": "file", + "description": "Reference genome index file", + "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Output BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "An optional BAM index file", + "pattern": "*.{bai}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100089,59 +127039,79 @@ "doi": "10.1158/1538-7445.AM2017-3590", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "bed": { - "type": "file", - "description": "Input bed file", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary", - "pattern": "*.dict" - } - }, - { - "arguments_file": { - "type": "file", - "description": "File containing command line arguments (optional)", - "pattern": "*" - } - } - ], - "output": [ - { - "interval_list": { - "type": "file", - "description": "gatk interval list file", - "pattern": "*.interval_list" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bed": { + "type": "file", + "description": "Input bed file", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "interval_list": [ + { + "meta": { + "type": "file", + "description": "gatk interval list file", + "pattern": "*.interval_list" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "gatk interval list file", + "pattern": "*.interval_list" + } + }, + { + "_list": { + "type": "file", + "description": "gatk interval list file", + "pattern": "*.interval_list" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100177,45 +127147,56 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] + ], + "identifier": "biotools:picard_tools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Cleaned BAM file", + "pattern": "*.{bam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Cleaned BAM file", - "pattern": "*.{bam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100255,105 +127236,122 @@ "tool_dev_url": "https://github.com/broadinstitute/picard/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "An aligned BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "Optional aligned BAM/CRAM/SAM file index", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "bait_intervals": { - "type": "file", - "description": "An interval file that contains the locations of the baits used.", - "pattern": "*.{interval_list,bed,bed.gz}" - } - }, - { - "target_intervals": { - "type": "file", - "description": "An interval file that contains the locations of the targets.", - "pattern": "*.{interval_list,bed,bed.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference file to calculate dropout metrics measuring reduced representation of reads.\nOptional input.\n", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of FASTA file. Only needed when fasta is supplied.", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard", - "pattern": "*_{metrics}" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "An aligned BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "Optional aligned BAM/CRAM/SAM file index", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "bait_intervals": { + "type": "file", + "description": "An interval file that contains the locations of the baits used.", + "pattern": "*.{interval_list,bed,bed.gz}" + } + }, + { + "target_intervals": { + "type": "file", + "description": "An interval file that contains the locations of the targets.", + "pattern": "*.{interval_list,bed,bed.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A reference file to calculate dropout metrics measuring reduced representation of reads.\nOptional input.\n", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of FASTA file. Only needed when fasta is supplied.", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard", + "pattern": "*_{metrics}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100399,52 +127397,73 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pdf": { - "type": "file", - "description": "Histogram plots of the insert size metrics computed by Picard", - "pattern": "*.pdf" - } - }, - { - "metrics": { - "type": "file", - "description": "Values used by Picard to generate the insert size histograms", - "pattern": "*.txt" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Values used by Picard to generate the insert size histograms", + "pattern": "*.txt" + } + } + ] + }, + { + "histogram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Insert size histogram in PDF format", + "pattern": "*.pdf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100484,88 +127503,113 @@ "documentation": "https://broadinstitute.github.io/picard/", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "SAM/BAM/CRAM file", + "pattern": "*.{sam,bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "Optional SAM/BAM/CRAM file index", + "pattern": "*.{sai,bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of FASTA file. Only needed when fasta is supplied.", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard", + "pattern": "*_{metrics}" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF plots of metrics", + "pattern": "*.{pdf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "SAM/BAM/CRAM file", - "pattern": "*.{sam,bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "Optional SAM/BAM/CRAM file index", - "pattern": "*.{sai,bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome']\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of FASTA file. Only needed when fasta is supplied.", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard", - "pattern": "*_{metrics}" - } - }, - { - "pdf": { - "type": "file", - "description": "PDF plots of metrics", - "pattern": "*.{pdf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@drpatelh" + "authors": [ + "@drpatelh" ], "maintainers": [ "@drpatelh" @@ -100622,75 +127666,96 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, strandedness:true ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "ref_flat": { - "type": "file", - "description": "Genome ref_flat file" - } - }, - { - "gene_pred": { - "type": "file", - "description": "genome gene_pred file as an alternative to the ref_flat file" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file" - } - }, - { - "rrna_intervals": { - "type": "file", - "description": "Interval file of ribosomal RNA regions" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "metrics": { - "type": "file", - "description": "RNA alignment metrics files generated by picard", - "pattern": "*.rna_metrics" - } - }, - { - "pdf": { - "type": "file", - "description": "Plot normalized position vs. coverage in a pdf file generated by picard" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, strandedness:true ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "ref_flat": { + "type": "file", + "description": "Genome ref_flat file" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Genome fasta file" + } + } + ], + [ + { + "rrna_intervals": { + "type": "file", + "description": "Interval file of ribosomal RNA regions" + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rna_metrics": { + "type": "file", + "description": "RNA alignment metrics files generated by picard", + "pattern": "*.rna_metrics" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Plot normalized position vs. coverage in a pdf file generated by picard" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100723,84 +127788,101 @@ "documentation": "https://broadinstitute.github.io/picard/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Aligned reads file", - "pattern": "*.{bam, cram}" - } - }, - { - "bai": { - "type": "file", - "description": "(Optional) Aligned reads file index", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Genome fasta file index", - "pattern": "*.{fai}" - } - }, - { - "intervallist": { - "type": "file", - "description": "Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "metrics": { - "type": "file", - "description": "Alignment metrics files generated by picard", - "pattern": "*_{metrics}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Aligned reads file", + "pattern": "*.{bam, cram}" + } + }, + { + "bai": { + "type": "file", + "description": "(Optional) Aligned reads file index", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Genome fasta file index", + "pattern": "*.{fai}" + } + } + ], + [ + { + "intervallist": { + "type": "file", + "description": "Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList." + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_metrics": { + "type": "file", + "description": "Alignment metrics files generated by picard", + "pattern": "*_{metrics}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100852,45 +127934,56 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] + ], + "identifier": "biotools:picard_tools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "reference_dict": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dict": { + "type": "file", + "description": "picard dictionary file", + "pattern": "*.{dict}" + } + } + ] }, { - "reference_dict": { - "type": "file", - "description": "picard dictionary file", - "pattern": "*.{dict}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -100942,93 +128035,99 @@ "tool_dev_url": "https://github.com/broadinstitute/picard/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input1": { - "type": "file", - "description": "List containing 1 or more bam/vcf files or a file containing filepaths", - "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}" - } - }, - { - "input1_index": { - "type": "file", - "description": "List containing 1 or more bam/vcf files indexes", - "pattern": "*.{bai,csi,crai,tbi}" - } - }, - { - "input2": { - "type": "file", - "description": "Optional list containing 1 or more bam/vcf files or a file containing filepaths", - "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}" - } - }, - { - "input2_index": { - "type": "file", - "description": "List containing 1 or more bam/vcf files indexes", - "pattern": "*.{bai,csi,crai,tbi}" - } - }, - { - "haplotype_map": { - "type": "file", - "description": "Haplotype map file", - "pattern": "*.{txt,vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" - } - }, - { - "fasta_index": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "crosscheck_metrics": { - "type": "file", - "description": "Metrics created by crosscheckfingerprints", - "pattern": "*.{crosscheck_metrics.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input1": { + "type": "file", + "description": "List containing 1 or more bam/vcf files or a file containing filepaths", + "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}" + } + }, + { + "input1_index": { + "type": "file", + "description": "List containing 1 or more bam/vcf files indexes", + "pattern": "*.{bai,csi,crai,tbi}" + } + }, + { + "input2": { + "type": "file", + "description": "Optional list containing 1 or more bam/vcf files or a file containing filepaths", + "pattern": "*.{bam,vcf,vcf.gz,txt,fofn}" + } + }, + { + "input2_index": { + "type": "file", + "description": "List containing 1 or more bam/vcf files indexes", + "pattern": "*.{bai,csi,crai,tbi}" + } + }, + { + "haplotype_map": { + "type": "file", + "description": "Haplotype map file", + "pattern": "*.{txt,vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ] + ], + "output": [ + { + "crosscheck_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crosscheck_metrics.txt": { + "type": "file", + "description": "Metrics created by crosscheckfingerprints", + "pattern": "*.{crosscheck_metrics.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101061,44 +128160,115 @@ "tool_dev_url": "https://github.com/broadinstitute/picard/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "file", - "description": "Input SAM/BAM/CRAM file\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference sequence file\n" - } - }, - { - "haplotype_map": { - "type": "file", - "description": "A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting.\nSee https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.\n", - "pattern": "*.{txt,vcf,vcf.gz}" - } - } - ], - "output": [ - { - "fingerprint": { - "type": "file", - "description": "Output fingerprint file (VCF)\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "file", + "description": "Input SAM/BAM/CRAM file\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}" + } + } + ], + [ + { + "haplotype_map": { + "type": "file", + "description": "A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting.\nSee https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.\n", + "pattern": "*.{txt,vcf,vcf.gz}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference sequence file", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Reference sequence index file", + "pattern": "*.{fai}" + } + } + ], + [ + { + "sequence_dictionary": { + "type": "file", + "description": "Reference sequence dictionary file" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Tabix index file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101132,44 +128302,55 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] + ], + "identifier": "biotools:picard_tools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Unaligned bam file", + "pattern": "*.{bam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Unaligned bam file", - "pattern": "*.{bam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101202,58 +128383,71 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam", - "pattern": "*.{bam}" - } - }, - { - "filter": { - "type": "string", - "description": "Picard filter type", - "pattern": "includeAligned|excludeAligned|includeReadList|excludeReadList" - } - }, - { - "readlist": { - "type": "file", - "description": "Optional text file containing reads IDs to include or exclude" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Filtered BAM file", - "pattern": "*.{bam}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam", + "pattern": "*.{bam}" + } + }, + { + "readlist": { + "type": "file", + "description": "Optional text file containing reads IDs to include or exclude" + } + } + ], + [ + { + "filter": { + "type": "string", + "description": "Picard filter type", + "pattern": "includeAligned|excludeAligned|includeReadList|excludeReadList" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Filtered BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101292,45 +128486,56 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] + ], + "identifier": "biotools:picard_tools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "mate-pair verified BAM file", + "pattern": "*.{bam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "mate-pair verified BAM file", - "pattern": "*.{bam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101366,90 +128571,117 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "input_vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "dictionary for fasta file", - "pattern": "*.{dict}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "chain": { - "type": "file", - "description": "The liftover chain file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf_lifted": { - "type": "file", - "description": "VCF file containing successfully lifted variants", - "pattern": "*.{lifted.vcf.gz}" - } - }, - { - "vcf_unlifted": { - "type": "file", - "description": "VCF file containing unsuccessfully lifted variants", - "pattern": "*.{unlifted.vcf.gz}" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "input_vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "dictionary for fasta file", + "pattern": "*.{dict}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "chain": { + "type": "file", + "description": "The liftover chain file" + } + } + ] + ], + "output": [ + { + "vcf_lifted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "*.lifted.vcf.gz": { + "type": "file", + "description": "VCF file containing successfully lifted variants", + "pattern": "*.{lifted.vcf.gz}" + } + } + ] + }, + { + "vcf_unlifted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]" + } + }, + { + "*.unlifted.vcf.gz": { + "type": "file", + "description": "VCF file containing unsuccessfully lifted variants", + "pattern": "*.{unlifted.vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101495,92 +128727,137 @@ "documentation": "https://broadinstitute.github.io/picard/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Sequence reads file, can be SAM/BAM/CRAM format", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome fasta file, required for CRAM input", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome fasta index", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with duplicate reads marked/removed", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", - "pattern": "*.{bai}" - } - }, - { - "cram": { - "type": "file", - "description": "Output CRAM file", - "pattern": "*.{cram}" - } - }, - { - "metrics": { - "type": "file", - "description": "Duplicate metrics file generated by picard", - "pattern": "*.{metrics.txt}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Sequence reads file, can be SAM/BAM/CRAM format", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome fasta file, required for CRAM input", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome fasta index", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with duplicate reads marked/removed", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", + "pattern": "*.{bai}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Output CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.txt": { + "type": "file", + "description": "Duplicate metrics file generated by picard", + "pattern": "*.{metrics.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101662,45 +128939,56 @@ "documentation": "https://broadinstitute.github.io/picard/", "licence": [ "MIT" - ] + ], + "identifier": "biotools:picard_tools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "List of BAM files", - "pattern": "*.{bam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "list", + "description": "List of input BAM files to be merged", + "pattern": "*.{bam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Merged BAM file", - "pattern": "*.{bam}" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Merged BAM file", + "pattern": "*.{bam}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101742,64 +129030,95 @@ "documentation": "https://broadinstitute.github.io/picard/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fraction": { - "type": "float", - "description": "Fraction of reads to downsample to" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "A downsampled BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", - "pattern": "*.{bai}" - } - }, - { - "num_reads": { - "type": "integer", - "description": "The actual number of downsampled reads" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "fraction": { + "type": "float", + "description": "Fraction of reads to downsample to" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ds*.bam": { + "type": "file", + "description": "A downsampled BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ds*.bai": { + "type": "file", + "description": "An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag", + "pattern": "*.{bai}" + } + } + ] + }, + { + "num_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ACTUAL_NUM_READS": { + "type": "integer", + "description": "The actual number of downsampled reads" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101828,45 +129147,56 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] + ], + "identifier": "biotools:picard_tools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -101904,71 +129234,93 @@ "tool_dev_url": "https://github.com/broadinstitute/picard", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file to derive the intervals from", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fai information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the fasta file", - "pattern": "*.fai" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing dictionary information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Sequence dictionary of the fasta file", - "pattern": "*.dict" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "intervals": { - "type": "file", - "description": "The scattered intervals", - "pattern": "*.interval_list" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file to derive the intervals from", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fai information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing dictionary information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Sequence dictionary of the fasta file", + "pattern": "*.dict" + } + } + ] + ], + "output": [ + { + "intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interval_list": { + "type": "file", + "description": "The scattered intervals", + "pattern": "*.interval_list" + } + }, + { + "s": { + "type": "file", + "description": "The scattered intervals", + "pattern": "*.interval_list" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102000,52 +129352,65 @@ "documentation": "https://broadinstitute.github.io/picard/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "sort_order": { - "type": "string", - "description": "Picard sort order type", - "pattern": "unsorted|queryname|coordinate|duplicate|unknown" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam}" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,sam}" + } + } + ], + [ + { + "sort_order": { + "type": "string", + "description": "Picard sort order type", + "pattern": "unsorted|queryname|coordinate|duplicate|unknown" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102086,71 +129451,86 @@ "documentation": "https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "Reference genome dictionary file", - "pattern": "*.{dict}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Sorted VCF file", - "pattern": "*.{vcf}" - } + ], + "identifier": "biotools:picard_tools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "Reference genome dictionary file", + "pattern": "*.{dict}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_sorted.vcf.gz": { + "type": "file", + "description": "Sorted VCF file", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102184,45 +129564,56 @@ "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "raw_file": { - "type": "file", - "description": "File to be compressed", - "pattern": "*.*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "raw_file": { + "type": "file", + "description": "File to be compressed", + "pattern": "*.*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "archive": { - "type": "file", - "description": "The compressed file", - "pattern": "*.gz" - } + "archive": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$archive": { + "type": "file", + "description": "The compressed file", + "pattern": "*.gz" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102268,45 +129659,56 @@ "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "zip": { - "type": "file", - "description": "Gzipped file", - "pattern": "*.{gzip}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "zip": { + "type": "file", + "description": "Gzipped file", + "pattern": "*.{gzip}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "file": { - "type": "file", - "description": "File to compress", - "pattern": "*" - } + "file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "${uncompressed_filename}": { + "type": "file", + "description": "File to compress", + "pattern": "*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102350,105 +129752,160 @@ "doi": "10.1371/journal.pone.0112963", "licence": [ "GPL-2.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information for the fasta\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA of the input genome", - "pattern": "*.{fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for the bam file\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file of reads aligned to the input genome", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAI file (BAM index) of BAM reads aligned to the input genome", - "pattern": "*.{bai}" - } - }, - { - "pilon_mode": { - "type": "string", - "description": "Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).", - "enum": [ - "frags", - "jumps", - "unpaired", - "bam" - ] - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "improved_assembly": { - "type": "file", - "description": "fasta file, improved assembly", - "pattern": "*.{fasta}" - } - }, - { - "change_record": { - "type": "file", - "description": "file containing a space-delimited record of every change made in the assembly as instructed by the --fix option", - "pattern": "*.{change}" - } - }, - { - "vcf": { - "type": "file", - "description": "Pilon variant output", - "pattern": "*.{vcf}" - } - }, - { - "tracks_bed": { - "type": "file", - "description": "files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats", - "pattern": "*.{bed}" - } - }, - { - "tracks_wig": { - "type": "file", - "description": "files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats", - "pattern": "*.{wig}" - } + ], + "identifier": "biotools:pilon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information for the fasta\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA of the input genome", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for the bam file\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file of reads aligned to the input genome", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAI file (BAM index) of BAM reads aligned to the input genome", + "pattern": "*.{bai}" + } + } + ], + [ + { + "pilon_mode": { + "type": "string", + "description": "Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).", + "enum": [ + "frags", + "jumps", + "unpaired", + "bam" + ] + } + } + ] + ], + "output": [ + { + "improved_assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "fasta file, improved assembly", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Pilon variant output", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "change_record": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.change": { + "type": "file", + "description": "file containing a space-delimited record of every change made in the assembly as instructed by the --fix option", + "pattern": "*.{change}" + } + } + ] + }, + { + "tracks_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats", + "pattern": "*.{bed}" + } + } + ] + }, + { + "tracks_wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats", + "pattern": "*.{wig}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102479,133 +129936,240 @@ "documentation": "https://gmt.genome.wustl.edu/packages/pindel/user-manual.html", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics\nor a sensible default - setting ext.args2 to either in modules.conf\ne.g. [ id:'test', single_end:false, insert_size:500 ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "bed": { - "type": "file", - "description": "BED file containing regions of interest" - } - }, - { - "fasta": { - "type": "file", - "description": "Input reference genome fasta file" - } - }, - { - "fai": { - "type": "file", - "description": "Input reference genome fasta index file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bp": { - "type": "file", - "description": "File containing breakpoints", - "pattern": "*_{BP}" - } - }, - { - "cem": { - "type": "file", - "description": "File containing close end reads", - "pattern": "*_{CloseEndMapped}" - } - }, - { - "del": { - "type": "file", - "description": "File containing deletions", - "pattern": "*_{D}" - } - }, - { - "dd": { - "type": "file", - "description": "File containing dispersed duplications", - "pattern": "*_{DD}" - } - }, - { - "int_{final": { - "type": "file", - "description": "File containing interchromosomal events", - "pattern": "*_{INT_final}" - } - }, - { - "inv": { - "type": "file", - "description": "File containing inversions", - "pattern": "*_{INV}" - } - }, - { - "li": { - "type": "file", - "description": "File containing long insertions", - "pattern": "*_{LI}" - } - }, - { - "rp": { - "type": "file", - "description": "File containing read-pair evidence", - "pattern": "*_{RP}" - } - }, - { - "si": { - "type": "file", - "description": "File containing short insertions", - "pattern": "*_{SI}" - } - }, - { - "td": { - "type": "file", - "description": "File containing tandem duplications", - "pattern": "*_{TD}" - } + ], + "identifier": "biotools:pindel" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics\nor a sensible default - setting ext.args2 to either in modules.conf\ne.g. [ id:'test', single_end:false, insert_size:500 ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Input reference genome fasta file" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Input reference genome fasta index file" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "BED file containing regions of interest" + } + } + ] + ], + "output": [ + { + "bp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_BP": { + "type": "file", + "description": "File containing breakpoints", + "pattern": "*_{BP}" + } + } + ] + }, + { + "cem": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_CloseEndMapped": { + "type": "file", + "description": "File containing close end reads", + "pattern": "*_{CloseEndMapped}" + } + } + ] + }, + { + "del": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_D": { + "type": "file", + "description": "File containing deletions", + "pattern": "*_{D}" + } + } + ] + }, + { + "dd": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_DD": { + "type": "file", + "description": "File containing dispersed duplications", + "pattern": "*_{DD}" + } + } + ] + }, + { + "int_final": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_INT_final": { + "type": "file", + "description": "int file", + "pattern": "*_INT_final" + } + } + ] + }, + { + "inv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_INV": { + "type": "file", + "description": "File containing inversions", + "pattern": "*_{INV}" + } + } + ] + }, + { + "li": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_LI": { + "type": "file", + "description": "File containing long insertions", + "pattern": "*_{LI}" + } + } + ] + }, + { + "rp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_RP": { + "type": "file", + "description": "File containing read-pair evidence", + "pattern": "*_{RP}" + } + } + ] + }, + { + "si": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_SI": { + "type": "file", + "description": "File containing short insertions", + "pattern": "*_{SI}" + } + } + ] + }, + { + "td": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_TD": { + "type": "file", + "description": "File containing tandem duplications", + "pattern": "*_{TD}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102646,86 +130210,129 @@ "doi": "10.1038/s41587-022-01211-7", "licence": [ "GPL v3" - ] - } + ], + "identifier": "biotools:pyPINTS" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "One or more BAM files", + "pattern": "*.{bam}" + } + }, + { + "bais": { + "type": "file", + "description": "Corresponding BAM file indexes", + "pattern": "*.bam.bai" + } + } + ], + [ + { + "assay_type": { + "type": "string", + "description": "Assay type" + } + } + ] + ], + "output": [ + { + "divergent_TREs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_divergent_peaks.bed": { + "type": "file", + "description": "Divergent TREs", + "pattern": "*_divergent_peaks.bed", + "optional": true + } + } + ] + }, + { + "bidirectional_TREs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_bidirectional_peaks.bed": { + "type": "file", + "description": "Divergent TREs and convergent TREs", + "pattern": "*_bidirectional_peaks.bed", + "optional": true + } + } + ] + }, + { + "unidirectional_TREs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_unidirectional_peaks.bed": { + "type": "file", + "description": "Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)", + "pattern": "*_unidirectional_peaks.bed", + "optional": true + } + } + ] + }, + { + "peakcalling_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "peakcalling_*.log": { + "type": "file", + "description": "Peakcalling log for debugging purposes", + "pattern": "peakcalling_*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "One or more BAM files", - "pattern": "*.{bam}" - } - }, - { - "bais": { - "type": "file", - "description": "Corresponding BAM file indexes", - "pattern": "*.bam.bai" - } - }, - { - "assay": { - "type": "string", - "description": "Assay name" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "divergent_TREs": { - "type": "file", - "description": "Divergent TREs", - "pattern": "*_divergent_peaks.bed", - "optional": true - } - }, - { - "bidirectional_TREs": { - "type": "file", - "description": "Divergent TREs and convergent TREs", - "pattern": "*_bidirectional_peaks.bed", - "optional": true - } - }, - { - "unidirectional_TREs": { - "type": "file", - "description": "Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)", - "pattern": "*_unidirectional_peaks.bed", - "optional": true - } - }, - { - "peakcalling_log": { - "type": "file", - "description": "Peakcalling log for debugging purposes", - "pattern": "peakcalling_*.log" - } - } - ], - "authors": [ - "@edmundmiller" + "authors": [ + "@edmundmiller" ], "maintainers": [ "@edmundmiller" @@ -102760,52 +130367,73 @@ "doi": "10.1093/gigascience/giz119", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "A set of GFF3 formatted files", - "pattern": "*.{gff}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "directory", - "description": "Directory containing PIRATE result files", - "pattern": "*/*" - } - }, - { - "aln": { - "type": "file", - "description": "Core-genome alignment produced by PIRATE (Optional)", - "pattern": "*.{fasta}" - } + ], + "identifier": "biotools:PIRATE" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "A set of GFF3 formatted files", + "pattern": "*.{gff}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*": { + "type": "directory", + "description": "Directory containing PIRATE result files", + "pattern": "*/*" + } + } + ] + }, + { + "aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/core_alignment.fasta": { + "type": "file", + "description": "Core-genome alignment produced by PIRATE (Optional)", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102844,73 +130472,124 @@ "doi": "10.1128/AAC.02412-14", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "Input FASTA or FASTQ formatted genome sequences", - "pattern": "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "The results from analysis in JSON format", - "pattern": "*.json" - } - }, - { - "txt": { - "type": "file", - "description": "The summary of results from analysis", - "pattern": "*.txt" - } - }, - { - "tsv": { - "type": "file", - "description": "The results from analysis in TSV format", - "pattern": "*.tsv" - } - }, - { - "genome_seq": { - "type": "file", - "description": "FASTA of sequences in the input with a hit", - "pattern": "*-hit_in_genome_seq.fsa" - } - }, - { - "plasmid_seq": { - "type": "file", - "description": "FASTA of plasmid sequences with a hit against the input", - "pattern": "*-plasmid_seqs.fsa" - } + ], + "identifier": "biotools:PlasmidFinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "Input FASTA or FASTQ formatted genome sequences", + "pattern": "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "The results from analysis in JSON format", + "pattern": "*.json" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "The summary of results from analysis", + "pattern": "*.txt" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The results from analysis in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "genome_seq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-hit_in_genome_seq.fsa": { + "type": "file", + "description": "FASTA of sequences in the input with a hit", + "pattern": "*-hit_in_genome_seq.fsa" + } + } + ] + }, + { + "plasmid_seq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-plasmid_seqs.fsa": { + "type": "file", + "description": "FASTA of plasmid sequences with a hit against the input", + "pattern": "*-plasmid_seqs.fsa" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -102942,100 +130621,183 @@ "tool_dev_url": "https://github.com/BU-ISCIII/plasmidID", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "scaffold": { - "type": "file", - "description": "Fasta file containing scaffold\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "html": { - "type": "file", - "description": "html file with results rendered", - "pattern": "*.{html}" - } - }, - { - "tab": { - "type": "file", - "description": "Results in a tabular file", - "pattern": "*.{tab}" - } - }, - { - "images": { - "type": "directory", - "description": "Directory containing the images produced by plasmidid", - "pattern": "images" - } - }, - { - "logs": { - "type": "directory", - "description": "Directory containing the logs produced by plasmidid", - "pattern": "logs" - } - }, - { - "data": { - "type": "directory", - "description": "Directory containing the data produced by plasmidid", - "pattern": "data" - } - }, - { - "database": { - "type": "directory", - "description": "Directory containing the database produced by plasmidid", - "pattern": "database" - } - }, - { - "fasta_files": { - "type": "directory", - "description": "Directory containing the fasta files produced by plasmidid", - "pattern": "fasta_files" - } - }, - { - "kmer": { - "type": "directory", - "description": "Directory containing the kmer files produced by plasmidid", - "pattern": "database" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:plasmidid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "scaffold": { + "type": "file", + "description": "Fasta file containing scaffold\n" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*final_results.html": { + "type": "file", + "description": "html file with results rendered", + "pattern": "*.{html}" + } + } + ] + }, + { + "tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*final_results.tab": { + "type": "file", + "description": "Results in a tabular file", + "pattern": "*.{tab}" + } + } + ] + }, + { + "images": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/images/": { + "type": "directory", + "description": "Directory containing the images produced by plasmidid", + "pattern": "images" + } + } + ] + }, + { + "logs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/logs/": { + "type": "directory", + "description": "Directory containing the logs produced by plasmidid", + "pattern": "logs" + } + } + ] + }, + { + "data": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/data/": { + "type": "directory", + "description": "Directory containing the data produced by plasmidid", + "pattern": "data" + } + } + ] + }, + { + "database": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/database/": { + "type": "directory", + "description": "Directory containing the database produced by plasmidid", + "pattern": "database" + } + } + ] + }, + { + "fasta_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/fasta_files/": { + "type": "directory", + "description": "Directory containing the fasta files produced by plasmidid", + "pattern": "fasta_files" + } + } + ] + }, + { + "kmer": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/kmer/": { + "type": "directory", + "description": "Directory containing the kmer files produced by plasmidid", + "pattern": "database" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -103077,101 +130839,138 @@ "doi": "10.1038/ng.3036", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "tumor_file": { - "type": "file", - "description": "Tumor or metastatic sample, BAM or CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "tummor_file_bai": { - "type": "file", - "description": "Index of BAMfile", - "pattern": "*.{bai,crai}" - } - }, - { - "control_file": { - "type": "file", - "description": "Control (or blood) of matching tumor/metastatic sample, BAM or CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "control_file_bai": { - "type": "file", - "description": "Index of BAMfile", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fa" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai" - } - }, - { - "skipregions_file": { - "type": "file", - "description": "File with regions to skip, region as comma-separated list of chr:start-end, or just list of chr, or nothing", - "pattern": "*.bed|*.txt|*.tab" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "log": { - "type": "file", - "description": "Log file", - "pattern": "*.log" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.txt}" - } + ], + "identifier": "biotools:platypus" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "tumor_file": { + "type": "file", + "description": "Tumor or metastatic sample, BAM or CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "tumor_file_bai": { + "type": "file", + "description": "Index of BAM file", + "pattern": "*.{bai,crai}" + } + }, + { + "control_file": { + "type": "file", + "description": "Control (or blood) of matching tumor/metastatic sample, BAM or CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "control_file_bai": { + "type": "file", + "description": "Index of BAMfile", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fa" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "skipregions_file": { + "type": "file", + "description": "File with regions to skip, region as comma-separated list of chr:start-end, or just list of chr, or nothing", + "pattern": "*.bed|*.txt|*.tab" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log" + } + } + ] + }, + { + "version": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "*.{version.txt}" + } + } + ] } ], "authors": [ @@ -103203,80 +131002,111 @@ "doi": "10.1186/s13742-015-0047-8", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table", - "pattern": "*.{pgen}" - } - }, - { - "psam": { - "type": "file", - "description": "PLINK 2 sample information file", - "pattern": "*.{psam}" - } - }, - { - "pvar": { - "type": "file", - "description": "PLINK 2 variant information file", - "pattern": "*.{pvar}" - } - }, - { - "variants": { - "type": "file", - "description": "A text file containing variant identifiers to keep (one per line)", - "pattern": "*.{keep}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "extract_pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table, containing extracted variants", - "pattern": "*.{pgen}" - } - }, - { - "extract_psam": { - "type": "file", - "description": "PLINK 2 sample information file associated with the extracted data", - "pattern": "*.{psam}" - } - }, - { - "extract_pvar": { - "type": "file", - "description": "PLINK 2 variant information file, containing extracted variants", - "pattern": "*.{pvar.zst}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table", + "pattern": "*.{pgen}" + } + }, + { + "psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.{psam}" + } + }, + { + "pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.{pvar}" + } + }, + { + "variants": { + "type": "file", + "description": "A text file containing variant identifiers to keep (one per line)", + "pattern": "*.{keep}" + } + } + ] + ], + "output": [ + { + "extract_pgen": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table, containing extracted variants", + "pattern": "*.{pgen}" + } + } + ] + }, + { + "extract_psam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.psam": { + "type": "file", + "description": "PLINK 2 sample information file associated with the extracted data", + "pattern": "*.{psam}" + } + } + ] + }, + { + "extract_pvar": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvar.zst": { + "type": "file", + "description": "PLINK 2 variant information file, containing extracted variants", + "pattern": "*.{pvar.zst}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -103308,66 +131138,79 @@ "doi": "10.1186/s13742-015-0047-8", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table", - "pattern": "*.{pgen}" - } - }, - { - "psam": { - "type": "file", - "description": "PLINK 2 sample information file", - "pattern": "*.{psam}" - } - }, - { - "pvar": { - "type": "file", - "description": "PLINK 2 variant information file", - "pattern": "*.{pvar}" - } - }, - { - "scorefile": { - "type": "file", - "description": "A text file containing variant identifiers and weights", - "pattern": "*.{scores,txt,scorefile}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "score": { - "type": "file", - "description": "A text file containing sample scores, in plink 2 .sscore format", - "pattern": "*.{sscore}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table", + "pattern": "*.{pgen}" + } + }, + { + "psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.{psam}" + } + }, + { + "pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.{pvar}" + } + } + ], + [ + { + "scorefile": { + "type": "file", + "description": "A text file containing variant identifiers and weights", + "pattern": "*.{scores,txt,scorefile}" + } + } + ] + ], + "output": [ + { + "score": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sscore": { + "type": "file", + "description": "A text file containing sample scores, in plink 2 .sscore format", + "pattern": "*.{sscore}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -103398,66 +131241,107 @@ "documentation": "http://www.cog-genomics.org/plink/2.0/general_usage", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}, *.{vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pgen": { - "type": "file", - "description": "PLINK 2 binary genotype table", - "pattern": "*.{pgen}" - } - }, - { - "psam": { - "type": "file", - "description": "PLINK 2 sample information file", - "pattern": "*.{psam}" - } - }, - { - "pvar": { - "type": "file", - "description": "PLINK 2 variant information file", - "pattern": "*.{pvar.zst}" - } - }, - { - "pvar_zst": { - "type": "file", - "description": "PLINK 2 variant information zst file", - "pattern": "*.pvar.zst" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}, *.{vcf.gz}" + } + } + ] + ], + "output": [ + { + "pgen": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pgen": { + "type": "file", + "description": "PLINK 2 binary genotype table", + "pattern": "*.{pgen}" + } + } + ] + }, + { + "psam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.psam": { + "type": "file", + "description": "PLINK 2 sample information file", + "pattern": "*.{psam}" + } + } + ] + }, + { + "pvar": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvar": { + "type": "file", + "description": "PLINK 2 variant information file", + "pattern": "*.{pvar.zst}" + } + } + ] + }, + { + "pvar_zst": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pvar.zst": { + "type": "file", + "description": "PLINK 2 variant information zst file", + "pattern": "*.pvar.zst" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -103491,59 +131375,90 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bcf": { - "type": "file", - "description": "Binary variant call format file (bcf)", - "pattern": "*.{bcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bcf": { + "type": "file", + "description": "Binary variant call format file (bcf)", + "pattern": "*.{bcf}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}" + } + } + ] + }, + { + "bim": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + } + ] + }, + { + "fam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -103575,222 +131490,300 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" + } + }, + { + "bcf": { + "type": "file", + "description": "PLINK variant information + sample ID + genotype call binary file", + "pattern": "*.{bcf}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" + } + }, + { + "phe": { + "type": "file", + "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option.", + "pattern": "*.{phe}" + } + } + ] + ], + "output": [ + { + "epi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.epi.cc": { + "type": "file", + "description": "PLINK epistasis file", + "pattern": "*.{epi.cc}" + } + } + ] + }, + { + "episummary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.epi.cc.summary": { + "type": "file", + "description": "PLINK epistasis summary file", + "pattern": "*.{epi.cc.summary}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "PLINK epistasis log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "nosex": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.nosex": { + "type": "file", + "description": "Ambiguous sex ID file", + "pattern": "*.{nosex}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "bcf": { - "type": "file", - "description": "PLINK variant information + sample ID + genotype call binary file", - "pattern": "*.{bcf}" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}" - } - }, - { - "phe": { - "type": "file", - "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option.", - "pattern": "*.{phe}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "epi": { - "type": "file", - "description": "PLINK epistasis file", - "pattern": "*.{epi.cc}" - } - }, - { - "episummary": { - "type": "file", - "description": "PLINK epistasis summary file", - "pattern": "*.{epi.cc.summary}" - } - }, - { - "log": { - "type": "file", - "description": "PLINK epistasis log file", - "pattern": "*.{log}" - } - }, - { - "nosex": { - "type": "file", - "description": "Ambiguous sex ID file", - "pattern": "*.{nosex}" - } - } - ], - "authors": [ - "@davidebag" - ], - "maintainers": [ - "@davidebag" - ] - } - }, - { - "name": "plink_exclude", - "path": "modules/nf-core/plink/exclude/meta.yml", - "type": "module", - "meta": { - "name": "plink_exclude", - "description": "Exclude variant identifiers from plink bfiles", - "keywords": [ - "exclude", - "plink", - "variant identifiers" - ], - "tools": [ + "authors": [ + "@davidebag" + ], + "maintainers": [ + "@davidebag" + ] + } + }, + { + "name": "plink_exclude", + "path": "modules/nf-core/plink/exclude/meta.yml", + "type": "module", + "meta": { + "name": "plink_exclude", + "description": "Exclude variant identifiers from plink bfiles", + "keywords": [ + "exclude", + "plink", + "variant identifiers" + ], + "tools": [ { "plink": { "description": "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", "homepage": "https://www.cog-genomics.org/plink", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "variants": { - "type": "file", - "description": "A text file containing variant identifiers to remove (one per line)", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + }, + { + "variants": { + "type": "file", + "description": "A text file containing variant identifiers to remove (one per line)", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + } + ] + }, + { + "bim": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + } + ] + }, + { + "fam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -103821,80 +131814,111 @@ "homepage": "https://www.cog-genomics.org/plink", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "variants": { - "type": "file", - "description": "A text file containing variant identifiers to keep (one per line)", - "pattern": "*.{keep}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + }, + { + "variants": { + "type": "file", + "description": "A text file containing variant identifiers to keep (one per line)", + "pattern": "*.{keep}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}" + } + } + ] + }, + { + "bim": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + } + ] + }, + { + "fam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -103926,119 +131950,166 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "bcf": { - "type": "file", - "description": "PLINK variant information + sample ID + genotype call binary file", - "pattern": "*.{bcf}" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}" - } - }, - { - "phe": { - "type": "file", - "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option.", - "pattern": "*.{phe}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fepi": { - "type": "file", - "description": "PLINK fast-epistasis file", - "pattern": "*.{epi.cc}" - } - }, - { - "fepisummary": { - "type": "file", - "description": "PLINK fast-epistasis summary file", - "pattern": "*.{epi.cc.summary}" - } - }, - { - "flog": { - "type": "file", - "description": "PLINK fast-epistasis log file", - "pattern": "*.{log}" - } - }, - { - "fnosex": { - "type": "file", - "description": "Ambiguous sex ID file", - "pattern": "*.{nosex}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" + } + }, + { + "bcf": { + "type": "file", + "description": "PLINK variant information + sample ID + genotype call binary file", + "pattern": "*.{bcf}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" + } + }, + { + "phe": { + "type": "file", + "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option.", + "pattern": "*.{phe}" + } + } + ] + ], + "output": [ + { + "fepi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.epi.cc": { + "type": "file", + "description": "PLINK fast-epistasis file", + "pattern": "*.{epi.cc}" + } + } + ] + }, + { + "fepisummary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.epi.cc.summary": { + "type": "file", + "description": "PLINK fast-epistasis summary file", + "pattern": "*.{epi.cc.summary}" + } + } + ] + }, + { + "flog": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "PLINK fast-epistasis log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "fnosex": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.nosex": { + "type": "file", + "description": "Ambiguous sex ID file", + "pattern": "*.{nosex}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -104070,112 +132141,149 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "bcf": { - "type": "file", - "description": "PLINK variant information + sample ID + genotype call binary file", - "pattern": "*.{bcf}" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}" - } - }, - { - "phe": { - "type": "file", - "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option", - "pattern": "*.{phe}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assoc": { - "type": "file", - "description": "PLINK GWAS association file", - "pattern": "*.{assoc}" - } - }, - { - "log": { - "type": "file", - "description": "PLINK GWAS association log file", - "pattern": "*.{log}" - } - }, - { - "nosex": { - "type": "file", - "description": "PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option --allow-no-sex", - "pattern": "*.{nosex}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to the PLINK native file input\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF file input\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta3 is associated to BCF file input\n" + } + }, + { + "bcf": { + "type": "file", + "description": "PLINK variant information + sample ID + genotype call binary file", + "pattern": "*.{bcf}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information,\ne.g. [ id:'test', single_end:false ]\nmeta4 is associated to phenotype file input\n" + } + }, + { + "phe": { + "type": "file", + "description": "PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option", + "pattern": "*.{phe}" + } + } + ] + ], + "output": [ + { + "assoc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.assoc": { + "type": "file", + "description": "PLINK GWAS association file", + "pattern": "*.{assoc}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "PLINK GWAS association log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "nosex": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.nosex": { + "type": "file", + "description": "PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option --allow-no-sex", + "pattern": "*.{nosex}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -104207,84 +132315,99 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to PLINK native files input\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF files input\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to BCF files input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF format input file", - "pattern": "*.{vcf} | *{vcf.gz}" - } - }, - { - "bcf": { - "type": "file", - "description": "BCF format input file", - "pattern": "*.{bcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "hwe": { - "type": "file", - "description": "Summary file containing observed vs expected heterozygous frequencies and the\np-value of the hardy-weinberg statistics\n" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to PLINK native files input\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF files input\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF format input file", + "pattern": "*.{vcf} | *{vcf.gz}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to BCF files input\n" + } + }, + { + "bcf": { + "type": "file", + "description": "BCF format input file", + "pattern": "*.{bcf}" + } + } + ] + ], + "output": [ + { + "hwe": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hwe": { + "type": "file", + "description": "Summary file containing observed vs expected heterozygous frequencies and the\np-value of the hardy-weinberg statistics\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -104318,84 +132441,111 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "window_size": { - "type": "string", - "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold." - } - }, - { - "variant_count": { - "type": "string", - "description": "Variant count to shift the window at the end of each step." - } - }, - { - "variance_inflation_factor": { - "type": "string", - "description": "Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "prunein": { - "type": "file", - "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", - "pattern": "*.{prune.in}" - } - }, - { - "pruneout": { - "type": "file", - "description": "File with IDs of excluded variants", - "pattern": "*.{prune.out}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ], + [ + { + "window_size": { + "type": "string", + "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold." + } + } + ], + [ + { + "variant_count": { + "type": "string", + "description": "Variant count to shift the window at the end of each step." + } + } + ], + [ + { + "variance_inflation_factor": { + "type": "string", + "description": "Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed." + } + } + ] + ], + "output": [ + { + "prunein": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.in": { + "type": "file", + "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", + "pattern": "*.{prune.in}" + } + } + ] + }, + { + "pruneout": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.out": { + "type": "file", + "description": "File with IDs of excluded variants", + "pattern": "*.{prune.out}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -104429,84 +132579,111 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "window_size": { - "type": "string", - "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold." - } - }, - { - "variant_count": { - "type": "string", - "description": "Variant count to shift the window at the end of each step." - } - }, - { - "r2_threshold": { - "type": "string", - "description": "Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "prunein": { - "type": "file", - "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", - "pattern": "*.{prune.in}" - } - }, - { - "pruneout": { - "type": "file", - "description": "File with IDs of excluded variants", - "pattern": "*.{prune.out}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ], + [ + { + "window_size": { + "type": "string", + "description": "Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold." + } + } + ], + [ + { + "variant_count": { + "type": "string", + "description": "Variant count to shift the window at the end of each step." + } + } + ], + [ + { + "r2_threshold": { + "type": "string", + "description": "Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain" + } + } + ] + ], + "output": [ + { + "prunein": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.in": { + "type": "file", + "description": "File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other", + "pattern": "*.{prune.in}" + } + } + ] + }, + { + "pruneout": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.prune.out": { + "type": "file", + "description": "File with IDs of excluded variants", + "pattern": "*.{prune.out}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -104538,109 +132715,146 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to PLINK native files input\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF files input\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to BCF files input\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to randomly selected snp files input\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF format input file", - "pattern": "*.{vcf} | *{vcf.gz}" - } - }, - { - "bcf": { - "type": "file", - "description": "BCF format input file", - "pattern": "*.{bcf}" - } - }, - { - "snpfile": { - "type": "file", - "description": "randomly selected snp identifiers, used to calculate linkage disequilibrium", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "ld": { - "type": "file", - "description": "The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R².\n" - } - }, - { - "log": { - "type": "file", - "description": "Log file of the ld process\n" - } - }, - { - "nosex": { - "type": "file", - "description": "Ambiguous sex ID file\n" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to PLINK native files input\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta2 is associated to VCF files input\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF format input file", + "pattern": "*.{vcf} | *{vcf.gz}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to BCF files input\n" + } + }, + { + "bcf": { + "type": "file", + "description": "BCF format input file", + "pattern": "*.{bcf}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\nmeta is associated to randomly selected snp files input\n" + } + }, + { + "snpfile": { + "type": "file", + "description": "randomly selected snp identifiers, used to calculate linkage disequilibrium", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "ld": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.ld": { + "type": "file", + "description": "The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R².\n" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of the ld process\n" + } + } + ] + }, + { + "nosex": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.nosex": { + "type": "file", + "description": "Ambiguous sex ID file\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -104673,220 +132887,461 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table file", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "ped": { - "type": "file", - "description": "PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default \"--recode\" or by \"--recode 12\".", - "pattern": "*.{ped}" - } - }, - { - "map": { - "type": "file", - "description": "PLINK text fileset variant information file. Produced by the default \"--recode\" or by \"--recode 12\".", - "pattern": "*.{map}" - } - }, - { - "txt": { - "type": "file", - "description": "Text file. Produced by \"--recode 23\". Can only be used in a file with only one sample.", - "pattern": "*.{txt}" - } - }, - { - "raw": { - "type": "file", - "description": "Additive + dominant component file. Produced by \"--recode AD\" or \"--recode A\".", - "pattern": "*.{raw}" - } - }, - { - "traw": { - "type": "file", - "description": "Variant-major additive component file. Produced by \"--recode A-transpose\".", - "pattern": "*.{traw}" - } - }, - { - "beagle-dat": { - "type": "file", - "description": "Single BEAGLE unphased genotype file. Produced by \"--recode beagle\" in 'beagle-nomap' mode.", - "pattern": "*.{beagle.dat}" - } - }, - { - "chr-dat": { - "type": "file", - "description": "BEAGLE unphased genotype and variant information files. Produced by \"--recode beagle\".", - "pattern": "*.{*.chr-*.dat}" - } - }, - { - "chr-map": { - "type": "file", - "description": "BEAGLE variant information files. Produced by \"--recode beagle\".", - "pattern": "*.{*chr-*.map}" - } - }, - { - "geno": { - "type": "file", - "description": "BIMBAM genotype file. Produced by \"--recode bimbam\".", - "pattern": "*.{recode.geno.txt}" - } - }, - { - "pheno": { - "type": "file", - "description": "BIMBAM phenotype file. Produced by \"--recode bimbam\".", - "pattern": "*.{recode.pheno.txt}" - } - }, - { - "pos": { - "type": "file", - "description": "BIMBAM variant position file. Produced by \"--recode bimbam\".", - "pattern": "*.{recode.pos.txt}" - } - }, - { - "phase": { - "type": "file", - "description": "fastPHASE format. Produced by \"--recode fastphase\".", - "pattern": "*.{recode.phase.inp}" - } - }, - { - "info": { - "type": "file", - "description": "Haploview map file. Produced by \"--recode HV\".", - "pattern": "*.{info}" - } - }, - { - "lgen": { - "type": "file", - "description": "PLINK long-format genotype file. Produced by \"--recode lgen\".", - "pattern": "*.{lgen}" - } - }, - { - "list": { - "type": "file", - "description": "Genotype list file. Produced by \"--recode list\".", - "pattern": "*.{list}" - } - }, - { - "gen": { - "type": "file", - "description": "Oxford genotype file format. Produced by \"--recode oxford\".", - "pattern": "*.{gen}" - } - }, - { - "genz": { - "type": "file", - "description": "Compressed Oxford genotype file format. Produced by \"--recode oxford gen-gz\".", - "pattern": "*.{genz}" - } - }, - { - "sample": { - "type": "file", - "description": "Oxford sample information file. Produced by \"--recode oxford\".", - "pattern": "*.{sample}" - } - }, - { - "rlist": { - "type": "file", - "description": "Rare genotype list file. Produced by \"--recode rlist\".", - "pattern": "*.{rlist}" - } - }, - { - "strctin": { - "type": "file", - "description": "Structure-format file. Produced by \"--recode structure\".", - "pattern": "*.{strct_in}" - } - }, - { - "tped": { - "type": "file", - "description": "Transposed text PED file. Produced by \"--recode transpose\".", - "pattern": "*.{tped}" - } - }, - { - "tfam": { - "type": "file", - "description": "Transposed text FAM file. Produced by \"--recode transpose\".", - "pattern": "*.{tfam}" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (VCF). Produced by \"--recode vcf\".", - "pattern": "*.{vcf}" - } - }, - { - "vcfgz": { - "type": "file", - "description": "Compressed variant calling file (VCF). Produced by \"--recode vcf bgz\".", - "pattern": "*.{vcf.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table file", + "pattern": "*.{bed}" + } + }, + { + "bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + }, + { + "fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ] + ], + "output": [ + { + "ped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ped": { + "type": "file", + "description": "PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default \"--recode\" or by \"--recode 12\".", + "pattern": "*.{ped}" + } + } + ] + }, + { + "map": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.map": { + "type": "file", + "description": "PLINK text fileset variant information file. Produced by the default \"--recode\" or by \"--recode 12\".", + "pattern": "*.{map}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Text file. Produced by \"--recode 23\". Can only be used in a file with only one sample.", + "pattern": "*.{txt}" + } + } + ] + }, + { + "raw": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.raw": { + "type": "file", + "description": "Additive + dominant component file. Produced by \"--recode AD\" or \"--recode A\".", + "pattern": "*.{raw}" + } + } + ] + }, + { + "traw": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.traw": { + "type": "file", + "description": "Variant-major additive component file. Produced by \"--recode A-transpose\".", + "pattern": "*.{traw}" + } + } + ] + }, + { + "beagledat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.beagle.dat": { + "type": "file", + "description": "BEAGLE file", + "pattern": "*.{beagle.dat}" + } + } + ] + }, + { + "chrdat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.chr-*.dat": { + "type": "file", + "description": "chr file", + "pattern": "*.{chr-*.dat}" + } + } + ] + }, + { + "chrmap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + ".*chr-*.map": { + "type": "file", + "description": "chr map file", + "pattern": "*.{chr-*.map}" + } + } + ] + }, + { + "geno": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.geno.txt": { + "type": "file", + "description": "BIMBAM genotype file. Produced by \"--recode bimbam\".", + "pattern": "*.{recode.geno.txt}" + } + } + ] + }, + { + "pheno": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.pheno.txt": { + "type": "file", + "description": "BIMBAM phenotype file. Produced by \"--recode bimbam\".", + "pattern": "*.{recode.pheno.txt}" + } + } + ] + }, + { + "pos": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.pos.txt": { + "type": "file", + "description": "BIMBAM variant position file. Produced by \"--recode bimbam\".", + "pattern": "*.{recode.pos.txt}" + } + } + ] + }, + { + "phase": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.recode.phase.inp": { + "type": "file", + "description": "fastPHASE format. Produced by \"--recode fastphase\".", + "pattern": "*.{recode.phase.inp}" + } + } + ] + }, + { + "info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.info": { + "type": "file", + "description": "Haploview map file. Produced by \"--recode HV\".", + "pattern": "*.{info}" + } + } + ] + }, + { + "lgen": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lgen": { + "type": "file", + "description": "PLINK long-format genotype file. Produced by \"--recode lgen\".", + "pattern": "*.{lgen}" + } + } + ] + }, + { + "list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list": { + "type": "file", + "description": "Genotype list file. Produced by \"--recode list\".", + "pattern": "*.{list}" + } + } + ] + }, + { + "gen": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gen": { + "type": "file", + "description": "Oxford genotype file format. Produced by \"--recode oxford\".", + "pattern": "*.{gen}" + } + } + ] + }, + { + "gengz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gen.gz": { + "type": "file", + "description": "Compressed Oxford genotype file format", + "pattern": "*.{gen.gz}" + } + } + ] + }, + { + "sample": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sample": { + "type": "file", + "description": "Oxford sample information file. Produced by \"--recode oxford\".", + "pattern": "*.{sample}" + } + } + ] + }, + { + "rlist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.rlist": { + "type": "file", + "description": "Rare genotype list file. Produced by \"--recode rlist\".", + "pattern": "*.{rlist}" + } + } + ] + }, + { + "strctin": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.strct_in": { + "type": "file", + "description": "Structure-format file. Produced by \"--recode structure\".", + "pattern": "*.{strct_in}" + } + } + ] + }, + { + "tped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tped": { + "type": "file", + "description": "Transposed text PED file. Produced by \"--recode transpose\".", + "pattern": "*.{tped}" + } + } + ] + }, + { + "tfam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tfam": { + "type": "file", + "description": "Transposed text FAM file. Produced by \"--recode transpose\".", + "pattern": "*.{tfam}" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Variant calling file (VCF). Produced by \"--recode vcf\".", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "vcfgz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed variant calling file (VCF). Produced by \"--recode vcf bgz\".", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -104918,59 +133373,90 @@ "tool_dev_url": "https://www.cog-genomics.org/plink/1.9/dev", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant calling file (vcf)", - "pattern": "*.{vcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "PLINK binary biallelic genotype table", - "pattern": "*.{bed}" - } - }, - { - "bim": { - "type": "file", - "description": "PLINK extended MAP file", - "pattern": "*.{bim}" - } - }, - { - "fam": { - "type": "file", - "description": "PLINK sample information file", - "pattern": "*.{fam}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Variant calling file (vcf)", + "pattern": "*.{vcf}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "PLINK binary biallelic genotype table", + "pattern": "*.{bed}" + } + } + ] + }, + { + "bim": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bim": { + "type": "file", + "description": "PLINK extended MAP file", + "pattern": "*.{bim}" + } + } + ] + }, + { + "fam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fam": { + "type": "file", + "description": "PLINK sample information file", + "pattern": "*.{fam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105006,65 +133492,80 @@ "doi": "10.1073/pnas.1318934111", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "threshold": { - "type": "float", - "description": "Post-mortem damage score threshold" - } - }, - { - "reference": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Filtered BAM file", - "pattern": "*.bam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ], + [ + { + "threshold": { + "type": "float", + "description": "Post-mortem damage score threshold" + } + } + ], + [ + { + "reference": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Filtered BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105097,52 +133598,73 @@ "doi": "10.7717/peerj.2477", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input Illunina paired-end FASTQ files", - "pattern": "*.{fq.gz,fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "xml": { - "type": "file", - "description": "The predicted serotype in XML format", - "pattern": "*.xml" - } - }, - { - "txt": { - "type": "file", - "description": "A detailed description of the predicted serotype", - "pattern": "*.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input Illunina paired-end FASTQ files", + "pattern": "*.{fq.gz,fastq.gz}" + } + } + ] + ], + "output": [ + { + "xml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.xml": { + "type": "file", + "description": "The predicted serotype in XML format", + "pattern": "*.xml" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "A detailed description of the predicted serotype", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105174,85 +133696,126 @@ "licence": [ "Apache-2.0" ], - "args_id": "$args" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "mpileup": { - "type": "file", - "description": "MPILEUP file. This file contains the base calls and alignment information\nfor each position in the reference genome.\nIt is used as input for variant calling and other downstream analyses.\n", - "pattern": "*.mpileup" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "reference": { - "type": "file", - "description": "Reference genome in FASTA format.\nMay NOT contain any special characters such as \"/|,:\"\n", - "pattern": "*.{fasta,fa}" - } - }, - { - "max_cov": { - "type": "float", - "description": "Maximum coverage is calculated for every library and chromosomal arm\nas the percentile of a coverage distribution,\ne.g. max-cov=0.98 will only consider positions within the 98% coverage percentile\nfor a given sample and chromosomal arm.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n" - } - }, - { - "max_cov_file": { - "type": "file", - "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries.\nThis file needs to be tab-delimited with two columns:\n1. Chromosomal name\n2. Comma-separated list of coverage thresholds for each sample in the mpileup file.\ne.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples\nand 200 for the last two samples on chromosomal arm 2L.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Gzipped VCF file containing allele counts and frequencies for every position and library", - "pattern": "*.vcf.gz" - } - }, - { - "max_cov": { - "type": "file", - "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries", - "pattern": "*cov-*.txt" - } - }, - { - "bad_sites": { - "type": "file", - "description": "File containing a list of sites (variable and invariable) that did not pass the SNP calling criteria", - "pattern": "*BS.txt.gz", - "optional": true - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "args_id": "$args", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "mpileup": { + "type": "file", + "description": "MPILEUP file. This file contains the base calls and alignment information\nfor each position in the reference genome.\nIt is used as input for variant calling and other downstream analyses.\n", + "pattern": "*.mpileup" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference genome in FASTA format.\nMay NOT contain any special characters such as \"/|,:\"\n", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "max_cov": { + "type": "float", + "description": "Maximum coverage is calculated for every library and chromosomal arm\nas the percentile of a coverage distribution,\ne.g. max-cov=0.98 will only consider positions within the 98% coverage percentile\nfor a given sample and chromosomal arm.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n" + } + }, + { + "max_cov_file": { + "type": "file", + "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries.\nThis file needs to be tab-delimited with two columns:\n1. Chromosomal name\n2. Comma-separated list of coverage thresholds for each sample in the mpileup file.\ne.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples\nand 200 for the last two samples on chromosomal arm 2L.\nNote: Provide `max_cov` or `max_cov_file` but not both.\nRead more: https://github.com/capoony/PoolSNP\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing allele counts and frequencies for every position and library", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "max_cov": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*cov-*.txt": { + "type": "file", + "description": "File containing the maximum coverage thresholds for all chromosomal arms and libraries", + "pattern": "*cov-*.txt" + } + } + ] + }, + { + "bad_sites": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*BS.txt.gz": { + "type": "file", + "description": "File containing a list of sites (variable and invariable) that did not pass the SNP calling criteria", + "pattern": "*BS.txt.gz", + "optional": true + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105286,58 +133849,69 @@ "doi": "10.1038/nbt.4042", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "plp_prefix": { - "type": "string", - "description": "Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." - } - }, - { - "bam": { - "type": "file", - "description": "Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must be sorted by coordinates and indexed.", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "donor_genotype": { - "type": "file", - "description": "Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file.", - "pattern": "*.{vcf,bcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "demuxlet_result": { - "type": "file", - "description": "Result of demuxlet containing the best guess of the sample identity, with detailed statistics to reach to the best guess.", - "pattern": "*.best" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "plp_prefix": { + "type": "string", + "description": "Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." + } + }, + { + "bam": { + "type": "file", + "description": "Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must be sorted by coordinates and indexed.", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "donor_genotype": { + "type": "file", + "description": "Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file.", + "pattern": "*.{vcf,bcf}" + } + } + ] + ], + "output": [ + { + "demuxlet_result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.best": { + "type": "file", + "description": "Result of demuxlet containing the best guess of the sample identity, with detailed statistics to reach to the best guess.", + "pattern": "*.best" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105378,73 +133952,114 @@ "doi": "10.1038/nbt.4042", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq.", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g).", - "pattern": "*.{vcf,bcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cel": { - "type": "file", - "description": "Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet.", - "pattern": "*.cel.gz" - } - }, - { - "plp": { - "type": "file", - "description": "Contains the overlapping SNP and the corresponding read and base quality for each barcode ID.", - "pattern": "*.plp.gz" - } - }, - { - "var": { - "type": "file", - "description": "Contains the position, reference allele and allele frequency for each SNP.", - "pattern": "*.var.gz" - } - }, - { - "umi": { - "type": "file", - "description": "Contains the position covered by each umi.", - "pattern": "*.umi.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq.", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g).", + "pattern": "*.{vcf,bcf}" + } + } + ] + ], + "output": [ + { + "cel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.cel.gz": { + "type": "file", + "description": "Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet.", + "pattern": "*.cel.gz" + } + } + ] + }, + { + "plp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.plp.gz": { + "type": "file", + "description": "Contains the overlapping SNP and the corresponding read and base quality for each barcode ID.", + "pattern": "*.plp.gz" + } + } + ] + }, + { + "var": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.var.gz": { + "type": "file", + "description": "Contains the position, reference allele and allele frequency for each SNP.", + "pattern": "*.var.gz" + } + } + ] + }, + { + "umi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "*.umi.gz": { + "type": "file", + "description": "Contains the position covered by each umi.", + "pattern": "*.umi.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105484,78 +134099,129 @@ "doi": "10.1038/nbt.4042", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "plp": { - "type": "directory", - "description": "Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." - } - }, - { - "n_sample": { - "type": "integer", - "description": "Number of samples multiplexed together." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "result": { - "type": "file", - "description": "Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.", - "pattern": "*.clust1.samples.gz" - } - }, - { - "vcf": { - "type": "file", - "description": "Output vcf file for each sample inferred and clustered from freemuxlet.", - "pattern": "*.clust1.vcf.gz" - } - }, - { - "lmix": { - "type": "file", - "description": "Output file contains basic statistics for each barcode.", - "pattern": "*.lmix" - } - }, - { - "singlet_result": { - "type": "file", - "description": "Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.", - "pattern": "*.clust0.samples.gz" - } - }, - { - "singlet_vcf": { - "type": "file", - "description": "Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.", - "pattern": "*.clust0.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "plp": { + "type": "directory", + "description": "Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup." + } + }, + { + "n_sample": { + "type": "integer", + "description": "Number of samples multiplexed together." + } + } + ] + ], + "output": [ + { + "result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust1.samples.gz": { + "type": "file", + "description": "Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.", + "pattern": "*.clust1.samples.gz" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust1.vcf.gz": { + "type": "file", + "description": "Output vcf file for each sample inferred and clustered from freemuxlet.", + "pattern": "*.clust1.vcf.gz" + } + } + ] + }, + { + "lmix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.lmix": { + "type": "file", + "description": "Output file contains basic statistics for each barcode.", + "pattern": "*.lmix" + } + } + ] + }, + { + "singlet_result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust0.samples.gz": { + "type": "file", + "description": "Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.", + "pattern": "*.clust0.samples.gz" + } + } + ] + }, + { + "singlet_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.clust0.vcf.gz": { + "type": "file", + "description": "Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.", + "pattern": "*.clust0.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105588,52 +134254,73 @@ "doi": "10.1101/2022.07.07.499093", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq/fastq.gz file", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Adapter-trimmed fastq.gz file", - "pattern": "*.fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing stdout information", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq/fastq.gz file", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Adapter-trimmed fastq.gz file", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stdout information", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105668,52 +134355,73 @@ "doi": "10.1099/mgen.0.000132", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq/fastq.gz file", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Demultiplexed and/or adapter-trimmed fastq.gz file", - "pattern": "*.{fastq.gz}" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing stdout information", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq/fastq.gz file", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Demultiplexed and/or adapter-trimmed fastq.gz file", + "pattern": "*.{fastq.gz}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stdout information", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105775,52 +134483,73 @@ "tool_dev_url": "https://github.com/smithlabcode/preseq", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "ccurve": { - "type": "file", - "description": "File containing output of Preseq c curve", - "pattern": "*.{c_curve.txt}" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing stderr produced by Preseq", - "pattern": "*.{log}" - } + ], + "identifier": "biotools:preseq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "c_curve": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.c_curve.txt": { + "type": "file", + "description": "Preseq c_curve output file", + "pattern": "*.{c_curve.txt}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stderr produced by Preseq", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105864,52 +134593,73 @@ "tool_dev_url": "https://github.com/smithlabcode/preseq", "licence": [ "GPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "lc_extrap": { - "type": "file", - "description": "File containing output of Preseq lcextrap", - "pattern": "*.{lc_extrap.txt}" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing stderr produced by Preseq", - "pattern": "*.{log}" - } + ], + "identifier": "biotools:preseq" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "lc_extrap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lc_extrap.txt": { + "type": "file", + "description": "File containing output of Preseq lcextrap", + "pattern": "*.{lc_extrap.txt}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file containing stderr produced by Preseq", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -105970,79 +134720,148 @@ "tool_dev_url": "https://github.com/rki-mf1/president", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information, e.g. [ id:'test', single_end:false ]" - } - }, - { - "fasta": { - "type": "file", - "description": "One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed!", - "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about the reference genome" - } - }, - { - "reference": { - "type": "file", - "description": "Fasta of a reference genome. Has to be uncompressed!", - "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Set to \"true\" if fasta output should be compressed" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "valid_fasta": { - "type": "file", - "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", - "pattern": "*.{fasta.gz, fasta}" - } - }, - { - "invalid_fasta": { - "type": "file", - "description": "Fasta file containing sequences which didn't pass the qc (\"invalid.fasta\"). If true is set on the \"compress\" input value, the files are gz-compressed.", - "pattern": "*_invalid.{fasta.gz, fasta}" - } - }, - { - "report": { - "type": "file", - "description": "Report with some information for every sample, like statistic values. See docs for details", - "pattern": "*.tsv" - } - }, - { - "log": { - "type": "file", - "description": "Log file of president", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information, e.g. [ id:'test', single_end:false ]" + } + }, + { + "fasta": { + "type": "file", + "description": "One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed!", + "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about the reference genome" + } + }, + { + "reference": { + "type": "file", + "description": "Fasta of a reference genome. Has to be uncompressed!", + "pattern": "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Set to \"true\" if fasta output should be compressed" + } + } + ] + ], + "output": [ + { + "valid_fasta": [ + { + "meta": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}" + } + }, + { + "${prefix}_valid.fasta*": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}" + } + }, + { + "id_fasta": { + "type": "file", + "description": "Fasta file containing sequences which passed the qc (\"valid.fasta\"). If true is set on the \"compress\" input value, the file is gz-compressed.", + "pattern": "*.{fasta.gz, fasta}" + } + } + ] + }, + { + "invalid_fasta": [ + { + "meta": { + "type": "file", + "description": "Fasta file containing sequences which didn't pass the qc (\"invalid.fasta\"). If true is set on the \"compress\" input value, the files are gz-compressed.", + "pattern": "*_invalid.{fasta.gz, fasta}" + } + }, + { + "${prefix}_invalid.fasta*": { + "type": "file", + "description": "Fasta file containing sequences which didn't pass the qc (\"invalid.fasta\"). If true is set on the \"compress\" input value, the files are gz-compressed.", + "pattern": "*_invalid.{fasta.gz, fasta}" + } + }, + { + "id_fasta": { + "type": "file", + "description": "Fasta file containing sequences which didn't pass the qc (\"invalid.fasta\"). If true is set on the \"compress\" input value, the files are gz-compressed.", + "pattern": "*_invalid.{fasta.gz, fasta}" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "file", + "description": "Report with some information for every sample, like statistic values. See docs for details", + "pattern": "*.tsv" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Report with some information for every sample, like statistic values. See docs for details", + "pattern": "*.tsv" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log file of president", + "pattern": "*.log" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of president", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106077,59 +134896,78 @@ "doi": "10.1093/bioinformatics/btu138", "licence": [ "AGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq file", - "pattern": "*.{fastq}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "filtered fastq file", - "pattern": "*.{fastq}" - } - }, - { - "logs": { - "type": "file", - "description": "command logs", - "pattern": "*.txt" - } - }, - { - "log_tab": { - "type": "file", - "description": "parsed log table", - "pattern": "*.tab" - } + ], + "identifier": "biotools:presto-measure" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq file", + "pattern": "*.{fastq}" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*_quality-pass.fastq": { + "type": "file", + "description": "filtered fastq file", + "pattern": "*.{fastq}" + } + } + ] + }, + { + "logs": [ + { + "*_command_log.txt": { + "type": "file", + "description": "command logs", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "log_tab": [ + { + "*.tab": { + "type": "file", + "description": "parsed log table", + "pattern": "*.tab" + } + } + ] } ], "authors": [ @@ -106157,65 +134995,78 @@ "documentation": "https://github.com/wtsi-hpag/PretextMap/blob/master/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file or pairs formatted reads file", - "pattern": "*.{bam,cram,sam,pairs.gz}" - } - }, - { - "input": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test2', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "input": { - "type": "file", - "description": "Fasta index", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pretext": { - "type": "file", - "description": "pretext map", - "pattern": "*.pretext" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file or pairs formatted reads file", + "pattern": "*.{bam,cram,sam,pairs.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference sequence file", + "pattern": "*.{fasta,fna,fa}" + } + }, + { + "fai": { + "type": "file", + "description": "Reference sequence index file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "pretext": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pretext": { + "type": "file", + "description": "pretext map", + "pattern": "*.pretext" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106252,45 +135103,56 @@ "tool_dev_url": "https://github.com/wtsi-hpag/PretextSnapshot", "licence": [ "https://github.com/wtsi-hpag/PretextSnapshot/blob/master/LICENSE" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "pretext_map": { - "type": "file", - "description": "pretext hic map", - "pattern": "*.pretext" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pretext_map": { + "type": "file", + "description": "pretext hic map", + "pattern": "*.pretext" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "image": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{jpeg,png,bmp}": { + "type": "file", + "description": "image of a hic contact map", + "pattern": "*.{png,jpg,bmp}" + } + } + ] }, { - "image": { - "type": "file", - "description": "image of a hic contact map", - "pattern": "*.{png,jpg,bmp}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106324,65 +135186,106 @@ "doi": "10.7287/peerj.preprints.27553v1", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end\ndata, respectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "good_reads": { - "type": "file", - "description": "Reads passing filter(s) in gzipped FASTQ format", - "pattern": "*_good_out_{R1,R2}.fastq.gz" - } - }, - { - "single_reads": { - "type": "file", - "description": "Single reads without the pair passing filter(s) in gzipped FASTQ format\n", - "pattern": "*_single_out_{R1,R2}.fastq.gz" - } - }, - { - "bad_reads": { - "type": "file", - "description": "Reads without not passing filter(s) in gzipped FASTQ format\n", - "pattern": "*_bad_out_{R1,R2}.fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "Verbose level 2 STDOUT information in a log file\n", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end\ndata, respectively.\n" + } + } + ] + ], + "output": [ + { + "good_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_good_out*.fastq.gz": { + "type": "file", + "description": "Reads passing filter(s) in gzipped FASTQ format", + "pattern": "*_good_out_{R1,R2}.fastq.gz" + } + } + ] + }, + { + "single_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_single_out*.fastq.gz": { + "type": "file", + "description": "Single reads without the pair passing filter(s) in gzipped FASTQ format\n", + "pattern": "*_single_out_{R1,R2}.fastq.gz" + } + } + ] + }, + { + "bad_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_bad_out*.fastq.gz": { + "type": "file", + "description": "Reads without not passing filter(s) in gzipped FASTQ format\n", + "pattern": "*_bad_out_{R1,R2}.fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Verbose level 2 STDOUT information in a log file\n", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106421,71 +135324,114 @@ "doi": "10.1186/1471-2105-11-119", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genome": { - "type": "file", - "description": "fasta/fasta.gz file" - } - }, - { - "output_format": { - "type": "string", - "description": "Output format (\"gbk\"/\"gff\"/\"sqn\"/\"sco\")" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "nucleotide_fasta": { - "type": "file", - "description": "nucleotide sequences file", - "pattern": "*.{fna}" - } - }, - { - "amino_acid_fasta": { - "type": "file", - "description": "protein translations file", - "pattern": "*.{faa}" - } - }, - { - "all_gene_annotations": { - "type": "file", - "description": "complete starts file", - "pattern": "*.{_all.txt}" - } - }, - { - "gene_annotations": { - "type": "file", - "description": "gene annotations in output_format given as input", - "pattern": "*.{output_format}" - } + ], + "identifier": "biotools:prodigal" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genome": { + "type": "file", + "description": "fasta/fasta.gz file" + } + } + ], + [ + { + "output_format": { + "type": "string", + "description": "Output format (\"gbk\"/\"gff\"/\"sqn\"/\"sco\")" + } + } + ] + ], + "output": [ + { + "gene_annotations": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${output_format}.gz": { + "type": "file", + "description": "gene annotations in output_format given as input", + "pattern": "*.{output_format}" + } + } + ] + }, + { + "nucleotide_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.fna.gz": { + "type": "file", + "description": "nucleotide sequences file", + "pattern": "*.{fna}" + } + } + ] + }, + { + "amino_acid_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.faa.gz": { + "type": "file", + "description": "protein translations file", + "pattern": "*.{faa}" + } + } + ] + }, + { + "all_gene_annotations": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}_all.txt.gz": { + "type": "file", + "description": "complete starts file", + "pattern": "*.{_all.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106534,133 +135480,258 @@ "doi": "10.1093/bioinformatics/btu153", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file to be annotated. Has to contain at least a non-empty string dummy value.\n" - } - }, - { - "proteins": { - "type": "file", - "description": "FASTA file of trusted proteins to first annotate from (optional)" - } - }, - { - "prodigal_tf": { - "type": "file", - "description": "Training file to use for Prodigal (optional)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gff": { - "type": "file", - "description": "annotation in GFF3 format, containing both sequences and annotations", - "pattern": "*.{gff}" - } - }, - { - "gbk": { - "type": "file", - "description": "annotation in GenBank format, containing both sequences and annotations", - "pattern": "*.{gbk}" - } - }, - { - "fna": { - "type": "file", - "description": "nucleotide FASTA file of the input contig sequences", - "pattern": "*.{fna}" - } - }, - { - "faa": { - "type": "file", - "description": "protein FASTA file of the translated CDS sequences", - "pattern": "*.{faa}" - } - }, - { - "ffn": { - "type": "file", - "description": "nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)", - "pattern": "*.{ffn}" - } - }, - { - "sqn": { - "type": "file", - "description": "an ASN1 format \"Sequin\" file for submission to Genbank", - "pattern": "*.{sqn}" - } - }, - { - "fsa": { - "type": "file", - "description": "nucleotide FASTA file of the input contig sequences, used by \"tbl2asn\" to create the .sqn file", - "pattern": "*.{fsa}" - } - }, - { - "tbl": { - "type": "file", - "description": "feature Table file, used by \"tbl2asn\" to create the .sqn file", - "pattern": "*.{tbl}" - } - }, - { - "err": { - "type": "file", - "description": "unacceptable annotations - the NCBI discrepancy report.", - "pattern": "*.{err}" - } - }, - { - "log": { - "type": "file", - "description": "contains all the output that Prokka produced during its run", - "pattern": "*.{log}" - } - }, - { - "txt": { - "type": "file", - "description": "statistics relating to the annotated features found", - "pattern": "*.{txt}" - } - }, - { - "tsv": { - "type": "file", - "description": "tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)", - "pattern": "*.{tsv}" - } + ], + "identifier": "biotools:prokka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file to be annotated. Has to contain at least a non-empty string dummy value.\n" + } + } + ], + [ + { + "proteins": { + "type": "file", + "description": "FASTA file of trusted proteins to first annotate from (optional)" + } + } + ], + [ + { + "prodigal_tf": { + "type": "file", + "description": "Training file to use for Prodigal (optional)" + } + } + ] + ], + "output": [ + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.gff": { + "type": "file", + "description": "annotation in GFF3 format, containing both sequences and annotations", + "pattern": "*.{gff}" + } + } + ] + }, + { + "gbk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.gbk": { + "type": "file", + "description": "annotation in GenBank format, containing both sequences and annotations", + "pattern": "*.{gbk}" + } + } + ] + }, + { + "fna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.fna": { + "type": "file", + "description": "nucleotide FASTA file of the input contig sequences", + "pattern": "*.{fna}" + } + } + ] + }, + { + "faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.faa": { + "type": "file", + "description": "protein FASTA file of the translated CDS sequences", + "pattern": "*.{faa}" + } + } + ] + }, + { + "ffn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.ffn": { + "type": "file", + "description": "nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)", + "pattern": "*.{ffn}" + } + } + ] + }, + { + "sqn": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.sqn": { + "type": "file", + "description": "an ASN1 format \"Sequin\" file for submission to Genbank", + "pattern": "*.{sqn}" + } + } + ] + }, + { + "fsa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.fsa": { + "type": "file", + "description": "nucleotide FASTA file of the input contig sequences, used by \"tbl2asn\" to create the .sqn file", + "pattern": "*.{fsa}" + } + } + ] + }, + { + "tbl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.tbl": { + "type": "file", + "description": "feature Table file, used by \"tbl2asn\" to create the .sqn file", + "pattern": "*.{tbl}" + } + } + ] + }, + { + "err": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.err": { + "type": "file", + "description": "unacceptable annotations - the NCBI discrepancy report.", + "pattern": "*.{err}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.log": { + "type": "file", + "description": "contains all the output that Prokka produced during its run", + "pattern": "*.{log}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.txt": { + "type": "file", + "description": "statistics relating to the annotated features found", + "pattern": "*.{txt}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/*.tsv": { + "type": "file", + "description": "tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106718,65 +135789,82 @@ "doi": "10.2202/1544-6115.1175", "licence": [ "GPL-2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the knowledge database\n" - } - }, - { - "adj": { - "type": "file", - "description": "adjacency matrix for gene ratio proportionality/differential proportionality", - "pattern": "*.{csv,tsv}" - } - }, - { - "gmt": { - "type": "file", - "description": "relational database containing genes and GO terms (generated by mygene module)", - "pattern": "*.{gmt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "enrichedGO": { - "type": "file", - "description": "File containing GO terms and their enrichment values", - "pattern": "*.{csv}" - } - }, - { - "session_info": { - "type": "file", - "description": "R session log", - "pattern": "*.R_sessionInfo.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:propr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "adj": { + "type": "file", + "description": "adjacency matrix for gene ratio proportionality/differential proportionality", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the knowledge database\n" + } + }, + { + "gmt": { + "type": "file", + "description": "relational database containing genes and GO terms (generated by mygene module)", + "pattern": "*.{gmt}" + } + } + ] + ], + "output": [ + { + "enrichedGO": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.go.tsv": { + "type": "file", + "description": "File containing GO terms and their enrichment values", + "pattern": "*.{csv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "session_info": [ + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "R session log", + "pattern": "*.R_sessionInfo.log" + } + } + ] } ], "authors": [ @@ -106812,52 +135900,67 @@ "doi": "10.1038/s41598-017-16520-0", "licence": [ "GPL-2" - ] + ], + "identifier": "biotools:propr" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" - } - }, - { - "count": { - "type": "file", - "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be first replaced by the minimun value.\nYou may want to handle the zeros with a different method beforehand.\n", - "pattern": "*.{csv,tsv}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" + } + }, + { + "count": { + "type": "file", + "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be first replaced by the minimun value.\nYou may want to handle the zeros with a different method beforehand.\n", + "pattern": "*.{csv,tsv}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" - } - }, - { - "logratio": { - "type": "file", - "description": "ALR/CLR transformed data matrix. With rows = variables or genes, columns = samples or cells.", - "pattern": "*.logratio.tsv" - } + "logratio": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nmeta.id can be used to name the output files.\n[id: 'test', ...]\n" + } + }, + { + "*.logratio.tsv": { + "type": "file", + "description": "ALR/CLR transformed data matrix. With rows = variables or genes, columns = samples or cells.", + "pattern": "*.logratio.tsv" + } + } + ] }, { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log" - } + "session_info": [ + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -106894,92 +135997,143 @@ "doi": "10.1038/s41598-017-16520-0", "licence": [ "GPL-2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing additional information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "count": { - "type": "file", - "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. One should plug this module after another one that handles the zeros.\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy map containing study-wide metadata related to the sample sheet and matrix\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing additional information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "propd": { - "type": "file", - "description": "R propd object", - "pattern": "*.propd.rds" - } - }, - { - "results": { - "type": "file", - "description": "Results table", - "pattern": "*.propd.tsv" - } - }, - { - "fdr": { - "type": "file", - "description": "(optional) propd fdr table", - "pattern": "*.fdr.tsv" - } - }, - { - "adj": { - "type": "file", - "description": "(optional) propd adj table", - "pattern": "*.adj.csv" - } - }, - { - "warnings": { - "type": "file", - "description": "propd warnings", - "pattern": "*.warnings.txt" - } - }, - { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:propr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "count": { + "type": "file", + "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. One should plug this module after another one that handles the zeros.\n", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing study-wide metadata related to the sample sheet and matrix\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata\n" + } + } + ] + ], + "output": [ + { + "propd": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.propd.rds": { + "type": "file", + "description": "R propd object", + "pattern": "*.propd.rds" + } + } + ] + }, + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.propd.tsv": { + "type": "file", + "description": "Results table", + "pattern": "*.propd.tsv" + } + } + ] + }, + { + "fdr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.fdr.tsv": { + "type": "file", + "description": "(optional) propd fdr table", + "pattern": "*.fdr.tsv" + } + } + ] + }, + { + "adj": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing additional information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.adj.csv": { + "type": "file", + "description": "(optional) propd adj table", + "pattern": "*.adj.csv" + } + } + ] + }, + { + "warnings": [ + { + "*.warnings.log": { + "type": "file", + "description": "propd warnings", + "pattern": "*.warnings.txt" + } + } + ] + }, + { + "session_info": [ + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107015,7 +136169,8 @@ "doi": "10.1038/s41598-017-16520-0", "licence": [ "GPL-2" - ] + ], + "identifier": "biotools:propr" } }, { @@ -107026,80 +136181,129 @@ "doi": "10.2202/1544-6115.1175", "licence": [ "GPL >=3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "count": { - "type": "file", - "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be replaced by the minimun number.\nIt is recommended to handle the zeros beforehand with the method of preference.\n", - "pattern": "*.{csv,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" - } - }, - { - "propr": { - "type": "file", - "description": "R propr object", - "pattern": "*.propr.rds" - } - }, - { - "matrix": { - "type": "file", - "description": "Coefficient matrix", - "pattern": "*.propr.tsv" - } - }, - { - "fdr": { - "type": "file", - "description": "(optional) propr fdr table", - "pattern": "*.fdr.tsv" - } - }, - { - "adj": { - "type": "file", - "description": "(optional) propr adjacency table", - "pattern": "*.adj.csv" - } - }, - { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.R_sessionInfo.log" - } - }, - { - "warnings": { - "type": "file", - "description": "Warnings", - "pattern": "*.warnings.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:propr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "count": { + "type": "file", + "description": "Count matrix, where rows = variables or genes, columns = samples or cells.\nThis matrix should not contain zeros. Otherwise, they will be replaced by the minimun number.\nIt is recommended to handle the zeros beforehand with the method of preference.\n", + "pattern": "*.{csv,tsv}" + } + } + ] + ], + "output": [ + { + "propr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.propr.rds": { + "type": "file", + "description": "R propr object", + "pattern": "*.propr.rds" + } + } + ] + }, + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.propr.tsv": { + "type": "file", + "description": "Coefficient matrix", + "pattern": "*.propr.tsv" + } + } + ] + }, + { + "fdr": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.fdr.tsv": { + "type": "file", + "description": "(optional) propr fdr table", + "pattern": "*.fdr.tsv" + } + } + ] + }, + { + "adj": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nThis can be used at the workflow level to pass optional parameters to the module.\n[id: 'test', ...]\n" + } + }, + { + "*.adj.csv": { + "type": "file", + "description": "(optional) propr adjacency table", + "pattern": "*.adj.csv" + } + } + ] + }, + { + "warnings": [ + { + "*.warnings.log": { + "type": "file", + "description": "Warnings", + "pattern": "*.warnings.log" + } + } + ] + }, + { + "session_info": [ + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.R_sessionInfo.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107133,53 +136337,93 @@ "doi": "10.3389/fbinf.2023.1322477", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta_files": { - "type": "file", - "description": "Input fasta files (proteomes or transcriptomes), at least 2 are needed", - "pattern": "*.{fa,fasta,faa,fna,fn}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "orthologgroups": { - "type": "file", - "description": "Orthology table", - "pattern": "*.proteinortho.tsv" - } - }, - { - "orthologgraph": { - "type": "file", - "description": "Orthology graph", - "pattern": "*.proteinortho-graph" - } - }, - { - "blastgraph": { - "type": "file", - "description": "BLAST graph", - "pattern": "*.blast-graph" - } + ], + "identifier": "biotools:proteinortho" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta_files": { + "type": "file", + "description": "Input fasta files (proteomes or transcriptomes), at least 2 are needed", + "pattern": "*.{fa,fasta,faa,fna,fn}" + } + } + ] + ], + "output": [ + { + "orthologgroups": [ + { + "meta": { + "type": "file", + "description": "Orthology table", + "pattern": "*.proteinortho.tsv" + } + }, + { + "${meta.id}.proteinortho.tsv": { + "type": "file", + "description": "Orthology table", + "pattern": "*.proteinortho.tsv" + } + } + ] + }, + { + "orthologgraph": [ + { + "meta": { + "type": "file", + "description": "Orthology graph", + "pattern": "*.proteinortho-graph" + } + }, + { + "${meta.id}.proteinortho-graph": { + "type": "file", + "description": "Orthology graph", + "pattern": "*.proteinortho-graph" + } + } + ] + }, + { + "blastgraph": [ + { + "meta": { + "type": "file", + "description": "BLAST graph", + "pattern": "*.blast-graph" + } + }, + { + "${meta.id}.blast-graph": { + "type": "file", + "description": "BLAST graph", + "pattern": "*.blast-graph" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107212,103 +136456,188 @@ "doi": "10.1101/416511", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "samplesheet": { - "type": "file", - "description": "CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html\n" - } - }, - { - "intensities": { - "type": "file", - "description": "proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "contrast_variable": { - "type": "string", - "description": "The column in the sample sheet that should be used to define groups for comparison\n" - } - } - ], - "output": [ - { - "dendro_plot": { - "type": "file", - "description": "PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities\n" - } - }, - { - "mean_var_plot": { - "type": "file", - "description": "PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples\n" - } - }, - { - "raw_dist_plot": { - "type": "file", - "description": "PNG file; plot of the intensity/ratio distributions of the raw samples\n" - } - }, - { - "norm_dist_plot": { - "type": "file", - "description": "PNG file; plot of the intensity/ratio distributions of the normalized samples\n" - } - }, - { - "raw_rdata": { - "type": "file", - "description": "RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info\n" - } - }, - { - "norm_rdata": { - "type": "file", - "description": "RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info\n" - } - }, - { - "raw_tab": { - "type": "file", - "description": "TSV-format intensities table from Proteus, contains raw protein intensities\n" - } - }, - { - "norm_tab": { - "type": "file", - "description": "TSV-format intensities table from Proteus, contains normalized protein intensities\n" - } - }, - { - "session_info": { - "type": "file", - "description": "LOG file of the R sessionInfo from the module run\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:proteus-engineering" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "samplesheet": { + "type": "file", + "description": "CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html\n" + } + }, + { + "intensities": { + "type": "file", + "description": "proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html\n" + } + } + ] + ], + "output": [ + { + "dendro_plot": [ + { + "meta": { + "type": "file", + "description": "PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities\n" + } + }, + { + "*dendrogram.png": { + "type": "file", + "description": "PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities\n" + } + } + ] + }, + { + "mean_var_plot": [ + { + "meta": { + "type": "file", + "description": "PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples\n" + } + }, + { + "*mean_variance_relationship.png": { + "type": "file", + "description": "PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples\n" + } + } + ] + }, + { + "raw_dist_plot": [ + { + "meta": { + "type": "file", + "description": "PNG file; plot of the intensity/ratio distributions of the raw samples\n" + } + }, + { + "*raw_distributions.png": { + "type": "file", + "description": "PNG file; plot of the intensity/ratio distributions of the raw samples\n" + } + } + ] + }, + { + "norm_dist_plot": [ + { + "meta": { + "type": "file", + "description": "PNG file; plot of the intensity/ratio distributions of the normalized samples\n" + } + }, + { + "*normalized_distributions.png": { + "type": "file", + "description": "PNG file; plot of the intensity/ratio distributions of the normalized samples\n" + } + } + ] + }, + { + "raw_rdata": [ + { + "meta": { + "type": "file", + "description": "RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info\n" + } + }, + { + "*raw_proteingroups.rds": { + "type": "file", + "description": "RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info\n" + } + } + ] + }, + { + "norm_rdata": [ + { + "meta": { + "type": "file", + "description": "RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info\n" + } + }, + { + "*normalized_proteingroups.rds": { + "type": "file", + "description": "RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info\n" + } + } + ] + }, + { + "raw_tab": [ + { + "meta": { + "type": "file", + "description": "TSV-format intensities table from Proteus, contains raw protein intensities\n" + } + }, + { + "*raw_proteingroups_tab.tsv": { + "type": "file", + "description": "TSV-format intensities table from Proteus, contains raw protein intensities\n" + } + } + ] + }, + { + "norm_tab": [ + { + "meta": { + "type": "file", + "description": "TSV-format intensities table from Proteus, contains normalized protein intensities\n" + } + }, + { + "*normalized_proteingroups_tab.tsv": { + "type": "file", + "description": "TSV-format intensities table from Proteus, contains normalized protein intensities\n" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "file", + "description": "LOG file of the R sessionInfo from the module run\n" + } + }, + { + "*R_sessionInfo.log": { + "type": "file", + "description": "LOG file of the R sessionInfo from the module run\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107347,92 +136676,125 @@ "doi": "10.1186/s13059-017-1364-2", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ipbam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "controlbam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "ipbai": { - "type": "file", - "description": "BAM index", - "pattern": "*.{bai}" - } - }, - { - "controlbai": { - "type": "file", - "description": "BAM index", - "pattern": "*.{bai}" - } - }, - { - "input_control": { - "type": "boolean", - "description": "Whether to run PureCLIP with an input control" - } - }, - { - "genome_fasta": { - "type": "file", - "description": "FASTA file of reference genome", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "crosslinks": { - "type": "file", - "description": "Bed file of crosslinks", - "pattern": "*.{bed}" - } - }, - { - "peaks": { - "type": "file", - "description": "Bed file of peaks", - "pattern": "*.{bed}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "ipbam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "controlbam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "ipbai": { + "type": "file", + "description": "BAM index", + "pattern": "*.{bai}" + } + }, + { + "controlbai": { + "type": "file", + "description": "BAM index", + "pattern": "*.{bai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genome_fasta": { + "type": "file", + "description": "FASTA file of reference genome", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "input_control": { + "type": "boolean", + "description": "Whether to run PureCLIP with an input control" + } + } + ] + ], + "output": [ + { + "crosslinks": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${crosslinks_output_name}": { + "type": "file", + "description": "Bed file of crosslinks", + "pattern": "*.{bed}" + } + } + ] + }, + { + "peaks": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${peaks_output_name}": { + "type": "file", + "description": "Bed file of peaks", + "pattern": "*.{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107470,80 +136832,123 @@ "license": [ "Artistic-2.0" ], - "args_id": "$args" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.{bai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Annotated targets optimized for copy number calling", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "txt": { - "type": "file", - "description": "Intervals coverage file", - "pattern": "*.txt.gz" - } - }, - { - "png": { - "type": "file", - "description": "GC-normalized intervals coverage plot.\nGenerated only when GC-normalization is enabled.\n", - "pattern": "*.png" - } - }, - { - "loess_qc_txt": { - "type": "file", - "description": "GC-normalized intervals coverage metrics.\nGenerated only when GC-normalization is enabled.\n", - "pattern": "*_loess_qc.txt" - } - }, - { - "loess_txt": { - "type": "file", - "description": "GC-normalized intervals coverage file.\nGenerated only when GC-normalization is enabled.\n", - "pattern": "*_loess.txt.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "args_id": "$args", + "identifier": "biotools:purecn" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.{bai}" + } + } + ], + [ + { + "intervals": { + "type": "file", + "description": "Annotated targets optimized for copy number calling", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Intervals coverage file", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "GC-normalized intervals coverage plot.\nGenerated only when GC-normalization is enabled.\n", + "pattern": "*.png" + } + } + ] + }, + { + "loess_qc_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_loess_qc.txt": { + "type": "file", + "description": "GC-normalized intervals coverage metrics.\nGenerated only when GC-normalization is enabled.\n", + "pattern": "*_loess_qc.txt" + } + } + ] + }, + { + "loess_txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_loess.txt.gz": { + "type": "file", + "description": "GC-normalized intervals coverage file.\nGenerated only when GC-normalization is enabled.\n", + "pattern": "*_loess.txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107580,71 +136985,96 @@ "doi": "10.1186/s13029-016-0060-z.", "licence": [ "Artistic-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file of target intervals", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference sequence of the genome being used", - "pattern": "*.fasta" - } - }, - { - "genome": { - "type": "string", - "description": "Genome used for the BED file (e.g., \"hg38\", \"mm10\"...)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "txt": { - "type": "file", - "pattern": "*.txt", - "description": "Annotated targets optimized for copy number calling\n" - } - }, - { - "bed": { - "type": "file", - "pattern": "*.bed", - "description": "Modified and optimized targets exported as a BED file.\nGenerate the file using the --export command-line switch\nIntervalFile.R.\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:purecn" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file of target intervals", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference sequence of the genome being used", + "pattern": "*.fasta" + } + } + ], + [ + { + "genome": { + "type": "string", + "description": "Genome used for the BED file (e.g., \"hg38\", \"mm10\"...)" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "pattern": "*.txt", + "description": "Annotated targets optimized for copy number calling\n" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "pattern": "*.bed", + "description": "Modified and optimized targets exported as a BED file.\nGenerate the file using the --export command-line switch\nIntervalFile.R.\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107683,86 +137113,159 @@ "licence": [ "Artistic-2.0" ], - "args_id": "$args" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "coverage_files": { - "type": "file", - "description": "Coverage files from normal samples", - "pattern": "*.txt.gz" - } - }, - { - "normal_vcf": { - "type": "file", - "description": "Normal panel in VCF format, used to precompute mapping bias\nfor faster runtimes. Optional.\n", - "pattern": "*.vcf.gz" - } - }, - { - "genome": { - "type": "string", - "description": "Genome build" - } - }, - { - "assay": { - "type": "string", - "description": "Assay name" - } - } - ], - "output": [ - { - "rds": { - "type": "file", - "description": "File containing the generated panel of normals", - "pattern": "normalDB*.rds" - } - }, - { - "png": { - "type": "file", - "description": "Plot of interval weights calculated from the panel of normals", - "pattern": "interval_weights*.png" - } - }, - { - "bias_rds": { - "type": "file", - "description": "Calculated mapping bias from the normal files", - "pattern": "mapping_bias*.rds" - } - }, - { - "bias_bed": { - "type": "file", - "description": "Calculated mapping bias sites from the normal files", - "pattern": "mapping_bias_hq_sites*.bed" - } - }, - { - "low_cov_bed": { - "type": "file", - "description": "BED with possibly low coverage targets identified, only\ngenerated if there are low coverage targets\n", - "pattern": "low_coverage_targets*.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "args_id": "$args", + "identifier": "biotools:purecn" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "coverage_files": { + "type": "file", + "description": "Coverage files from normal samples", + "pattern": "*.txt.gz" + } + }, + { + "normal_vcf": { + "type": "file", + "description": "Normal panel in VCF format, used to precompute mapping bias\nfor faster runtimes. Optional.\n", + "pattern": "*.vcf.gz" + } + }, + { + "normal_vcf_tbi": { + "type": "file", + "description": "Normal panel in VCF format", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "genome": { + "type": "string", + "description": "Genome build" + } + } + ], + [ + { + "assay": { + "type": "string", + "description": "Assay name" + } + } + ] + ], + "output": [ + { + "rds": [ + { + "meta": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds" + } + }, + { + "normalDB*.rds": { + "type": "file", + "description": "File containing the generated panel of normals", + "pattern": "normalDB*.rds" + } + } + ] + }, + { + "png": [ + { + "meta": { + "type": "file", + "description": "Plot of interval weights calculated from the panel of normals", + "pattern": "interval_weights*.png" + } + }, + { + "interval_weights*.png": { + "type": "file", + "description": "Plot of interval weights calculated from the panel of normals", + "pattern": "interval_weights*.png" + } + } + ] + }, + { + "bias_rds": [ + { + "meta": { + "type": "file", + "description": "Calculated mapping bias from the normal files", + "pattern": "mapping_bias*.rds" + } + }, + { + "mapping_bias*.rds": { + "type": "file", + "description": "Calculated mapping bias from the normal files", + "pattern": "mapping_bias*.rds" + } + } + ] + }, + { + "bias_bed": [ + { + "meta": { + "type": "file", + "description": "Calculated mapping bias sites from the normal files", + "pattern": "mapping_bias_hq_sites*.bed" + } + }, + { + "mapping_bias_hq_sites*.bed": { + "type": "file", + "description": "Calculated mapping bias sites from the normal files", + "pattern": "mapping_bias_hq_sites*.bed" + } + } + ] + }, + { + "low_cov_bed": [ + { + "meta": { + "type": "file", + "description": "BED with possibly low coverage targets identified, only\ngenerated if there are low coverage targets\n", + "pattern": "low_coverage_targets*.bed" + } + }, + { + "low_coverage_targets*.bed": { + "type": "file", + "description": "BED with possibly low coverage targets identified, only\ngenerated if there are low coverage targets\n", + "pattern": "low_coverage_targets*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107799,129 +137302,266 @@ "license": [ "Artistic-2.0" ], - "args_id": "$args" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "BED file of target intervals, generated from IntervalFile.R\n", - "pattern": "{*.bed,*.txt}" - } - }, - { - "coverage": { - "type": "file", - "description": "Coverage file generated from Coverage.R", - "pattern": "*.txt" - } - }, - { - "normaldb": { - "type": "file", - "description": "Normal panel in RDS format, generated from NormalDB.R\n", - "pattern": "*.rds" - } - }, - { - "genome": { - "type": "string", - "description": "Genome build" - } - } - ], - "output": [ - { - "pdf": { - "type": "file", - "description": "PDF file containing copy number plots\n", - "pattern": "*.pdf" - } - }, - { - "local_optima_pdf": { - "type": "file", - "description": "PDF file containing local optima plots\n", - "pattern": "*_local_optima.pdf" - } - }, - { - "seg": { - "type": "file", - "description": "Tab-delimited file containing segmentation results\n", - "pattern": "*_dnacopy.seg" - } - }, - { - "genes_csv": { - "type": "file", - "description": "CSV file containing gene copy number calls. Optional\n", - "pattern": "*_genes.csv" - } - }, - { - "amplification_pvalues_csv": { - "type": "file", - "description": "CSV file containing amplification p-values. Optional\n", - "pattern": "*_amplification_pvalues.csv" - } - }, - { - "vcf_gz": { - "type": "file", - "description": "GZipped VCF file containing SNV calls. Optional\n", - "pattern": "*.vcf.gz" - } - }, - { - "variants_csv": { - "type": "file", - "description": "CSV file containing SNV calls. Optional\n", - "pattern": "*_variants.csv" - } - }, - { - "loh_csv": { - "type": "file", - "description": "CSV file containing LOH calls. Optional\n", - "pattern": "*_loh.csv" - } - }, - { - "chr_pdf": { - "type": "file", - "description": "PDF file containing chromosome plots. Optional\n", - "pattern": "*_chromosomes.pdf" - } - }, - { - "segmentation_pdf": { - "type": "file", - "description": "PDF file containing segmentation plots. Optional\n", - "pattern": "*_segmentation.pdf" - } - }, - { - "multisample.seg": { - "type": "file", - "description": "Tab-delimited file containing segmentation data from multiple samples. Optional\n", - "pattern": "*_multisample.seg" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "args_id": "$args", + "identifier": "biotools:purecn" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "BED file of target intervals, generated from IntervalFile.R\n", + "pattern": "{*.bed,*.txt}" + } + }, + { + "coverage": { + "type": "file", + "description": "Coverage file generated from Coverage.R", + "pattern": "*.txt" + } + } + ], + [ + { + "normal_db": { + "type": "file", + "description": "normal pannel database" + } + } + ], + [ + { + "genome": { + "type": "string", + "description": "Genome build" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "PDF file containing copy number plots\n", + "pattern": "*.pdf" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF file containing copy number plots\n", + "pattern": "*.pdf" + } + } + ] + }, + { + "local_optima_pdf": [ + { + "meta": { + "type": "file", + "description": "PDF file containing local optima plots\n", + "pattern": "*_local_optima.pdf" + } + }, + { + "*_local_optima.pdf": { + "type": "file", + "description": "PDF file containing local optima plots\n", + "pattern": "*_local_optima.pdf" + } + } + ] + }, + { + "seg": [ + { + "meta": { + "type": "file", + "description": "Tab-delimited file containing segmentation results\n", + "pattern": "*_dnacopy.seg" + } + }, + { + "*_dnacopy.seg": { + "type": "file", + "description": "Tab-delimited file containing segmentation results\n", + "pattern": "*_dnacopy.seg" + } + } + ] + }, + { + "genes_csv": [ + { + "meta": { + "type": "file", + "description": "CSV file containing gene copy number calls. Optional\n", + "pattern": "*_genes.csv" + } + }, + { + "*_genes.csv": { + "type": "file", + "description": "CSV file containing gene copy number calls. Optional\n", + "pattern": "*_genes.csv" + } + } + ] + }, + { + "amplification_pvalues_csv": [ + { + "meta": { + "type": "file", + "description": "CSV file containing amplification p-values. Optional\n", + "pattern": "*_amplification_pvalues.csv" + } + }, + { + "*_amplification_pvalues.csv": { + "type": "file", + "description": "CSV file containing amplification p-values. Optional\n", + "pattern": "*_amplification_pvalues.csv" + } + }, + { + "ues_csv": { + "type": "file", + "description": "CSV file containing amplification p-values. Optional\n", + "pattern": "*_amplification_pvalues.csv" + } + } + ] + }, + { + "vcf_gz": [ + { + "meta": { + "type": "file", + "description": "GZipped VCF file containing SNV calls. Optional\n", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "GZipped VCF file containing SNV calls. Optional\n", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "variants_csv": [ + { + "meta": { + "type": "file", + "description": "CSV file containing SNV calls. Optional\n", + "pattern": "*_variants.csv" + } + }, + { + "*_variants.csv": { + "type": "file", + "description": "CSV file containing SNV calls. Optional\n", + "pattern": "*_variants.csv" + } + } + ] + }, + { + "loh_csv": [ + { + "meta": { + "type": "file", + "description": "CSV file containing LOH calls. Optional\n", + "pattern": "*_loh.csv" + } + }, + { + "*_loh.csv": { + "type": "file", + "description": "CSV file containing LOH calls. Optional\n", + "pattern": "*_loh.csv" + } + } + ] + }, + { + "chr_pdf": [ + { + "meta": { + "type": "file", + "description": "PDF file containing chromosome plots. Optional\n", + "pattern": "*_chromosomes.pdf" + } + }, + { + "*_chromosomes.pdf": { + "type": "file", + "description": "PDF file containing chromosome plots. Optional\n", + "pattern": "*_chromosomes.pdf" + } + } + ] + }, + { + "segmentation_pdf": [ + { + "meta": { + "type": "file", + "description": "PDF file containing segmentation plots. Optional\n", + "pattern": "*_segmentation.pdf" + } + }, + { + "*_segmentation.pdf": { + "type": "file", + "description": "PDF file containing segmentation plots. Optional\n", + "pattern": "*_segmentation.pdf" + } + } + ] + }, + { + "multisample_seg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_multisample.seg": { + "type": "file", + "description": "multisample segmentation results", + "pattern": "*_multisample.seg" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -107956,52 +137596,73 @@ "doi": "10.1093/bioinformatics/btaa025", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "stat": { - "type": "file", - "description": "Histogram of coverage", - "pattern": "*.stat" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cutoff": { - "type": "file", - "description": "Cutoff file", - "pattern": "*.cutoffs" - } - }, - { - "log": { - "type": "file", - "description": "Log file", - "pattern": ".calcuts.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "stat": { + "type": "file", + "description": "Histogram of coverage", + "pattern": "*.stat" + } + } + ] + ], + "output": [ + { + "cutoff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cutoffs": { + "type": "file", + "description": "Cutoff file", + "pattern": "*.cutoffs" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.calcuts.log": { + "type": "file", + "description": "Log file", + "pattern": ".calcuts.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108035,59 +137696,80 @@ "doi": "10.1093/bioinformatics/btaa025", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "Draft assembly in fasta format", - "pattern": "*.fasta" - } - }, - { - "bed": { - "type": "file", - "description": "Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "haplotigs": { - "type": "file", - "description": "Fasta file containing purged haplotigs", - "pattern": "*.hap.fa" - } - }, - { - "purged": { - "type": "file", - "description": "Fasta file purged of duplicated haplotigs", - "pattern": "*.purged.fa" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "Draft assembly in fasta format", + "pattern": "*.fasta" + } + }, + { + "bed": { + "type": "file", + "description": "Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "haplotigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap.fa": { + "type": "file", + "description": "Fasta file containing purged haplotigs", + "pattern": "*.hap.fa" + } + } + ] + }, + { + "purged": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.purged.fa": { + "type": "file", + "description": "Fasta file purged of duplicated haplotigs", + "pattern": "*.purged.fa" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108120,52 +137802,63 @@ "doi": "10.1093/bioinformatics/btaa025", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "statfile": { - "type": "file", - "description": "A Purge dups statistic file", - "pattern": "*.stat" - } - }, - { - "cutoff": { - "type": "file", - "description": "A Purge dups cutoff file", - "pattern": "*.cutoffs" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "png": { - "type": "file", - "description": "A png file of the read depth coverage.", - "pattern": "*.png" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "statfile": { + "type": "file", + "description": "A Purge dups statistic file", + "pattern": "*.stat" + } + }, + { + "cutoff": { + "type": "file", + "description": "A Purge dups cutoff file", + "pattern": "*.cutoffs" + } + } + ] + ], + "output": [ + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "A png file of the read depth coverage.", + "pattern": "*.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108199,52 +137892,73 @@ "doi": "10.1093/bioinformatics/btaa025", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "paf_alignment": { - "type": "file", - "description": "PAF alignment file", - "pattern": "*.paf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "stat": { - "type": "file", - "description": "PacBio Statistic file", - "pattern": "*.PB.stat" - } - }, - { - "basecov": { - "type": "file", - "description": "PacBio Base coverage file", - "pattern": "*.PB.base.cov" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "paf_alignment": { + "type": "file", + "description": "PAF alignment file", + "pattern": "*.paf" + } + } + ] + ], + "output": [ + { + "stat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.PB.stat": { + "type": "file", + "description": "PacBio Statistic file", + "pattern": "*.PB.stat" + } + } + ] + }, + { + "basecov": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.PB.base.cov": { + "type": "file", + "description": "PacBio Base coverage file", + "pattern": "*.PB.base.cov" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108279,66 +137993,87 @@ "doi": "10.1093/bioinformatics/btaa025", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "basecov": { - "type": "file", - "description": "A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT", - "pattern": "*.PB.base.cov" - } - }, - { - "cutoff": { - "type": "file", - "description": "A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS", - "pattern": "*.cutoffs" - } - }, - { - "paf": { - "type": "file", - "description": "A file of assembly alignments to itself", - "pattern": "*.paf(.gz)?" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "A bed file of sequences purged of false duplications", - "pattern": "*.bed" - } - }, - { - "log": { - "type": "file", - "description": "A log of the tool output", - "pattern": "*.log" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "basecov": { + "type": "file", + "description": "A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT", + "pattern": "*.PB.base.cov" + } + }, + { + "cutoff": { + "type": "file", + "description": "A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS", + "pattern": "*.cutoffs" + } + }, + { + "paf": { + "type": "file", + "description": "A file of assembly alignments to itself", + "pattern": "*.paf(.gz)?" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dups.bed": { + "type": "file", + "description": "A bed file of sequences purged of false duplications", + "pattern": "*.bed" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.purge_dups.log": { + "type": "file", + "description": "A log of the tool output", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108372,45 +138107,56 @@ "doi": "10.1093/bioinformatics/btaa025", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "assembly": { - "type": "file", - "description": "Draft assembly file", - "pattern": "*.fasta" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "assembly": { + "type": "file", + "description": "Draft assembly file", + "pattern": "*.fasta" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "split_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.split.fasta.gz": { + "type": "file", + "description": "Fasta split by N's", + "pattern": "*.fasta.gz" + } + } + ] }, { - "split_fasta": { - "type": "file", - "description": "Fasta split by N's", - "pattern": "*.fasta.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108444,56 +138190,77 @@ "doi": "10.21105/joss.01236", "licence": [ "GNU General Public v3 (GPL v3)" - ] - } + ], + "identifier": "biotools:pycoqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "summary": { + "type": "file", + "description": "sequencing summary file", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "Results in HTML format" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Results in JSON format", + "pattern": "*.{json}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "summary": { - "type": "file", - "description": "sequencing summary file", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "html": { - "type": "file", - "description": "Results in HTML format" - } - }, - { - "json": { - "type": "file", - "description": "Results in JSON format", - "pattern": "*.{json}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@joseespinosa", - "@drpatelh" + "authors": [ + "@joseespinosa", + "@drpatelh" ], "maintainers": [ "@joseespinosa", @@ -108537,52 +138304,63 @@ "tool_dev_url": "https://github.com/maxibor/pydamage", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "PyDamage results as csv files", - "pattern": "*.csv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pydamage_results/pydamage_results.csv": { + "type": "file", + "description": "PyDamage results as csv files", + "pattern": "*.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108629,45 +138407,56 @@ "tool_dev_url": "https://github.com/maxibor/pydamage", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "csv": { - "type": "file", - "description": "csv file from pydamage analyze", - "pattern": "*.csv" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "csv": { + "type": "file", + "description": "csv file from pydamage analyze", + "pattern": "*.csv" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "pydamage_results/pydamage_filtered_results.csv": { + "type": "file", + "description": "PyDamage filtered results as csv file", + "pattern": "*.csv" + } + } + ] }, { - "csv": { - "type": "file", - "description": "PyDamage filtered results as csv file", - "pattern": "*.csv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108707,73 +138496,116 @@ "doi": "10.21105/joss.04296", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta.gz,fa.gz,fna.gz}" - } - }, - { - "output_format": { - "type": "string", - "description": "Output format", - "pattern": "{gbk,gff}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "annotations": { - "type": "file", - "description": "Gene annotations. The file format is specified via input channel \"output_format\".", - "pattern": "*.{gbk,gff}.gz" - } - }, - { - "faa": { - "type": "file", - "description": "protein translations file", - "pattern": "*.{faa.gz}" - } - }, - { - "fna": { - "type": "file", - "description": "nucleotide sequences file", - "pattern": "*.{fna.gz}" - } - }, - { - "score": { - "type": "file", - "description": "all potential genes (with scores)", - "pattern": "*.{score.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta.gz,fa.gz,fna.gz}" + } + } + ], + [ + { + "output_format": { + "type": "string", + "description": "Output format", + "pattern": "{gbk,gff}" + } + } + ] + ], + "output": [ + { + "annotations": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.${output_format}.gz": { + "type": "file", + "description": "Gene annotations. The file format is specified via input channel \"output_format\".", + "pattern": "*.{gbk,gff}.gz" + } + } + ] + }, + { + "fna": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fna.gz": { + "type": "file", + "description": "nucleotide sequences file", + "pattern": "*.{fna.gz}" + } + } + ] + }, + { + "faa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.faa.gz": { + "type": "file", + "description": "protein translations file", + "pattern": "*.{faa.gz}" + } + } + ] + }, + { + "score": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.score.gz": { + "type": "file", + "description": "all potential genes (with scores)", + "pattern": "*.{score.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108810,44 +138642,63 @@ "documentation": "https://github.com/nanoporetech/qcat#qcat", "licence": [ "MPL-2.0" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Non-demultiplexed fastq files\n" + } } - }, - { - "reads": { - "type": "file", - "description": "Non-demultiplexed fastq files\n" + ], + [ + { + "barcode_kit": { + "type": "string", + "description": "Barcode kit used for demultiplexing" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Demultiplexed fastq samples", - "pattern": "*.fastq.gz" - } + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq/*.fastq.gz": { + "type": "file", + "description": "Demultiplexed fastq samples", + "pattern": "*.fastq.gz" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108881,52 +138732,65 @@ "doi": "10.1093/bioinformatics/bts503", "licence": [ "GPL-2.0-only" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } - }, - { - "gff": { - "type": "file", - "description": "Feature file with regions of interest", - "pattern": "*.{gff,gtf,bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "directory", - "description": "Qualimap results dir", - "pattern": "*/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:qualimap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "gff": { + "type": "file", + "description": "Feature file with regions of interest", + "pattern": "*.{gff,gtf,bed}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Qualimap results dir", + "pattern": "*/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -108972,59 +138836,90 @@ "doi": "10.1093/bioinformatics/bts503", "licence": [ "GPL-2.0-only" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bacramm": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } - }, - { - "gff": { - "type": "file", - "description": "Feature file with regions of interest", - "pattern": "*.{gff,gtf,bed}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file of cram file", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "directory", - "description": "Qualimap results dir", - "pattern": "*/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:qualimap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cram": { + "type": "file", + "description": "Input cram file", + "pattern": "*.{cram}" + } + }, + { + "crai": { + "type": "file", + "description": "Index file for cram file", + "pattern": "*.{crai}" + } + } + ], + [ + { + "gff": { + "type": "file", + "description": "Feature file with regions of interest", + "pattern": "*.{gff,gtf,bed}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference file of cram file", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Index file for reference file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Qualimap results dir", + "pattern": "*/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109062,58 +138957,71 @@ "doi": "10.1093/bioinformatics/bts503", "licence": [ "GPL-2.0-only" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file of the reference genome", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "results": { - "type": "directory", - "description": "Qualimap results dir", - "pattern": "*/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:qualimap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file of the reference genome", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Qualimap results dir", + "pattern": "*/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109153,7 +139061,8 @@ "tool_dev_url": "https://github.com/quarto-dev/quarto-cli", "licence": [ "MIT" - ] + ], + "identifier": "" } }, { @@ -109164,93 +139073,150 @@ "tool_dev_url": "https://github.com/nteract/papermill", "licence": [ "BSD 3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "notebook": { - "type": "file", - "description": "The Quarto notebook to be rendered.", - "pattern": "*.{qmd}" - } - }, - { - "parameters": { - "type": "map", - "description": "Groovy map with notebook parameters which will be passed to Quarto to\ngenerate parametrized reports.\n" - } - }, - { - "input_files": { - "type": "file", - "description": "One or multiple files serving as input data for the notebook.", - "pattern": "*" - } - }, - { - "extensions": { - "type": "file", - "description": "A quarto `_extensions` directory with custom template(s) to be\navailable for rendering.\n", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" - } - }, - { - "html": { - "type": "file", - "description": "HTML report generated by Quarto.", - "pattern": "*.html" - } - }, - { - "notebook": { - "type": "file", - "description": "The original, un-rendered notebook.", - "pattern": "*.[qmd,ipynb,rmd]" - } - }, - { - "artifacts": { - "type": "file", - "description": "Artifacts generated during report rendering.", - "pattern": "*" - } - }, - { - "params_yaml": { - "type": "file", - "description": "Parameters used during report rendering.", - "pattern": "*" - } - }, - { - "extensions": { - "type": "file", - "description": "Quarto extensions used during report rendering.", - "pattern": "*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "notebook": { + "type": "file", + "description": "The Quarto notebook to be rendered.", + "pattern": "*.{qmd}" + } + } + ], + [ + { + "parameters": { + "type": "map", + "description": "Groovy map with notebook parameters which will be passed to Quarto to\ngenerate parametrized reports.\n" + } + } + ], + [ + { + "input_files": { + "type": "file", + "description": "One or multiple files serving as input data for the notebook.", + "pattern": "*" + } + } + ], + [ + { + "extensions": { + "type": "file", + "description": "A quarto `_extensions` directory with custom template(s) to be\navailable for rendering.\n", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML report generated by Quarto.", + "pattern": "*.html" + } + } + ] + }, + { + "notebook": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "${notebook}": { + "type": "file", + "description": "The original, un-rendered notebook.", + "pattern": "*.[qmd,ipynb,rmd]" + } + } + ] + }, + { + "artifacts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "artifacts/*": { + "type": "file", + "description": "Artifacts generated during report rendering.", + "pattern": "*" + } + } + ] + }, + { + "params_yaml": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "params.yml": { + "type": "file", + "description": "Parameters used during report rendering.", + "pattern": "*" + } + } + ] + }, + { + "extensions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n" + } + }, + { + "_extensions": { + "type": "file", + "description": "Quarto extensions used during report rendering.", + "pattern": "*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109289,72 +139255,153 @@ "doi": "10.1093/bioinformatics/btt086", "licence": [ "GPL-2.0-only" - ] - } - } - ], - "input": [ - { - "consensus": { - "type": "file", - "description": "Fasta file containing the assembly of interest\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.\n" - } - }, - { - "gff": { - "type": "file", - "description": "The genome GFF file. Has to contain at least a non-empty string dummy value." - } - } - ], - "output": [ - { - "quast": { - "type": "directory", - "description": "Directory containing complete quast report", - "pattern": "{prefix}/" - } - }, - { - "report": { - "type": "file", - "description": "tab-separated version of the summary, suitable for spreadsheets and mqc", - "pattern": "${prefix}.tsv" - } - }, - { - "misassemblies": { - "type": "file", - "description": "Report containing misassemblies, only when a reference fasta is provided\n", - "pattern": "${prefix}_misassemblies.tsv" - } - }, - { - "transcriptome": { - "type": "file", - "description": "Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided\n", - "pattern": "${prefix}_transcriptome.tsv" - } - }, - { - "unaligned": { - "type": "file", - "description": "Report containing unaligned contigs, only when a reference fasta is provided\n", - "pattern": "${prefix}_unaligned.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:quast" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "consensus": { + "type": "file", + "description": "Fasta file containing the assembly of interest\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "The genome GFF file. Has to contain at least a non-empty string dummy value." + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Directory containing the results of the QUAST analysis\n" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "TSV file", + "pattern": "${prefix}.tsv" + } + } + ] + }, + { + "transcriptome": [ + { + "meta": { + "type": "file", + "description": "Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided\n", + "pattern": "${prefix}_transcriptome.tsv" + } + }, + { + "${prefix}_transcriptome.tsv": { + "type": "file", + "description": "Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided\n", + "pattern": "${prefix}_transcriptome.tsv" + } + } + ] + }, + { + "misassemblies": [ + { + "meta": { + "type": "file", + "description": "Report containing misassemblies, only when a reference fasta is provided\n", + "pattern": "${prefix}_misassemblies.tsv" + } + }, + { + "${prefix}_misassemblies.tsv": { + "type": "file", + "description": "Report containing misassemblies, only when a reference fasta is provided\n", + "pattern": "${prefix}_misassemblies.tsv" + } + } + ] + }, + { + "unaligned": [ + { + "meta": { + "type": "file", + "description": "Report containing unaligned contigs, only when a reference fasta is provided\n", + "pattern": "${prefix}_unaligned.tsv" + } + }, + { + "${prefix}_unaligned.tsv": { + "type": "file", + "description": "Report containing unaligned contigs, only when a reference fasta is provided\n", + "pattern": "${prefix}_unaligned.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109409,280 +139456,336 @@ "doi": "10.1038/s41588-021-00877-0", "licence": [ "GPL v3" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "(Mandatory) BAM/CRAM files", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bais": { + "type": "file", + "description": "(Mandatory) BAM/CRAM index files", + "pattern": "*.{bai}" + } + }, + { + "reference_haplotype_file": { + "type": "file", + "description": "(Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1)", + "pattern": "*.{hap.gz}" + } + }, + { + "reference_legend_file": { + "type": "file", + "description": "(Mandatory) Reference haplotype legend file in IMPUTE format (file with one row per SNP, and a header including position for the physical position in 1 based coordinates, a0 for the reference allele, and a1 for the alternate allele).", + "pattern": "*.{legend.gz}" + } + }, + { + "chr": { + "type": "string", + "description": "(Mandatory) What chromosome to run. Should match BAM headers." + } + }, + { + "regions_start": { + "type": "integer", + "description": "(Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd." + } + }, + { + "regions_end": { + "type": "integer", + "description": "(Mandatory) When running imputation, where to stop." + } + }, + { + "ngen": { + "type": "integer", + "description": "Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 * Ne / K if unsure." + } + }, + { + "buffer": { + "type": "integer", + "description": "Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd." + } + }, + { + "genetic_map_file": { + "type": "file", + "description": "(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).", + "pattern": "*.{txt.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "posfile": { + "type": "file", + "description": "(Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab seperated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized.", + "pattern": "*.{txt}" + } + }, + { + "phasefile": { + "type": "file", + "description": "(Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header.", + "pattern": "*.{txt}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "(Optional) File with reference genome.", + "pattern": "*.{txt.gz}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file with both SNP annotation information and per-sample genotype information.", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "TBI file of the VCF.", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "rdata": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "RData\", type: \"dir": { + "type": "directory", + "description": "Optional directory path to prepared RData file with reference objects (useful with --save_prepared_reference=TRUE)." + } + } + ] + }, + { + "plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "plots\", type: \"dir": { + "type": "directory", + "description": "Optional directory path to save plots." + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, + "authors": [ + "@atrigila" + ], + "maintainers": [ + "@atrigila" + ] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "dev" + } + ] + }, + { + "name": "racon", + "path": "modules/nf-core/racon/meta.yml", + "type": "module", + "meta": { + "name": "racon", + "description": "Consensus module for raw de novo DNA assembly of long uncorrected reads", + "keywords": [ + "assembly", + "pacbio", + "nanopore", + "polish" + ], + "tools": [ { - "bams": { - "type": "file", - "description": "(Mandatory) BAM/CRAM files", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bais": { - "type": "file", - "description": "(Mandatory) BAM/CRAM index files", - "pattern": "*.{bai}" - } - }, - { - "reference_haplotype_file": { - "type": "file", - "description": "(Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1)", - "pattern": "*.{hap.gz}" - } - }, - { - "reference_legend_file": { - "type": "file", - "description": "(Mandatory) Reference haplotype legend file in IMPUTE format (file with one row per SNP, and a header including position for the physical position in 1 based coordinates, a0 for the reference allele, and a1 for the alternate allele).", - "pattern": "*.{legend.gz}" - } - }, - { - "chr": { - "type": "string", - "description": "(Mandatory) What chromosome to run. Should match BAM headers." - } - }, - { - "regions_start": { - "type": "integer", - "description": "(Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd." - } - }, - { - "regions_end": { - "type": "integer", - "description": "(Mandatory) When running imputation, where to stop." - } - }, - { - "buffer": { - "type": "integer", - "description": "Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd." - } - }, - { - "ngen": { - "type": "integer", - "description": "Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 * Ne / K if unsure." - } - }, - { - "genetic_map_file": { - "type": "file", - "description": "(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).", - "pattern": "*.{txt.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "posfile": { - "type": "file", - "description": "(Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab seperated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized.", - "pattern": "*.{txt}" - } - }, - { - "phasefile": { - "type": "file", - "description": "(Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header.", - "pattern": "*.{txt}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "(Optional) File with reference genome.", - "pattern": "*.{txt.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file with both SNP annotation information and per-sample genotype information.", - "pattern": "*.{vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "TBI file of the VCF.", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "rdata": { - "type": "directory", - "description": "Optional directory path to prepared RData file with reference objects (useful with --save_prepared_reference=TRUE)." - } - }, - { - "plots": { - "type": "directory", - "description": "Optional directory path to save plots." - } - } - ], - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "dev" - } - ] - }, - { - "name": "racon", - "path": "modules/nf-core/racon/meta.yml", - "type": "module", - "meta": { - "name": "racon", - "description": "Consensus module for raw de novo DNA assembly of long uncorrected reads", - "keywords": [ - "assembly", - "pacbio", - "nanopore", - "polish" - ], - "tools": [ - { - "racon": { - "description": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.", - "homepage": "https://github.com/lbcb-sci/racon", - "documentation": "https://github.com/lbcb-sci/racon", - "tool_dev_url": "https://github.com/lbcb-sci/racon", - "doi": "10.1101/gr.214270.116", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files. Racon expects single end reads", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "assembly": { - "type": "file", - "description": "Genome assembly to be improved", - "pattern": "*.{fasta,fa}" - } - }, - { - "paf": { - "type": "file", - "description": "Alignment in PAF format", - "pattern": "*.paf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "improved_assembly": { - "type": "file", - "description": "Improved genome assembly", - "pattern": "*_assembly_consensus.fasta.gz" - } - } - ], - "authors": [ - "@avantonder" - ], - "maintainers": [ - "@avantonder" - ] - }, - "pipelines": [ - { - "name": "bacass", - "version": "2.3.1" - }, - { - "name": "crisprseq", - "version": "2.2.1" - } - ] - }, - { - "name": "rapidnj", - "path": "modules/nf-core/rapidnj/meta.yml", - "type": "module", - "meta": { - "name": "rapidnj", - "description": "Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.", - "keywords": [ - "phylogeny", - "newick", - "neighbour-joining" - ], - "tools": [ + "racon": { + "description": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.", + "homepage": "https://github.com/lbcb-sci/racon", + "documentation": "https://github.com/lbcb-sci/racon", + "tool_dev_url": "https://github.com/lbcb-sci/racon", + "doi": "10.1101/gr.214270.116", + "licence": [ + "MIT" + ], + "identifier": "biotools:Racon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files. Racon expects single end reads", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "assembly": { + "type": "file", + "description": "Genome assembly to be improved", + "pattern": "*.{fasta,fa}" + } + }, + { + "paf": { + "type": "file", + "description": "Alignment in PAF format", + "pattern": "*.paf" + } + } + ] + ], + "output": [ + { + "improved_assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_assembly_consensus.fasta.gz": { + "type": "file", + "description": "Improved genome assembly", + "pattern": "*_assembly_consensus.fasta.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@avantonder" + ], + "maintainers": [ + "@avantonder" + ] + }, + "pipelines": [ + { + "name": "bacass", + "version": "2.3.1" + }, + { + "name": "crisprseq", + "version": "2.2.1" + } + ] + }, + { + "name": "rapidnj", + "path": "modules/nf-core/rapidnj/meta.yml", + "type": "module", + "meta": { + "name": "rapidnj", + "description": "Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.", + "keywords": [ + "phylogeny", + "newick", + "neighbour-joining" + ], + "tools": [ { "rapidnj": { "description": "RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.", @@ -109692,40 +139795,55 @@ "doi": "10.1007/978-3-540-87361-7_10", "licence": [ "GPL v2" - ] + ], + "identifier": "biotools:rapidnj" } } ], "input": [ - { - "alignment": { - "type": "file", - "description": "A FASTA format multiple sequence alignment file", - "pattern": "*.{fasta,fas,fa,mfa}" + [ + { + "alignment": { + "type": "file", + "description": "A FASTA format multiple sequence alignment file", + "pattern": "*.{fasta,fas,fa,mfa}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "stockholm_alignment": [ + { + "*.sth": { + "type": "file", + "description": "An alignment in Stockholm format", + "pattern": "*.{sth}" + } + } + ] }, { - "phylogeny": { - "type": "file", - "description": "A phylogeny in Newick format", - "pattern": "*.{tre}" - } + "phylogeny": [ + { + "*.tre": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{tre}" + } + } + ] }, { - "stockholm_alignment": { - "type": "file", - "description": "An alignment in Stockholm format", - "pattern": "*.{sth}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109760,56 +139878,69 @@ "doi": "10.5281/zenodo.3731394", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input paired-end FastQ files" - } - }, - { - "genome_size": { - "type": "string", - "description": "Genome size of the species" - } - }, - { - "depth_cutoff": { - "type": "integer", - "description": "Depth of coverage cutoff" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Reads with subsampled coverage", - "pattern": "*.fastq.gz" - } + ], + "identifier": "biotools:rasusa" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired-end FastQ files" + } + }, + { + "genome_size": { + "type": "string", + "description": "Genome size of the species" + } + } + ], + [ + { + "depth_cutoff": { + "type": "integer", + "description": "Depth of coverage cutoff" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Reads with subsampled coverage", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109844,52 +139975,73 @@ "doi": "10.1038/s43588-021-00073-4", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', suffix:'bacteria' ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input file in FASTA/FASTQ format.", - "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', suffix:'bacteria' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembled FASTA file", - "pattern": "*.fasta.gz" - } - }, - { - "gfa": { - "type": "file", - "description": "Repeat graph", - "pattern": "*.gfa.gz" - } + ], + "identifier": "biotools:raven" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', suffix:'bacteria' ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input file in FASTA/FASTQ format.", + "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', suffix:'bacteria' ]\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "Assembled FASTA file", + "pattern": "*.fasta.gz" + } + } + ] + }, + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', suffix:'bacteria' ]\n" + } + }, + { + "*.gfa.gz": { + "type": "file", + "description": "Repeat graph", + "pattern": "*.gfa.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109922,40 +140074,55 @@ "doi": "10.1093/bioinformatics/btz305", "licence": [ "GPL v2-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "alignment": { - "type": "file", - "description": "A FASTA format multiple sequence alignment file", - "pattern": "*.{fasta,fas,fa,mfa}" + [ + { + "alignment": { + "type": "file", + "description": "A FASTA format multiple sequence alignment file", + "pattern": "*.{fasta,fas,fa,mfa}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "phylogeny": [ + { + "*.raxml.bestTree": { + "type": "file", + "description": "A phylogeny in Newick format", + "pattern": "*.{raxml.bestTree}" + } + } + ] }, { - "phylogeny": { - "type": "file", - "description": "A phylogeny in Newick format", - "pattern": "*.{raxml.bestTree}" - } + "phylogeny_bootstrapped": [ + { + "*.raxml.support": { + "type": "file", + "description": "A phylogeny in Newick format with bootstrap values", + "pattern": "*.{raxml.support}" + } + } + ] }, { - "phylogeny_bootstrapped": { - "type": "file", - "description": "A phylogeny in Newick format with bootstrap values", - "pattern": "*.{raxml.support}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -109989,45 +140156,56 @@ "tool_dev_url": "https://github.com/Dfam-consortium/RepeatModeler", "licence": [ "Open Software License v2.1" - ] + ], + "identifier": "biotools:repeatmodeler" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file", - "pattern": "*.{fasta,fsa,fa}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file", + "pattern": "*.{fasta,fsa,fa}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "db": { - "type": "file", - "description": "Database files for repeatmodeler", - "pattern": "`${prefix}.*`" - } + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Database files for repeatmodeler", + "pattern": "`${prefix}.*`" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110060,59 +140238,90 @@ "tool_dev_url": "https://github.com/Dfam-consortium/RepeatModeler", "licence": [ "Open Software License v2.1" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "db": { - "type": "file", - "description": "RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Consensus repeat sequences", - "pattern": "*.fa" - } - }, - { - "stk": { - "type": "file", - "description": "Seed alignments", - "pattern": "*.stk" - } - }, - { - "log": { - "type": "file", - "description": "A summarized log of the run", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:repeatmodeler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "db": { + "type": "file", + "description": "RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Consensus repeat sequences", + "pattern": "*.fa" + } + } + ] + }, + { + "stk": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.stk": { + "type": "file", + "description": "Seed alignments", + "pattern": "*.stk" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "A summarized log of the run", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110147,162 +140356,317 @@ "doi": "10.1099/mgen.0.000748", "licence": [ "APACHE-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "fastq file(s)", - "pattern": "*.{fastq,fq}{.gz}" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fa,fna}" - } - }, - { - "db_point": { - "type": "directory", - "description": "database directory containing known point mutations" - } - }, - { - "db_res": { - "type": "directory", - "description": "database directory containing known resistance genes" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "json": { - "type": "file", - "description": "CGE standardized json file", - "pattern": "*.json" - } - }, - { - "disinfinder_kma": { - "type": "directory", - "description": "directory holding kma results", - "pattern": "disinfinder_kma" - } - }, - { - "pheno_table_species": { - "type": "file", - "description": "table with species specific AMR phenotypes", - "pattern": "pheno_table_species.tsv" - } - }, - { - "pheno_table": { - "type": "file", - "description": "table with all AMR phenotypes", - "pattern": "pheno_table.tsv" - } - }, - { - "pointfinder_kma": { - "type": "directory", - "description": "directory holding kma results", - "pattern": "pointfinder_kma" - } - }, - { - "pointfinder_prediction": { - "type": "file", - "description": "tab separated table; 1 is given to a predicted resistance against an antibiotic class, 0 is given to not resistance detected", - "pattern": "PointFinder_prediction.txt" - } - }, - { - "pointfinder_results": { - "type": "file", - "description": "tab separated table with predicted point mutations leading to antibiotic resistance", - "pattern": "PointFinder_results.txt" - } - }, - { - "pointfinder_table": { - "type": "file", - "description": "predicted point mutations grouped into genes to which they belong", - "pattern": "PointFinder_table.txt" - } - }, - { - "resfinder_blast": { - "type": "directory", - "description": "directory holding blast results", - "pattern": "resfinder_kma" - } - }, - { - "resfinder_hit_in_genome_seq": { - "type": "file", - "description": "fasta sequence of resistance gene hits found in the input data (query)", - "pattern": "ResFinder_Hit_in_genome_seq.fsa" - } - }, - { - "resfinder_kma": { - "type": "directory", - "description": "directory holding kma results", - "pattern": "resfinder_kma" - } - }, - { - "resfinder_resistance_gene_seq": { - "type": "file", - "description": "fasta sequence of resistance gene hits found in the database (reference)", - "pattern": "ResFinder_Resistance_gene_seq.fsa" - } - }, - { - "resfinder_results_table": { - "type": "file", - "description": "predicted resistance genes grouped by antibiotic class", - "pattern": "ResFinder_results_table.txt" - } - }, - { - "resfinder_results_tab": { - "type": "file", - "description": "tab separated table with predicted resistance genes", - "pattern": "ResFinder_results_tab.txt" - } - }, - { - "resfinder_results": { - "type": "file", - "description": "predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes", - "pattern": "ResFinder_results.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:resfinder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "fastq file(s)", + "pattern": "*.{fastq,fq}{.gz}" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fa,fna}" + } + } + ], + [ + { + "db_point": { + "type": "directory", + "description": "database directory containing known point mutations" + } + } + ], + [ + { + "db_res": { + "type": "directory", + "description": "database directory containing known resistance genes" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "CGE standardized json file", + "pattern": "*.json" + } + } + ] + }, + { + "disinfinder_kma": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "disinfinder_kma": { + "type": "directory", + "description": "directory holding kma results", + "pattern": "disinfinder_kma" + } + } + ] + }, + { + "pheno_table_species": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pheno_table_species.txt": { + "type": "file", + "description": "table with species specific AMR phenotypes", + "pattern": "pheno_table_species.tsv" + } + } + ] + }, + { + "pheno_table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pheno_table.txt": { + "type": "file", + "description": "table with all AMR phenotypes", + "pattern": "pheno_table.tsv" + } + } + ] + }, + { + "pointfinder_kma": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "pointfinder_kma": { + "type": "directory", + "description": "directory holding kma results", + "pattern": "pointfinder_kma" + } + } + ] + }, + { + "pointfinder_prediction": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "PointFinder_prediction.txt": { + "type": "file", + "description": "tab separated table; 1 is given to a predicted resistance against an antibiotic class, 0 is given to not resistance detected", + "pattern": "PointFinder_prediction.txt" + } + } + ] + }, + { + "pointfinder_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "PointFinder_results.txt": { + "type": "file", + "description": "tab separated table with predicted point mutations leading to antibiotic resistance", + "pattern": "PointFinder_results.txt" + } + } + ] + }, + { + "pointfinder_table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "PointFinder_table.txt": { + "type": "file", + "description": "predicted point mutations grouped into genes to which they belong", + "pattern": "PointFinder_table.txt" + } + } + ] + }, + { + "resfinder_hit_in_genome_seq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_Hit_in_genome_seq.fsa": { + "type": "file", + "description": "fasta sequence of resistance gene hits found in the input data (query)", + "pattern": "ResFinder_Hit_in_genome_seq.fsa" + } + } + ] + }, + { + "resfinder_blast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "resfinder_blast": { + "type": "directory", + "description": "directory holding blast results", + "pattern": "resfinder_kma" + } + } + ] + }, + { + "resfinder_kma": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "resfinder_kma": { + "type": "directory", + "description": "directory holding kma results", + "pattern": "resfinder_kma" + } + } + ] + }, + { + "resfinder_resistance_gene_seq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_Resistance_gene_seq.fsa": { + "type": "file", + "description": "fasta sequence of resistance gene hits found in the database (reference)", + "pattern": "ResFinder_Resistance_gene_seq.fsa" + } + } + ] + }, + { + "resfinder_results_table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_results_table.txt": { + "type": "file", + "description": "predicted resistance genes grouped by antibiotic class", + "pattern": "ResFinder_results_table.txt" + } + } + ] + }, + { + "resfinder_results_tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_results_tab.txt": { + "type": "file", + "description": "tab separated table with predicted resistance genes", + "pattern": "ResFinder_results_tab.txt" + } + } + ] + }, + { + "resfinder_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ResFinder_results.txt": { + "type": "file", + "description": "predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes", + "pattern": "ResFinder_results.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110335,45 +140699,64 @@ "doi": "10.1093/nar/gkz935", "licence": [ "https://card.mcmaster.ca/about" - ] + ], + "identifier": "" } } ], "input": [ - { - "card": { - "type": "directory", - "description": "Directory containing the CARD database", - "pattern": "*/" + [ + { + "card": { + "type": "directory", + "description": "Directory containing the CARD database", + "pattern": "*/" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "card_database_processed": { + "type": "directory", + "description": "Directory containing the processed CARD database files", + "pattern": "*/" + } + } + ] }, { - "db": { - "type": "directory", - "description": "Directory containing the processed CARD database files", - "pattern": "*/" - } + "tool_version": [ + { + "RGI_VERSION": { + "type": "string", + "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" + } + } + ] }, { - "tool_version": { - "type": "string", - "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" - } + "db_version": [ + { + "DB_VERSION": { + "type": "string", + "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" + } + } + ] }, { - "db_version": { - "type": "string", - "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110416,85 +140799,128 @@ "doi": "10.1093/nar/gkz935", "licence": [ "https://card.mcmaster.ca/about" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Nucleotide or protein sequences in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - } - }, - { - "card": { - "type": "directory", - "description": "Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", - "pattern": "*/" - } - }, - { - "wildcard": { - "type": "directory", - "description": "Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "JSON formatted file with RGI results", - "pattern": "*.{json}" - } - }, - { - "tsv": { - "type": "file", - "description": "Tab-delimited file with RGI results", - "pattern": "*.{txt}" - } - }, - { - "tmp": { - "type": "directory", - "description": "Directory containing various intermediate files", - "pattern": "temp/" - } - }, - { - "tool_version": { - "type": "string", - "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" - } - }, - { - "db_version": { - "type": "string", - "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide or protein sequences in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + } + } + ], + [ + { + "card": { + "type": "directory", + "description": "Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", + "pattern": "*/" + } + } + ], + [ + { + "wildcard": { + "type": "directory", + "description": "Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON formatted file with RGI results", + "pattern": "*.{json}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab-delimited file with RGI results", + "pattern": "*.{txt}" + } + } + ] + }, + { + "tmp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "temp/": { + "type": "directory", + "description": "Directory containing various intermediate files", + "pattern": "temp/" + } + } + ] + }, + { + "tool_version": [ + { + "RGI_VERSION": { + "type": "string", + "description": "The version of the tool in string format (useful for downstream tools such as hAMRronization)" + } + } + ] + }, + { + "db_version": [ + { + "DB_VERSION": { + "type": "string", + "description": "The version of the used database in string format (useful for downstream tools such as hAMRronization)" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110536,72 +140962,87 @@ "tool_dev_url": "https://github.com/dnil", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "vcf index file", - "pattern": "*.{tbi}" - } - }, - { - "roh": { - "type": "file", - "description": "Bcftools roh style TSV file with CHR,POS,AZ,QUAL", - "pattern": "*.{roh}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file with AZ windows.", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "vcf index file", + "pattern": "*.{tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "roh": { + "type": "file", + "description": "Bcftools roh style TSV file with CHR,POS,AZ,QUAL", + "pattern": "*.{roh}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "BED file with AZ windows.", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_rhocall.vcf": { + "type": "file", + "description": "vcf file", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110639,59 +141080,88 @@ "tool_dev_url": "https://github.com/dnil", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf}" - } - }, - { - "roh": { - "type": "file", - "description": "Input RHO file produced from rhocall", - "pattern": "*.{roh}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "Bed file containing roh calls", - "pattern": "*.{bed}" - } - }, - { - "wig": { - "type": "file", - "description": "Wig file containing roh calls", - "pattern": "*.{wig}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "roh": { + "type": "file", + "description": "Input RHO file produced from rhocall", + "pattern": "*.{roh}" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/${prefix}.bed": { + "type": "file", + "description": "Bed file containing roh calls", + "pattern": "*.{bed}" + } + } + ] + }, + { + "wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/${prefix}.wig": { + "type": "file", + "description": "Wig file containing roh calls", + "pattern": "*.{wig}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110730,145 +141200,186 @@ "doi": "10.1038/s41467-017-01981-8", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "bam_ribo": { - "type": "file", - "description": "Sorted riboseq BAM file(s)", - "pattern": "*.{bam}" - } - }, - { - "bai_ribo": { - "type": "file", - "description": "Index for sorted riboseq bam file(s)", - "pattern": "*.{bai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing TI-Seq sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam_ti": { - "type": "file", - "description": "Sorted TI-Seq BAM file(s)", - "pattern": "*.{bam}" - } - }, - { - "bai_ti": { - "type": "file", - "description": "Index for sorted TI-Seq BAM file(s)", - "pattern": "*.{bai}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta-format sequence file for reference sequences used in the bam file\n", - "pattern": "*.gtf" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format annotation file for reference sequences used in the bam file\n", - "pattern": "*.gtf" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing information on candidate ORFs\n" - } - }, - { - "candidate_orfs": { - "type": "file", - "description": "3-column (transIDstarttstop) candidate ORFs file\n", - "pattern": "*.txt" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing information on riboseq P-site offfset parameter\nfiles\n" - } - }, - { - "para_ribo": { - "type": "file", - "description": "Input P-site offset parameter files for riboseq bam files\n", - "pattern": "*.py" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing information on TI-seq P-site offfset parameter\nfiles\n" - } - }, - { - "para_ribo": { - "type": "file", - "description": "Input P-site offset parameter files for TI-seq bam files\n", - "pattern": "*.py" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "predictions": { - "type": "file", - "description": "txt file all possible ORF results that fit the thresholds\n", - "pattern": "*.{txt}" - } - }, - { - "all": { - "type": "file", - "description": "txt file similar to the predictions but do not use FDR (q-value) cutoff\n", - "pattern": "*.{txt}" - } - }, - { - "transprofile": { - "type": "file", - "description": "Output RPF P-site profile for each transcript. The profile data is in\npython dict format, recording non-zero read counts at different\npositions on transcript.\n", - "pattern": "*.{py}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "bam_ribo": { + "type": "file", + "description": "Sorted riboseq BAM file(s)", + "pattern": "*.{bam}" + } + }, + { + "bai_ribo": { + "type": "file", + "description": "Index for sorted riboseq bam file(s)", + "pattern": "*.{bai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing TI-Seq sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam_ti": { + "type": "file", + "description": "Sorted TI-Seq BAM file(s)", + "pattern": "*.{bam}" + } + }, + { + "bai_ti": { + "type": "file", + "description": "Index for sorted TI-Seq BAM file(s)", + "pattern": "*.{bai}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta-format sequence file for reference sequences used in the bam file\n", + "pattern": "*.gtf" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for reference sequences used in the bam file\n", + "pattern": "*.gtf" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing information on candidate ORFs\n" + } + }, + { + "candidate_orfs": { + "type": "file", + "description": "3-column (transIDstarttstop) candidate ORFs file\n", + "pattern": "*.txt" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing information on riboseq P-site offfset parameter\nfiles\n" + } + }, + { + "para_ribo": { + "type": "file", + "description": "Input P-site offset parameter files for riboseq bam files\n", + "pattern": "*.py" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing information on TI-seq P-site offfset parameter\nfiles\n" + } + }, + { + "para_ti": { + "type": "file", + "description": "Input P-site offset parameter files for TI-seq bam files\n", + "pattern": "*.py" + } + } + ] + ], + "output": [ + { + "predictions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_pred.txt": { + "type": "file", + "description": "txt file all possible ORF results that fit the thresholds\n", + "pattern": "*.{txt}" + } + } + ] + }, + { + "all": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_all.txt": { + "type": "file", + "description": "txt file similar to the predictions but do not use FDR (q-value) cutoff\n", + "pattern": "*.{txt}" + } + } + ] + }, + { + "transprofile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_transprofile.py": { + "type": "file", + "description": "Output RPF P-site profile for each transcript. The profile data is in\npython dict format, recording non-zero read counts at different\npositions on transcript.\n", + "pattern": "*.{py}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -110907,79 +141418,112 @@ "doi": "10.1038/s41467-017-01981-8", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Index for sorted BAM/CRAM/SAM file", - "pattern": "*.{bai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format annotation file for reference sequences used in the bam file\n", - "pattern": "*.gtf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "txt": { - "type": "file", - "description": "txt file recording all distribution data in python format for each\ngroup of reads\n", - "pattern": "*.{txt}" - } - }, - { - "pdf": { - "type": "file", - "description": "Pdf figure file is plot of all the distributions and illustration of\nquality and P-site offset\n", - "pattern": "*.{pdf}" - } - }, - { - "offset": { - "type": "file", - "description": "This file saves P-site offsets for different reads lengths in python\ncode dict format, and can be used in further analysis\n", - "pattern": "*.{para.py}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for sorted BAM/CRAM/SAM file", + "pattern": "*.{bai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for reference sequences used in the bam file\n", + "pattern": "*.gtf" + } + } + ] + ], + "output": [ + { + "distribution": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "file containing distribution", + "pattern": "*.{txt}" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Pdf figure file is plot of all the distributions and illustration of\nquality and P-site offset\n", + "pattern": "*.{pdf}" + } + } + ] + }, + { + "offset": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.para.py": { + "type": "file", + "description": "This file saves P-site offsets for different reads lengths in python\ncode dict format, and can be used in further analysis\n", + "pattern": "*.{para.py}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111018,128 +141562,231 @@ "doi": "10.1093/bioinformatics/btz878", "licence": [ "GNU General Public v3 (GPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false, strandedness: 'single' ]\n" - } - }, - { - "bam_ribo": { - "type": "file", - "description": "Sorted riboseq BAM file(s)", - "pattern": "*.{bam}" - } - }, - { - "bai_ribo": { - "type": "file", - "description": "Index for sorted riboseq bam file(s)", - "pattern": "*.{bai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Map containing reference information for the candidate ORFs\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "candidate_orfs": { - "type": "file", - "description": "TSV file with candidate ORFs from 'ribotricer prepareorfs'", - "pattern": "*.tsv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" - } - }, - { - "protocol": { - "type": "file", - "description": "txt file containing inferred protocol if it was inferred (not supplied as input)", - "pattern": "*_protocol.txt" - } - }, - { - "bam_summary": { - "type": "file", - "description": "Text summary of reads found in the BAM", - "pattern": "*_bam_summary.txt" - } - }, - { - "read_length_dist": { - "type": "file", - "description": "PDF-format read length distribution as quality control", - "pattern": "*_read_length_dist.pdf" - } - }, - { - "metagene_profile_5p": { - "type": "file", - "description": "Metagene profile aligning with the start codon", - "pattern": "*_metagene_profiles_5p.tsv" - } - }, - { - "metagene_profile_3p": { - "type": "file", - "description": "Metagene profile aligning with the stop codon", - "pattern": "*_metagene_profiles_3p.tsv" - } - }, - { - "metagene_plots": { - "type": "file", - "description": "Metagene plots for quality control", - "pattern": "*_metagene_plots.pdf" - } - }, - { - "psite_offsets": { - "type": "file", - "description": "\"If the P-site offsets are not provided, txt file containing the\nderived relative offsets\"\n", - "pattern": "*_psite_offsets.txt" - } - }, - { - "pos_wig": { - "type": "file", - "description": "Positive strand WIG file for visualization in Genome Browser", - "pattern": "*_pos.wig" - } - }, - { - "neg_wig": { - "type": "file", - "description": "Negative strand WIG file for visualization in Genome Browser", - "pattern": "*_neg.wig" - } - }, - { - "orfs": { - "type": "file", - "description": "\"TSV with ORFs assessed as translating in this BAM file. You can output\nall ORFs regardless of the translation status with option --report_all\"\n", - "pattern": "*_translating_ORFs.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ribotricer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false, strandedness: 'single' ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for sorted BAM/CRAM/SAM file", + "pattern": "*.{bai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Map containing reference information for the candidate ORFs\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "candidate_orfs": { + "type": "file", + "description": "TSV file with candidate ORFs from 'ribotricer prepareorfs'", + "pattern": "*.tsv" + } + } + ] + ], + "output": [ + { + "protocol": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_protocol.txt": { + "type": "file", + "description": "txt file containing inferred protocol if it was inferred (not supplied as input)", + "pattern": "*_protocol.txt" + } + } + ] + }, + { + "bam_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_bam_summary.txt": { + "type": "file", + "description": "Text summary of reads found in the BAM", + "pattern": "*_bam_summary.txt" + } + } + ] + }, + { + "read_length_dist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_read_length_dist.pdf": { + "type": "file", + "description": "PDF-format read length distribution as quality control", + "pattern": "*_read_length_dist.pdf" + } + } + ] + }, + { + "metagene_profile_5p": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_metagene_profiles_5p.tsv": { + "type": "file", + "description": "Metagene profile aligning with the start codon", + "pattern": "*_metagene_profiles_5p.tsv" + } + } + ] + }, + { + "metagene_profile_3p": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_metagene_profiles_3p.tsv": { + "type": "file", + "description": "Metagene profile aligning with the stop codon", + "pattern": "*_metagene_profiles_3p.tsv" + } + } + ] + }, + { + "metagene_plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_metagene_plots.pdf": { + "type": "file", + "description": "Metagene plots for quality control", + "pattern": "*_metagene_plots.pdf" + } + } + ] + }, + { + "psite_offsets": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_psite_offsets.txt": { + "type": "file", + "description": "\"If the P-site offsets are not provided, txt file containing the\nderived relative offsets\"\n", + "pattern": "*_psite_offsets.txt" + } + } + ] + }, + { + "pos_wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_pos.wig": { + "type": "file", + "description": "Positive strand WIG file for visualization in Genome Browser", + "pattern": "*_pos.wig" + } + } + ] + }, + { + "neg_wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_neg.wig": { + "type": "file", + "description": "Negative strand WIG file for visualization in Genome Browser", + "pattern": "*_neg.wig" + } + } + ] + }, + { + "orfs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing riboseq sample information\ne.g. `[ id:'sample1', single_end:false ]\n" + } + }, + { + "*_translating_ORFs.tsv": { + "type": "file", + "description": "\"TSV with ORFs assessed as translating in this BAM file. You can output\nall ORFs regardless of the translation status with option --report_all\"\n", + "pattern": "*_translating_ORFs.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111178,52 +141825,63 @@ "doi": "10.1093/bioinformatics/btz878", "licence": [ "GNU General Public v3 (GPL v3)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta-format sequence file for reference sequences used in the bam file\n", - "pattern": "*.gtf" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF-format annotation file for reference sequences used in the bam file\n", - "pattern": "*.gtf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "candidate_orfs": { - "type": "file", - "description": "TSV file with candidate ORFs", - "pattern": "*.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ribotricer" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta-format sequence file for reference sequences used in the bam file\n", + "pattern": "*.gtf" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF-format annotation file for reference sequences used in the bam file\n", + "pattern": "*.gtf" + } + } + ] + ], + "output": [ + { + "candidate_orfs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "*_candidate_orfs.tsv": { + "type": "file", + "description": "TSV file with candidate ORFs", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111262,150 +141920,245 @@ "doi": "10.1371/journal.pcbi.1006169", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:ribowaltz" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Transcriptome BAM file", + "pattern": "*.{bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Map containing reference information for the reference genome GTF file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file of reference genome", + "pattern": "*.{gtf.gz,gtf}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Map containing reference information for the reference genome FASTA file\ne.g. `[ id:'Ensembl human v.111' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of reference genome", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ] + ], + "output": [ + { + "best_offset": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.best_offset.txt": { + "type": "file", + "description": "Text file with the extremity used for the offset correction step and the best offset for each sample (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)", + "pattern": "*.best_offset.txt" + } + } + ] + }, + { + "offset": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.psite_offset.tsv{,.gz}": { + "type": "file", + "description": "TSV file containing P-site offsets for each read length (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)", + "pattern": "*.psite_offset.tsv.gz" + } + } + ] + }, + { + "offset_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "offset_plot/*": { + "type": "file", + "description": "P-site offset plots for each read length (otional)", + "pattern": "offset_plot/*" + } + } + ] + }, + { + "psites": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file containing P-site transcriptomic coordinates and information for each alignment (optional)", + "pattern": "*.psite.tsv.gz" + } + } + ] + }, + { + "codon_coverage_rpf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.codon_coverage_rpf.tsv{,.gz}": { + "type": "file", + "description": "TSV file with codon-level RPF coverage for each transcript (optional)", + "pattern": "*.codon_coverage_rpf.tsv.gz" + } + } + ] + }, + { + "codon_coverage_psite": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.codon_coverage_psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file with codon-level P-site coverage for each transcript (optional)", + "pattern": "*.codon_coverage_psite.tsv.gz" + } + } + ] + }, + { + "cds_coverage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.cds_coverage_psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file with CDS P-site in-frame counts for each transcript (optional)", + "pattern": "*.cds_coverage_psite.tsv.gz" + } + } + ] + }, + { + "cds_window_coverage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*nt_coverage_psite.tsv{,.gz}": { + "type": "file", + "description": "TSV file with CDS P-site in-frame counts for each transcript, excluding P-sites within defined distances to start and stop codons (defined by passing --exclude_start and --exclude_stop with the number of nucleotides) (optional)", + "pattern": "*nt_coverage_psite.tsv.gz" + } + } + ] + }, + { + "ribowaltz_qc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "ribowaltz_qc/*.pdf": { + "type": "file", + "description": "riboWaltz diagnostic plots (optional)", + "pattern": "ribowaltz_qc/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Map containing reference information for the reference genome GTF file\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Map containing reference information for the reference genome FASTA file\ne.g. `[ id:'Ensembl human v.111' ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Transcriptome BAM file", - "pattern": "*.{bam}" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file of reference genome", - "pattern": "*.{gtf.gz,gtf}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of reference genome", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "best_offset": { - "type": "file", - "description": "Text file with the extremity used for the offset correction step and the best offset for each sample (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)", - "pattern": "*.best_offset.txt" - } - }, - { - "offset": { - "type": "file", - "description": "TSV file containing P-site offsets for each read length (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)", - "pattern": "*.psite_offset.tsv.gz" - } - }, - { - "offset_plot": { - "type": "file", - "description": "P-site offset plots for each read length (otional)", - "pattern": "offset_plot/*" - } - }, - { - "psites": { - "type": "file", - "description": "TSV file containing P-site transcriptomic coordinates and information for each alignment (optional)", - "pattern": "*.psite.tsv.gz" - } - }, - { - "codon_coverage_rpf": { - "type": "file", - "description": "TSV file with codon-level RPF coverage for each transcript (optional)", - "pattern": "*.codon_coverage_rpf.tsv.gz" - } - }, - { - "codon_coverage_psite": { - "type": "file", - "description": "TSV file with codon-level P-site coverage for each transcript (optional)", - "pattern": "*.codon_coverage_psite.tsv.gz" - } - }, - { - "cds_coverage": { - "type": "file", - "description": "TSV file with CDS P-site in-frame counts for each transcript (optional)", - "pattern": "*.cds_coverage_psite.tsv.gz" - } - }, - { - "cds_window_coverage": { - "type": "file", - "description": "TSV file with CDS P-site in-frame counts for each transcript, excluding P-sites within defined distances to start and stop codons (defined by passing --exclude_start and --exclude_stop with the number of nucleotides) (optional)", - "pattern": "*nt_coverage_psite.tsv.gz" - } - }, - { - "ribowaltz_qc": { - "type": "file", - "description": "riboWaltz diagnostic plots (optional)", - "pattern": "ribowaltz_qc/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@iraiosub" - ], - "maintainers": [ - "@iraiosub" - ] - } - }, - { - "name": "rmarkdownnotebook", - "path": "modules/nf-core/rmarkdownnotebook/meta.yml", - "type": "module", - "meta": { - "name": "rmarkdownnotebook", - "description": "Render an rmarkdown notebook. Supports parametrization.", - "keywords": [ - "R", - "notebook", - "reports" - ], - "tools": [ + "authors": [ + "@iraiosub" + ], + "maintainers": [ + "@iraiosub" + ] + } + }, + { + "name": "rmarkdownnotebook", + "path": "modules/nf-core/rmarkdownnotebook/meta.yml", + "type": "module", + "meta": { + "name": "rmarkdownnotebook", + "description": "Render an rmarkdown notebook. Supports parametrization.", + "keywords": [ + "R", + "notebook", + "reports" + ], + "tools": [ { "rmarkdown": { "description": "Dynamic Documents for R", @@ -111414,7 +142167,8 @@ "tool_dev_url": "https://github.com/rstudio/rmarkdown", "licence": [ "GPL-3" - ] + ], + "identifier": "" } } ], @@ -111439,60 +142193,118 @@ } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "notebook": { - "type": "file", - "description": "Rmarkdown file", - "pattern": "*.{Rmd}" - } - }, - { - "parameters": { - "type": "map", - "description": "Groovy map with notebook parameters which will be passed to\nrmarkdown to generate parametrized reports.\n" - } - }, - { - "input_files": { - "type": "file", - "description": "One or multiple files serving as input data for the notebook.", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report": { - "type": "file", - "description": "HTML report generated from Rmarkdown", - "pattern": "*.html" - } - }, - { - "session_info": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "notebook": { + "type": "file", + "description": "Rmarkdown file", + "pattern": "*.{Rmd}" + } + } + ], + [ + { + "parameters": { + "type": "map", + "description": "Groovy map with notebook parameters which will be passed to\nrmarkdown to generate parametrized reports.\n" + } + } + ], + [ + { + "input_files": { + "type": "file", + "description": "One or multiple files serving as input data for the notebook.", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "HTML report generated from Rmarkdown", + "pattern": "*.html" + } + } + ] + }, + { + "parameterised_notebook": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.parameterised.Rmd": { + "type": "file", + "description": "Parameterised Rmarkdown file", + "pattern": "*.parameterised.Rmd" + } + } + ] + }, + { + "artifacts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "artifacts/*": { + "type": "file", + "description": "Artifacts generated by the notebook", + "pattern": "artifacts/*" + } + } + ] + }, + { + "session_info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "session_info.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111531,52 +142343,73 @@ "doi": "10.1093/bioinformatics/btv421", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gff": { - "type": "file", - "description": "A set of GFF3 formatted files", - "pattern": "*.{gff}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results": { - "type": "directory", - "description": "Directory containing Roary result files", - "pattern": "*/*" - } - }, - { - "aln": { - "type": "file", - "description": "Core-genome alignment produced by Roary (Optional)", - "pattern": "*.{aln}" - } + ], + "identifier": "biotools:roary" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gff": { + "type": "file", + "description": "A set of GFF3 formatted files", + "pattern": "*.{gff}" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*": { + "type": "directory", + "description": "Directory containing Roary result files", + "pattern": "*/*" + } + } + ] + }, + { + "aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.aln": { + "type": "file", + "description": "Core-genome alignment produced by Roary (Optional)", + "pattern": "*.{aln}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111606,33 +142439,44 @@ "homepage": "https://github.com/nf-core/rnafusion", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}" + [ + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.{gtf}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "rrna_gtf": [ + { + "*rrna_intervals.gtf": { + "type": "file", + "description": "GTF file with ribosomal RNA only", + "pattern": "*.{gtf}" + } + } + ] }, { - "rrna_gtf": { - "type": "file", - "description": "GTF file with ribosomal RNA only", - "pattern": "*.{gtf}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111664,88 +142508,167 @@ "doi": "10.1186/1471-2105-12-323", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input reads for quantification", - "pattern": "*.fastq.gz" - } - }, - { - "index": { - "type": "file", - "description": "RSEM index", - "pattern": "rsem/*" - } - } - ], - "output": [ - { - "counts_gene": { - "type": "file", - "description": "Expression counts on gene level", - "pattern": "*.genes.results" - } - }, - { - "counts_transctips": { - "type": "file", - "description": "Expression counts on transcript level", - "pattern": "*.isoforms.results" - } - }, - { - "stat": { - "type": "file", - "description": "RSEM statistics", - "pattern": "*.stat" - } - }, - { - "logs": { - "type": "file", - "description": "RSEM logs", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam_star": { - "type": "file", - "description": "BAM file generated by STAR (optional)", - "pattern": "*.STAR.genome.bam" - } - }, - { - "bam_genome": { - "type": "file", - "description": "Genome BAM file (optional)", - "pattern": "*.genome.bam" - } - }, - { - "bam_transcript": { - "type": "file", - "description": "Transcript BAM file (optional)", - "pattern": "*.transcript.bam" - } + ], + "identifier": "biotools:rsem" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input reads for quantification", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "index": { + "type": "file", + "description": "RSEM index", + "pattern": "rsem/*" + } + } + ] + ], + "output": [ + { + "counts_gene": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.genes.results": { + "type": "file", + "description": "Expression counts on gene level", + "pattern": "*.genes.results" + } + } + ] + }, + { + "counts_transcript": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.isoforms.results": { + "type": "file", + "description": "Expression counts on transcript level", + "pattern": "*.isoforms.results" + } + } + ] + }, + { + "stat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.stat": { + "type": "file", + "description": "RSEM statistics", + "pattern": "*.stat" + } + } + ] + }, + { + "logs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "RSEM logs", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "bam_star": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.STAR.genome.bam": { + "type": "file", + "description": "BAM file generated by STAR (optional)", + "pattern": "*.STAR.genome.bam" + } + } + ] + }, + { + "bam_genome": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.genome.bam": { + "type": "file", + "description": "Genome BAM file (optional)", + "pattern": "*.genome.bam" + } + } + ] + }, + { + "bam_transcript": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.transcript.bam": { + "type": "file", + "description": "Transcript BAM file (optional)", + "pattern": "*.transcript.bam" + } + } + ] } ], "authors": [ @@ -111785,47 +142708,64 @@ "doi": "10.1186/1471-2105-12-323", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:rsem" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "The Fasta file of the reference genome", - "pattern": "*.{fasta,fa}" + [ + { + "fasta": { + "type": "file", + "description": "The Fasta file of the reference genome", + "pattern": "*.{fasta,fa}" + } } - }, - { - "gtf": { - "type": "file", - "description": "The GTF file of the reference genome", - "pattern": "*.gtf" + ], + [ + { + "gtf": { + "type": "file", + "description": "The GTF file of the reference genome", + "pattern": "*.gtf" + } } - } + ] ], "output": [ { - "rsem": { - "type": "directory", - "description": "RSEM index directory", - "pattern": "rsem" - } + "index": [ + { + "rsem": { + "type": "directory", + "description": "RSEM index directory", + "pattern": "rsem" + } + } + ] }, { - "transcript_fasta": { - "type": "file", - "description": "Fasta file of transcripts", - "pattern": "rsem/*transcripts.fa" - } + "transcript_fasta": [ + { + "*transcripts.fa": { + "type": "file", + "description": "Fasta file of transcripts", + "pattern": "rsem/*transcripts.fa" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111873,39 +142813,57 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:rseqc" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "the bam file to calculate statistics of", - "pattern": "*.{bam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "the bam file to calculate statistics of", + "pattern": "*.{bam}" + } } - } + ] ], "output": [ { - "txt": { - "type": "file", - "description": "bam statistics report", - "pattern": "*.bam_stat.txt" - } + "txt": [ + { + "meta": { + "type": "file", + "description": "bam statistics report", + "pattern": "*.bam_stat.txt" + } + }, + { + "*.bam_stat.txt": { + "type": "file", + "description": "bam statistics report", + "pattern": "*.bam_stat.txt" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -111949,46 +142907,66 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "the bam file to calculate statistics of", - "pattern": "*.{bam}" - } - }, - { - "bed": { - "type": "file", - "description": "a bed file for the reference gene model", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "txt": { - "type": "file", - "description": "infer_experiment results report", - "pattern": "*.infer_experiment.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:rseqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "the bam file to calculate statistics of", + "pattern": "*.{bam}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "a bed file for the reference gene model", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "file", + "description": "infer_experiment results report", + "pattern": "*.infer_experiment.txt" + } + }, + { + "*.infer_experiment.txt": { + "type": "file", + "description": "infer_experiment results report", + "pattern": "*.infer_experiment.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112036,74 +143014,138 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "the alignment in bam format", - "pattern": "*.{bam}" - } - }, - { - "bed": { - "type": "file", - "description": "a bed file for the reference gene model", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "distance": { - "type": "file", - "description": "the inner distances", - "pattern": "*.inner_distance.txt" - } - }, - { - "freq": { - "type": "file", - "description": "frequencies of different insert sizes", - "pattern": "*.inner_distance_freq.txt" - } - }, - { - "mean": { - "type": "file", - "description": "mean/median values of inner distances", - "pattern": "*.inner_distance_mean.txt" - } - }, - { - "pdf": { - "type": "file", - "description": "distribution plot of inner distances", - "pattern": "*.inner_distance_plot.pdf" - } - }, - { - "rscript": { - "type": "file", - "description": "script to reproduce the plot", - "pattern": "*.inner_distance_plot.R" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:rseqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "the alignment in bam format", + "pattern": "*.{bam}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "a bed file for the reference gene model", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "distance": [ + { + "meta": { + "type": "file", + "description": "the inner distances", + "pattern": "*.inner_distance.txt" + } + }, + { + "*distance.txt": { + "type": "file", + "description": "the inner distances", + "pattern": "*.inner_distance.txt" + } + } + ] + }, + { + "freq": [ + { + "meta": { + "type": "file", + "description": "frequencies of different insert sizes", + "pattern": "*.inner_distance_freq.txt" + } + }, + { + "*freq.txt": { + "type": "file", + "description": "frequencies of different insert sizes", + "pattern": "*.inner_distance_freq.txt" + } + } + ] + }, + { + "mean": [ + { + "meta": { + "type": "file", + "description": "mean/median values of inner distances", + "pattern": "*.inner_distance_mean.txt" + } + }, + { + "*mean.txt": { + "type": "file", + "description": "mean/median values of inner distances", + "pattern": "*.inner_distance_mean.txt" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "distribution plot of inner distances", + "pattern": "*.inner_distance_plot.pdf" + } + }, + { + "*.pdf": { + "type": "file", + "description": "distribution plot of inner distances", + "pattern": "*.inner_distance_plot.pdf" + } + } + ] + }, + { + "rscript": [ + { + "meta": { + "type": "file", + "description": "script to reproduce the plot", + "pattern": "*.inner_distance_plot.R" + } + }, + { + "*.r": { + "type": "file", + "description": "script to reproduce the plot", + "pattern": "*.inner_distance_plot.R" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112147,88 +143189,174 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "the alignment in bam format", - "pattern": "*.{bam}" - } - }, - { - "bed": { - "type": "file", - "description": "a bed file for the reference gene model", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "bed": { - "type": "file", - "description": "bed file of annotated junctions", - "pattern": "*.junction.bed" - } - }, - { - "interact_bed": { - "type": "file", - "description": "Interact bed file", - "pattern": "*.Interact.bed" - } - }, - { - "xls": { - "type": "file", - "description": "xls file with junction information", - "pattern": "*.xls" - } - }, - { - "pdf": { - "type": "file", - "description": "junction plot", - "pattern": "*.junction.pdf" - } - }, - { - "events_pdf": { - "type": "file", - "description": "events plot", - "pattern": "*.events.pdf" - } - }, - { - "rscript": { - "type": "file", - "description": "Rscript to reproduce the plots", - "pattern": "*.r" - } - }, - { - "log": { - "type": "file", - "description": "Log file of execution", - "pattern": "*.junction_annotation.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:rseqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "the alignment in bam format", + "pattern": "*.{bam}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "a bed file for the reference gene model", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "xls": [ + { + "meta": { + "type": "file", + "description": "xls file with junction information", + "pattern": "*.xls" + } + }, + { + "*.xls": { + "type": "file", + "description": "xls file with junction information", + "pattern": "*.xls" + } + } + ] + }, + { + "rscript": [ + { + "meta": { + "type": "file", + "description": "Rscript to reproduce the plots", + "pattern": "*.r" + } + }, + { + "*.r": { + "type": "file", + "description": "Rscript to reproduce the plots", + "pattern": "*.r" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "file", + "description": "Log file of execution", + "pattern": "*.junction_annotation.log" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file of execution", + "pattern": "*.junction_annotation.log" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "file", + "description": "bed file of annotated junctions", + "pattern": "*.junction.bed" + } + }, + { + "*.junction.bed": { + "type": "file", + "description": "bed file of annotated junctions", + "pattern": "*.junction.bed" + } + } + ] + }, + { + "interact_bed": [ + { + "meta": { + "type": "file", + "description": "Interact bed file", + "pattern": "*.Interact.bed" + } + }, + { + "*.Interact.bed": { + "type": "file", + "description": "Interact bed file", + "pattern": "*.Interact.bed" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "junction plot", + "pattern": "*.junction.pdf" + } + }, + { + "*junction.pdf": { + "type": "file", + "description": "junction plot", + "pattern": "*.junction.pdf" + } + } + ] + }, + { + "events_pdf": [ + { + "meta": { + "type": "file", + "description": "events plot", + "pattern": "*.events.pdf" + } + }, + { + "*events.pdf": { + "type": "file", + "description": "events plot", + "pattern": "*.events.pdf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112272,58 +143400,89 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] - } + ], + "identifier": "biotools:rseqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "the alignment in bam format", + "pattern": "*.{bam}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "a bed file for the reference gene model", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "Junction saturation report", + "pattern": "*.pdf" + } + }, + { + "*.pdf": { + "type": "file", + "description": "Junction saturation report", + "pattern": "*.pdf" + } + } + ] + }, + { + "rscript": [ + { + "meta": { + "type": "file", + "description": "Junction saturation R-script", + "pattern": "*.r" + } + }, + { + "*.r": { + "type": "file", + "description": "Junction saturation R-script", + "pattern": "*.r" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "the alignment in bam format", - "pattern": "*.{bam}" - } - }, - { - "bed": { - "type": "file", - "description": "a bed file for the reference gene model", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "pdf": { - "type": "file", - "description": "Junction saturation report", - "pattern": "*.pdf" - } - }, - { - "rscript": { - "type": "file", - "description": "Junction saturation R-script", - "pattern": "*.r" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@drpatelh", - "@kevinmenden" + "authors": [ + "@drpatelh", + "@kevinmenden" ], "maintainers": [ "@drpatelh", @@ -112362,46 +143521,66 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "the alignment in bam format", - "pattern": "*.{bam}" - } - }, - { - "bed": { - "type": "file", - "description": "a bed file for the reference gene model", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "txt": { - "type": "file", - "description": "the read distribution report", - "pattern": "*.read_distribution.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:rseqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "the alignment in bam format", + "pattern": "*.{bam}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "a bed file for the reference gene model", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "file", + "description": "the read distribution report", + "pattern": "*.read_distribution.txt" + } + }, + { + "*.read_distribution.txt": { + "type": "file", + "description": "the read distribution report", + "pattern": "*.read_distribution.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112454,67 +143633,111 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "the alignment in bam format", - "pattern": "*.{bam}" - } - }, - { - "bed": { - "type": "file", - "description": "a bed file for the reference gene model", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "seq_xls": { - "type": "file", - "description": "Read duplication rate determined from mapping position of read", - "pattern": "*seq.DupRate.xls" - } - }, - { - "pos_xls": { - "type": "file", - "description": "Read duplication rate determined from sequence of read", - "pattern": "*pos.DupRate.xls" - } - }, - { - "pdf": { - "type": "file", - "description": "plot of duplication rate", - "pattern": "*.pdf" - } - }, - { - "rscript": { - "type": "file", - "description": "script to reproduce the plot", - "pattern": "*.R" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:rseqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "the alignment in bam format", + "pattern": "*.{bam}" + } + } + ] + ], + "output": [ + { + "seq_xls": [ + { + "meta": { + "type": "file", + "description": "Read duplication rate determined from mapping position of read", + "pattern": "*seq.DupRate.xls" + } + }, + { + "*seq.DupRate.xls": { + "type": "file", + "description": "Read duplication rate determined from mapping position of read", + "pattern": "*seq.DupRate.xls" + } + } + ] + }, + { + "pos_xls": [ + { + "meta": { + "type": "file", + "description": "Read duplication rate determined from sequence of read", + "pattern": "*pos.DupRate.xls" + } + }, + { + "*pos.DupRate.xls": { + "type": "file", + "description": "Read duplication rate determined from sequence of read", + "pattern": "*pos.DupRate.xls" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "file", + "description": "plot of duplication rate", + "pattern": "*.pdf" + } + }, + { + "*.pdf": { + "type": "file", + "description": "plot of duplication rate", + "pattern": "*.pdf" + } + } + ] + }, + { + "rscript": [ + { + "meta": { + "type": "file", + "description": "script to reproduce the plot", + "pattern": "*.R" + } + }, + { + "*.r": { + "type": "file", + "description": "script to reproduce the plot", + "pattern": "*.R" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112562,60 +143785,91 @@ "doi": "10.1093/bioinformatics/bts356", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Input BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Index for input BAM file", - "pattern": "*.{bai}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file containing the reference gene model", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "txt": { - "type": "file", - "description": "TXT file containing tin.py results summary", - "pattern": "*.txt" - } - }, - { - "xls": { - "type": "file", - "description": "XLS file containing tin.py results", - "pattern": "*.xls" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:rseqc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Input BAM file", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for input BAM file", + "pattern": "*.{bai}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "BED file containing the reference gene model", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "txt": [ + { + "meta": { + "type": "file", + "description": "TXT file containing tin.py results summary", + "pattern": "*.txt" + } + }, + { + "*.txt": { + "type": "file", + "description": "TXT file containing tin.py results summary", + "pattern": "*.txt" + } + } + ] + }, + { + "xls": [ + { + "meta": { + "type": "file", + "description": "XLS file containing tin.py results", + "pattern": "*.xls" + } + }, + { + "*.xls": { + "type": "file", + "description": "XLS file containing tin.py results", + "pattern": "*.xls" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112659,59 +143913,70 @@ "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input1": { - "type": "file", - "description": "FASTA, FASTQ, BAM or SAM file. This should be the left input file when using paired end FASTQ/FASTA data", - "pattern": "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" - } - }, - { - "input2": { - "type": "file", - "description": "The right input file when using paired end FASTQ/FASTA data", - "pattern": "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" - } - }, - { - "sam_rg": { - "type": "file", - "description": "A file containing a single readgroup header as a SAM header. This can also be supplied as a string in `task.ext.args` as `--sam-rg `.", - "pattern": "*.{txt,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sdf": { - "type": "directory", - "description": "The sequence dictionary format folder created from the input file(s)", - "pattern": "*.sdf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input1": { + "type": "file", + "description": "FASTA, FASTQ, BAM or SAM file. This should be the left input file when using paired end FASTQ/FASTA data", + "pattern": "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" + } + }, + { + "input2": { + "type": "file", + "description": "The right input file when using paired end FASTQ/FASTA data", + "pattern": "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" + } + }, + { + "sam_rg": { + "type": "file", + "description": "A file containing a single readgroup header as a SAM header. This can also be supplied as a string in `task.ext.args` as `--sam-rg `.", + "pattern": "*.{txt,sam}" + } + } + ] + ], + "output": [ + { + "sdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sdf": { + "type": "directory", + "description": "The sequence dictionary format folder created from the input file(s)", + "pattern": "*.sdf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112754,45 +144019,56 @@ "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", "licence": [ "BSD" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "The input file, can be either a PED or a VCF file", - "pattern": "*.{vcf,vcf.gz,ped}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "The input file, can be either a PED or a VCF file", + "pattern": "*.{vcf,vcf.gz,ped}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf.gz,ped}": { + "type": "file", + "description": "The output file, can be either a filtered PED file\nor a VCF file containing the PED headers (needs --vcf as argument)\n", + "pattern": "*.{vcf.gz,ped}" + } + } + ] }, { - "output": { - "type": "file", - "description": "The output file, can be either a filtered PED file\nor a VCF file containing the PED headers (needs --vcf as argument)\n", - "pattern": "*.{vcf.gz,ped}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112825,52 +144101,73 @@ "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Input TSV ROC files created with RTGTOOLS_VCFEVAL", - "pattern": "*.tsv.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "png": { - "type": "file", - "description": "The resulting rocplot in PNG format", - "pattern": "*.png" - } - }, - { - "svg": { - "type": "file", - "description": "The resulting rocplot in SVG format", - "pattern": "*.svg" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input TSV ROC files created with RTGTOOLS_VCFEVAL", + "pattern": "*.tsv.gz" + } + } + ] + ], + "output": [ + { + "png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.png": { + "type": "file", + "description": "The resulting rocplot in PNG format", + "pattern": "*.png" + } + } + ] + }, + { + "svg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "The resulting rocplot in SVG format", + "pattern": "*.svg" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -112902,170 +144199,309 @@ "tool_dev_url": "https://github.com/RealTimeGenomics/rtg-tools", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "A VCF with called variants to benchmark against the standard", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "query_vcf_index": { - "type": "file", - "description": "The index of the called VCF (optional)", - "pattern": "*.tbi" - } - }, - { - "truth_vcf": { - "type": "file", - "description": "A standard VCF to compare against", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "truth_vcf_index": { - "type": "file", - "description": "The index of the standard VCF (optional)", - "pattern": "*.tbi" - } - }, - { - "truth_bed": { - "type": "file", - "description": "A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)", - "pattern": "*.bed" - } - }, - { - "evaluation_bed": { - "type": "file", - "description": "A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)", - "pattern": "*.bed" - } - }, - { - "sdf": { - "type": "file", - "description": "The SDF (RTG Sequence Data File) folder of the reference genome" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tp_vcf": { - "type": "file", - "description": "A VCF file for the true positive variants", - "pattern": "*.tp.vcf.gz" - } - }, - { - "tp_tbi": { - "type": "file", - "description": "The index of the VCF file for the true positive variants", - "pattern": "*.tp.vcf.gz.tbi" - } - }, - { - "fn_vcf": { - "type": "file", - "description": "A VCF file for the false negative variants", - "pattern": "*.fn.vcf.gz" - } - }, - { - "fn_tbi": { - "type": "file", - "description": "The index of the VCF file for the false negative variants", - "pattern": "*.fn.vcf.gz.tbi" - } - }, - { - "fp_vcf": { - "type": "file", - "description": "A VCF file for the false positive variants", - "pattern": "*.fp.vcf.gz" - } - }, - { - "fp_tbi": { - "type": "file", - "description": "The index of the VCF file for the false positive variants", - "pattern": "*.fp.vcf.gz.tbi" - } - }, - { - "baseline_vcf": { - "type": "file", - "description": "A VCF file for the true positive variants from the baseline", - "pattern": "*.tp-baseline.vcf.gz" - } - }, - { - "baseline_tbi": { - "type": "file", - "description": "The index of the VCF file for the true positive variants from the baseline", - "pattern": "*.tp-baseline.vcf.gz.tbi" - } - }, - { - "snp_roc": { - "type": "file", - "description": "TSV files containing ROC data for the SNPs", - "pattern": "*.snp_roc.tsv.gz" - } - }, - { - "non_snp_roc": { - "type": "file", - "description": "TSV files containing ROC data for all variants except SNPs", - "pattern": "*.non_snp_roc.tsv.gz" - } - }, - { - "weighted_roc": { - "type": "file", - "description": "TSV files containing weighted ROC data for all variants", - "pattern": "*.weighted_snp_roc.tsv.gz" - } - }, - { - "summary": { - "type": "file", - "description": "A TXT file containing the summary of the evaluation", - "pattern": "*.summary.txt" - } - }, - { - "phasing": { - "type": "file", - "description": "A TXT file containing the data on the phasing", - "pattern": "*.phasing.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "A VCF with called variants to benchmark against the standard", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "query_vcf_tbi": { + "type": "file", + "description": "The index of the VCF file with called variants to benchmark against the standard", + "pattern": "*.{vcf.gz.tbi, vcf.tbi}" + } + }, + { + "truth_vcf": { + "type": "file", + "description": "A standard VCF to compare against", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "truth_vcf_tbi": { + "type": "file", + "description": "The index of the standard VCF to compare against", + "pattern": "*.{vcf.gz.tbi, vcf.tbi}" + } + }, + { + "truth_bed": { + "type": "file", + "description": "A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)", + "pattern": "*.bed" + } + }, + { + "evaluation_bed": { + "type": "file", + "description": "A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sdf": { + "type": "file", + "description": "The SDF (RTG Sequence Data File) folder of the reference genome" + } + } + ] + ], + "output": [ + { + "tp_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tp.vcf.gz": { + "type": "file", + "description": "A VCF file for the true positive variants", + "pattern": "*.tp.vcf.gz" + } + } + ] + }, + { + "tp_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tp.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF file for the true positive variants", + "pattern": "*.tp.vcf.gz.tbi" + } + } + ] + }, + { + "fn_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fn.vcf.gz": { + "type": "file", + "description": "A VCF file for the false negative variants", + "pattern": "*.fn.vcf.gz" + } + } + ] + }, + { + "fn_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fn.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF file for the false negative variants", + "pattern": "*.fn.vcf.gz.tbi" + } + } + ] + }, + { + "fp_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fp.vcf.gz": { + "type": "file", + "description": "A VCF file for the false positive variants", + "pattern": "*.fp.vcf.gz" + } + } + ] + }, + { + "fp_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fp.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF file for the false positive variants", + "pattern": "*.fp.vcf.gz.tbi" + } + } + ] + }, + { + "baseline_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tp-baseline.vcf.gz": { + "type": "file", + "description": "A VCF file for the true positive variants from the baseline", + "pattern": "*.tp-baseline.vcf.gz" + } + } + ] + }, + { + "baseline_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tp-baseline.vcf.gz.tbi": { + "type": "file", + "description": "The index of the VCF file for the true positive variants from the baseline", + "pattern": "*.tp-baseline.vcf.gz.tbi" + } + } + ] + }, + { + "snp_roc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.snp_roc.tsv.gz": { + "type": "file", + "description": "TSV files containing ROC data for the SNPs", + "pattern": "*.snp_roc.tsv.gz" + } + } + ] + }, + { + "non_snp_roc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.non_snp_roc.tsv.gz": { + "type": "file", + "description": "TSV files containing ROC data for all variants except SNPs", + "pattern": "*.non_snp_roc.tsv.gz" + } + } + ] + }, + { + "weighted_roc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.weighted_roc.tsv.gz": { + "type": "file", + "description": "TSV files containing weighted ROC data for all variants", + "pattern": "*.weighted_snp_roc.tsv.gz" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary.txt": { + "type": "file", + "description": "A TXT file containing the summary of the evaluation", + "pattern": "*.summary.txt" + } + } + ] + }, + { + "phasing": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.phasing.txt": { + "type": "file", + "description": "A TXT file containing the data on the phasing", + "pattern": "*.phasing.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113108,54 +144544,111 @@ "doi": "10.1038/ncomms3464", "licence": [ "Artistic-2.0" - ] - } - } - ], - "input": [ - { - "expression_matrix": { - "type": "file", - "description": "expression matrix in TSV format", - "pattern": "*.tsv" - } - } - ], - "output": [ - { - "tni": { - "type": "file", - "description": "RDS R Object with the TNI object", - "pattern": "tni.rds" - } - }, - { - "tni_perm": { - "type": "file", - "description": "RDS R Object with the TNI object after permutation", - "pattern": "tni_permutated.rds" - } - }, - { - "tni_bootstrap": { - "type": "file", - "description": "RDS R Object with the TNI object after permutation and bootstrap", - "pattern": "tni_bootstrapped.rds" - } - }, - { - "tni_filtered": { - "type": "file", - "description": "RDS R Object with the TNI object after permutation, bootstrap and filtering", - "pattern": "tni_filtered.rds" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:rtn" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "expression_matrix": { + "type": "file", + "description": "expression matrix in TSV format", + "pattern": "*.tsv" + } + } + ] + ], + "output": [ + { + "tni": [ + { + "meta": { + "type": "file", + "description": "RDS R Object with the TNI object", + "pattern": "tni.rds" + } + }, + { + "tni.rds": { + "type": "file", + "description": "RDS R Object with the TNI object", + "pattern": "tni.rds" + } + } + ] + }, + { + "tni_perm": [ + { + "meta": { + "type": "file", + "description": "RDS R Object with the TNI object after permutation", + "pattern": "tni_permutated.rds" + } + }, + { + "tni_permutated.rds": { + "type": "file", + "description": "RDS R Object with the TNI object after permutation", + "pattern": "tni_permutated.rds" + } + } + ] + }, + { + "tni_bootstrap": [ + { + "meta": { + "type": "file", + "description": "RDS R Object with the TNI object after permutation and bootstrap", + "pattern": "tni_bootstrapped.rds" + } + }, + { + "tni_bootstrapped.rds": { + "type": "file", + "description": "RDS R Object with the TNI object after permutation and bootstrap", + "pattern": "tni_bootstrapped.rds" + } + } + ] + }, + { + "tni_filtered": [ + { + "meta": { + "type": "file", + "description": "RDS R Object with the TNI object after permutation, bootstrap and filtering", + "pattern": "tni_filtered.rds" + } + }, + { + "tni_filtered.rds": { + "type": "file", + "description": "RDS R Object with the TNI object after permutation, bootstrap and filtering", + "pattern": "tni_filtered.rds" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113188,99 +144681,154 @@ "doi": "10.1021/acs.jproteome.3c00486", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "\"*.mzML\"": { - "type": "file", - "description": "mzML open source mass spectrometry raw data format", - "pattern": "*.{mzML, mzML.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about fasta_proteome\ne.g. `[ id:'sample1']`\n" - } - }, - { - "fasta_proteome": { - "type": "file", - "description": "proteome database in fasta format", - "pattern": "*.{fasta, fasta.gz}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information about base_config\ne.g. `[ id:'sample1']`\n" - } - }, - { - "base_config": { - "type": "file", - "description": "sage configuration json", - "pattern": "*.{json}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "results_tsv": { - "type": "file", - "description": "tsv output results", - "pattern": "results.sage.tsv" - } - }, - { - "results_json": { - "type": "file", - "description": "json output results", - "pattern": "results.json" - } - }, - { - "results_pin": { - "type": "file", - "description": "pin format output results", - "pattern": "results.sage.pin" - } - }, - { - "tmt_tsv": { - "type": "file", - "description": "tandem mass tag quantification", - "pattern": "tmt.tsv" - } - }, - { - "lfq_tsv": { - "type": "file", - "description": "label free quantification", - "pattern": "lfq.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "\"*.mzML\"": { + "type": "file", + "description": "mzML open source mass spectrometry raw data format", + "pattern": "*.{mzML, mzML.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about fasta_proteome\ne.g. `[ id:'sample1']`\n" + } + }, + { + "fasta_proteome": { + "type": "file", + "description": "proteome database in fasta format", + "pattern": "*.{fasta, fasta.gz}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information about base_config\ne.g. `[ id:'sample1']`\n" + } + }, + { + "base_config": { + "type": "file", + "description": "sage configuration json", + "pattern": "*.{json}" + } + } + ] + ], + "output": [ + { + "results_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "results.sage.tsv": { + "type": "file", + "description": "tsv output results", + "pattern": "results.sage.tsv" + } + } + ] + }, + { + "results_json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "results.json": { + "type": "file", + "description": "json output results", + "pattern": "results.json" + } + } + ] + }, + { + "results_pin": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "results.sage.pin": { + "type": "file", + "description": "pin format output results", + "pattern": "results.sage.pin" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "tmt_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "tmt.tsv": { + "type": "file", + "description": "tandem mass tag quantification", + "pattern": "tmt.tsv" + } + } + ] + }, + { + "lfq_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "lfq.tsv": { + "type": "file", + "description": "label free quantification", + "pattern": "lfq.tsv" + } + } + ] } ], "authors": [ @@ -113313,38 +144861,51 @@ "doi": "10.1038/nmeth.4197", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "biotools:salmon" } } ], "input": [ - { - "genome_fasta": { - "type": "file", - "description": "Fasta file of the reference genome" + [ + { + "genome_fasta": { + "type": "file", + "description": "Fasta file of the reference genome" + } } - }, - { - "transcriptome_fasta": { - "type": "file", - "description": "Fasta file of the reference transcriptome" + ], + [ + { + "transcript_fasta": { + "type": "file", + "description": "Fasta file of the reference transcriptome" + } } - } + ] ], "output": [ { - "index": { - "type": "directory", - "description": "Folder containing the star index files", - "pattern": "salmon" - } + "index": [ + { + "salmon": { + "type": "directory", + "description": "Folder containing the star index files", + "pattern": "salmon" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113397,75 +144958,131 @@ "doi": "10.1038/nmeth.4197", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files for single-end or paired-end data.\nMultiple single-end fastqs or pairs of paired-end fastqs are\nhandled.\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the star index files" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF of the reference transcriptome" - } - }, - { - "transcript_fasta": { - "type": "file", - "description": "Fasta file of the reference transcriptome" - } - }, - { - "alignment_mode": { - "type": "boolean", - "description": "whether to run salmon in alignment mode" - } - }, - { - "lib_type": { - "type": "string", - "description": "Override library type inferred based on strandedness defined in meta object\n" - } - } - ], - "output": [ - { - "results": { - "type": "directory", - "description": "Folder containing the quantification results for a specific sample", - "pattern": "${prefix}" - } - }, - { - "json_info": { - "type": "file", - "description": "File containing meta information from Salmon quant", - "pattern": "*info.json" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:salmon" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files for single-end or paired-end data.\nMultiple single-end fastqs or pairs of paired-end fastqs are\nhandled.\n" + } + } + ], + [ + { + "index": { + "type": "directory", + "description": "Folder containing the star index files" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "GTF of the reference transcriptome" + } + } + ], + [ + { + "transcript_fasta": { + "type": "file", + "description": "Fasta file of the reference transcriptome" + } + } + ], + [ + { + "alignment_mode": { + "type": "boolean", + "description": "whether to run salmon in alignment mode" + } + } + ], + [ + { + "lib_type": { + "type": "string", + "description": "Override library type inferred based on strandedness defined in meta object\n" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "directory", + "description": "Folder containing the quantification results for a specific sample", + "pattern": "${prefix}" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Folder containing the quantification results for a specific sample", + "pattern": "${prefix}" + } + } + ] + }, + { + "json_info": [ + { + "meta": { + "type": "file", + "description": "File containing meta information from Salmon quant", + "pattern": "*info.json" + } + }, + { + "*info.json": { + "type": "file", + "description": "File containing meta information from Salmon quant", + "pattern": "*info.json" + } + } + ] + }, + { + "lib_format_counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*lib_format_counts.json": { + "type": "file", + "description": "File containing the library format counts", + "pattern": "*lib_format_counts.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113521,73 +145138,131 @@ "doi": "10.1186/s12864-017-3879-z", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of assembly. Headers must not contain ':'", - "pattern": "*.{fa, fasta}" - } - }, - { - "index": { - "type": "file", - "description": "Fasta index file of assembly containing the length of contigs.", - "pattern": "*.{fa.fai, fasta.fai}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file of alignments sorted by read names, e.g., from HiC-Pro", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequences for the scaffolds generated by the algorithm", - "pattern": "*_scaffolds_FINAL.fasta" - } - }, - { - "agp": { - "type": "file", - "description": "AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds", - "pattern": "*_scaffolds_FINAL.agp" - } - }, - { - "agp_original_coordinates": { - "type": "file", - "description": "Secondary output AGP file with names and coordinates matching the original input assembly (optional)", - "pattern": "*scaffolds_FINAL.original-coordinates.agp" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of assembly. Headers must not contain ':'", + "pattern": "*.{fa, fasta}" + } + }, + { + "index": { + "type": "file", + "description": "Fasta index file of assembly containing the length of contigs.", + "pattern": "*.{fa.fai, fasta.fai}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "BED file of alignments sorted by read names, e.g., from HiC-Pro", + "pattern": "*.{bed}" + } + } + ], + [ + { + "gfa": { + "type": "file", + "description": "GFA file of the assembly graph" + } + } + ], + [ + { + "dup": { + "type": "file", + "description": "File containing the duplicated contigs" + } + } + ], + [ + { + "filter_bed": { + "type": "file", + "description": "BED file of the filtered alignments", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_scaffolds_FINAL.fasta": { + "type": "file", + "description": "Sequences for the scaffolds generated by the algorithm", + "pattern": "*_scaffolds_FINAL.fasta" + } + } + ] + }, + { + "agp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_scaffolds_FINAL.agp": { + "type": "file", + "description": "AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds", + "pattern": "*_scaffolds_FINAL.agp" + } + } + ] + }, + { + "agp_original_coordinates": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*scaffolds_FINAL.original-coordinates.agp": { + "type": "file", + "description": "Secondary output AGP file with names and coordinates matching the original input assembly (optional)", + "pattern": "*scaffolds_FINAL.original-coordinates.agp" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113622,73 +145297,106 @@ "doi": "10.21105/joss.04360", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index", - "pattern": "*.{bai,.crai}" - } - }, - { - "database": { - "type": "file", - "description": "Directory containing the sam2lca database", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "CSV file containing the sam2lca results", - "pattern": "*.csv" - } - }, - { - "json": { - "type": "file", - "description": "JSON file containing the sam2lca results", - "pattern": "*.json" - } - }, - { - "bam": { - "type": "file", - "description": "Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic informations", - "pattern": "*.bam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM index", + "pattern": "*.{bai,.crai}" + } + } + ], + [ + { + "database": { + "type": "file", + "description": "Directory containing the sam2lca database", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "CSV file containing the sam2lca results", + "pattern": "*.csv" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file containing the sam2lca results", + "pattern": "*.json" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic informations", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113720,45 +145428,56 @@ "tool_dev_url": "https://github.com/biod/sambamba", "licence": [ "GPL v2" - ] + ], + "identifier": "biotools:sambamba" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "Stats file", + "pattern": "*.{stats}" + } + } + ] }, { - "stats": { - "type": "file", - "description": "Stats file", - "pattern": "*.{stats}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113790,52 +145509,73 @@ "tool_dev_url": "https://github.com/biod/sambamba", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "An optional BAM index file.", - "pattern": "*.{bai}" - } + ], + "identifier": "biotools:sambamba" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "An optional BAM index file.", + "pattern": "*.{bai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113867,45 +145607,56 @@ "doi": "10.1093/bioinformatics/btu314", "licence": [ "MIT" - ] + ], + "identifier": "biotools:samblaster" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.bam" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.bam" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Tagged or filtered BAM file", + "pattern": "*.bam" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Tagged or filtered BAM file", - "pattern": "*.bam" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -113949,78 +145700,115 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file of regions to be removed (e.g. amplicon primers)", - "pattern": "*.{bed}" - } - }, - { - "save_cliprejects": { - "type": "boolean", - "description": "Save filtered reads to a file" - } - }, - { - "save_clipstats": { - "type": "boolean", - "description": "Save clipping stats to a file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Clipped reads BAM file", - "pattern": "*.{bam}" - } - }, - { - "stats": { - "type": "file", - "description": "Clipping statistics text file", - "pattern": "*.{clipstats.txt}" - } - }, - { - "rejects_bam": { - "type": "file", - "description": "Filtered reads BAM file", - "pattern": "*.{cliprejects.bam}" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "BED file of regions to be removed (e.g. amplicon primers)", + "pattern": "*.{bed}" + } + } + ], + [ + { + "save_cliprejects": { + "type": "boolean", + "description": "Save filtered reads to a file" + } + } + ], + [ + { + "save_clipstats": { + "type": "boolean", + "description": "Save clipping stats to a file" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clipallowed.bam": { + "type": "file", + "description": "Clipped reads BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clipstats.txt": { + "type": "file", + "description": "Clipping statistics text file", + "pattern": "*.{clipstats.txt}" + } + } + ] + }, + { + "rejects_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cliprejects.bam": { + "type": "file", + "description": "Filtered reads BAM file", + "pattern": "*.{cliprejects.bam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114050,51 +145838,64 @@ "documentation": "http://www.htslib.org/doc/1.1/samtools.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "inputbam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "split": { - "type": "boolean", - "description": "TRUE/FALSE value to indicate if reads should be separated into\n/1, /2 and if present other, or singleton.\nNote: choosing TRUE will generate 4 different files.\nChoosing FALSE will produce a single file, which will be interleaved in case\nthe input contains paired reads.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)\nor a single interleaved .fq.gz file if the user chooses not to split the reads.\n", - "pattern": "*.fq.gz" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputbam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "split": { + "type": "boolean", + "description": "TRUE/FALSE value to indicate if reads should be separated into\n/1, /2 and if present other, or singleton.\nNote: choosing TRUE will generate 4 different files.\nChoosing FALSE will produce a single file, which will be interleaved in case\nthe input contains paired reads.\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fq.gz": { + "type": "file", + "description": "FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)\nor a single interleaved .fq.gz file if the user chooses not to split the reads.\n", + "pattern": "*.fq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114137,52 +145938,71 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA ref file", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA ref file", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114215,52 +146035,73 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_files": { - "type": "file", - "description": "BAM/CRAM files", - "pattern": "*.{bam,cram}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Concatenated BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Concatenated CRAM file", - "pattern": "*.{cram}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_files": { + "type": "file", + "description": "BAM/CRAM files", + "pattern": "*.{bam,cram}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "Concatenated BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "Concatenated CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114294,45 +146135,105 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "Collated BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA ref file", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Sorted CRAM", + "pattern": "*.{cram}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "Sorted SAM", + "pattern": "*.{sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114362,86 +146263,135 @@ "documentation": "http://www.htslib.org/doc/1.1/samtools.html", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "interleave": { - "type": "boolean", - "description": "If true, the output is a single interleaved paired-end FASTQ\nIf false, the output split paired-end FASTQ\n", - "default": false - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "R1 and R2 FASTQ files\n", - "pattern": "*_{1,2}.fq.gz" - } - }, - { - "fastq_interleaved": { - "type": "file", - "description": "Interleaved paired end FASTQ files\n", - "pattern": "*_interleaved.fq.gz" - } - }, - { - "fastq_other": { - "type": "file", - "description": "FASTQ files with reads where the READ1 and READ2 FLAG bits set are either both set or both unset.\n", - "pattern": "*_other.fq.gz" - } - }, - { - "fastq_singleton": { - "type": "file", - "description": "FASTQ files with singleton reads.\n", - "pattern": "*_singleton.fq.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "interleave": { + "type": "boolean", + "description": "If true, the output is a single interleaved paired-end FASTQ\nIf false, the output split paired-end FASTQ\n", + "default": false + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_{1,2}.fq.gz" + } + }, + { + "*_{1,2}.fq.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_{1,2}.fq.gz" + } + } + ] + }, + { + "fastq_interleaved": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_interleaved.fq.gz" + } + }, + { + "*_interleaved.fq": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_interleaved.fq.gz" + } + } + ] + }, + { + "fastq_other": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_other.fq.gz" + } + }, + { + "*_other.fq.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_other.fq.gz" + } + } + ] + }, + { + "fastq_singleton": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_singleton.fq.gz" + } + }, + { + "*_singleton.fq.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*_singleton.fq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114498,45 +146448,90 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "Consensus sequences", - "pattern": "*.{fasta,fastq,pileup}" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Consensus FASTA file", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fastq": { + "type": "file", + "description": "Consensus FASTQ file", + "pattern": "*.{fastq}" + } + } + ] + }, + { + "pileup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.pileup": { + "type": "file", + "description": "Consensus PILEUP file", + "pattern": "*.{pileup}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114569,80 +146564,144 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file to create the CRAM file", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "filtered/converted BAM file", - "pattern": "*{.bam}" - } - }, - { - "cram": { - "type": "file", - "description": "filtered/converted CRAM file", - "pattern": "*{cram}" - } - }, - { - "bai": { - "type": "file", - "description": "filtered/converted BAM index", - "pattern": "*{.bai}" - } - }, - { - "crai": { - "type": "file", - "description": "filtered/converted CRAM index", - "pattern": "*{.crai}" - } - }, - { - "version": { - "type": "file", - "description": "File containing software version", - "pattern": "*.{version.txt}" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "index": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file to create the CRAM file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference index file to create the CRAM file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "filtered/converted BAM file", + "pattern": "*{.bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "filtered/converted CRAM file", + "pattern": "*{cram}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "filtered/converted BAM index", + "pattern": "*{.bai}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "filtered/converted CRAM index", + "pattern": "*{.crai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114687,72 +146746,93 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Reference genome index file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "coverage": { - "type": "file", - "description": "Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with --histogram).", - "pattern": "*.txt" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference genome index file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "coverage": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with --histogram).", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114790,45 +146870,56 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] + ], + "identifier": "biotools:samtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cram": { - "type": "file", - "description": "CRAM file", - "pattern": "*.cram" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cram": { + "type": "file", + "description": "CRAM file", + "pattern": "*.cram" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "size": { - "type": "file", - "description": "Size information file", - "pattern": "*.size" - } + "size": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.size": { + "type": "file", + "description": "Size information file", + "pattern": "*.size" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114859,58 +146950,71 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "list of positions or regions in specified bed file", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta1": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position", - "pattern": "*.{tsv}" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "intervals": { + "type": "file", + "description": "list of positions or regions in specified bed file", + "pattern": "*.{bed}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -114950,45 +147054,56 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] + ], + "identifier": "biotools:samtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "dict": { - "type": "file", - "description": "FASTA dictionary file", - "pattern": "*.{dict}" - } + "dict": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.dict": { + "type": "file", + "description": "FASTA dictionary file", + "pattern": "*.{dict}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115030,72 +147145,105 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fa": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fa}" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}" - } - }, - { - "gzi": { - "type": "file", - "description": "Optional gzip index file for compressed inputs", - "pattern": "*.gzi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{fa,fasta}": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fa}" + } + } + ] + }, + { + "fai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}" + } + } + ] + }, + { + "gzi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gzi": { + "type": "file", + "description": "Optional gzip index file for compressed inputs", + "pattern": "*.gzi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115227,72 +147375,115 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "interleave": { - "type": "boolean", - "description": "Set true for interleaved fasta files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Compressed FASTA file(s) with reads with either the READ1 or READ2 flag set in separate files.", - "pattern": "*_{1,2}.fasta.gz" - } - }, - { - "interleaved": { - "type": "file", - "description": "Compressed FASTA file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.", - "pattern": "*_interleaved.fasta.gz" - } - }, - { - "singleton": { - "type": "file", - "description": "Compressed FASTA file with singleton reads", - "pattern": "*_singleton.fasta.gz" - } - }, - { - "other": { - "type": "file", - "description": "Compressed FASTA file with reads with either both READ1 and READ2 flags set or unset", - "pattern": "*_other.fasta.gz" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "interleave": { + "type": "boolean", + "description": "Set true for interleaved fasta files" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_{1,2}.fasta.gz": { + "type": "file", + "description": "Compressed FASTA file(s) with reads with either the READ1 or READ2 flag set in separate files.", + "pattern": "*_{1,2}.fasta.gz" + } + } + ] + }, + { + "interleaved": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_interleaved.fasta.gz": { + "type": "file", + "description": "Compressed FASTA file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.", + "pattern": "*_interleaved.fasta.gz" + } + } + ] + }, + { + "singleton": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_singleton.fasta.gz": { + "type": "file", + "description": "Compressed FASTA file with singleton reads", + "pattern": "*_singleton.fasta.gz" + } + } + ] + }, + { + "other": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_other.fasta.gz": { + "type": "file", + "description": "Compressed FASTA file with reads with either both READ1 and READ2 flags set or unset", + "pattern": "*_other.fasta.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115325,72 +147516,115 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "interleave": { - "type": "boolean", - "description": "Set true for interleaved fastq file" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.", - "pattern": "*_{1,2}.fastq.gz" - } - }, - { - "interleaved": { - "type": "file", - "description": "Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.", - "pattern": "*_interleaved.fastq.gz" - } - }, - { - "singleton": { - "type": "file", - "description": "Compressed FASTQ file with singleton reads", - "pattern": "*_singleton.fastq.gz" - } - }, - { - "other": { - "type": "file", - "description": "Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset", - "pattern": "*_other.fastq.gz" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "interleave": { + "type": "boolean", + "description": "Set true for interleaved fastq file" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_{1,2}.fastq.gz": { + "type": "file", + "description": "Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.", + "pattern": "*_{1,2}.fastq.gz" + } + } + ] + }, + { + "interleaved": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_interleaved.fastq": { + "type": "file", + "description": "Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.", + "pattern": "*_interleaved.fastq.gz" + } + } + ] + }, + { + "singleton": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_singleton.fastq.gz": { + "type": "file", + "description": "Compressed FASTQ file with singleton reads", + "pattern": "*_singleton.fastq.gz" + } + } + ] + }, + { + "other": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_other.fastq.gz": { + "type": "file", + "description": "Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset", + "pattern": "*_other.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115443,45 +147677,56 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] + ], + "identifier": "biotools:samtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file, must be sorted by name, not coordinate", - "pattern": "*.{bam,cram,sam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file, must be sorted by name, not coordinate", + "pattern": "*.{bam,cram,sam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "A BAM/CRAM/SAM file with mate information added and/or proper pairs recalled", + "pattern": "*.{bam,cram,sam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "A BAM/CRAM/SAM file with mate information added and/or proper pairs recalled", - "pattern": "*.{bam,cram,sam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115516,52 +147761,63 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "Index for BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "flagstat": { - "type": "file", - "description": "File containing samtools flagstat output", - "pattern": "*.{flagstat}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + } + ] + ], + "output": [ + { + "flagstat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.flagstat": { + "type": "file", + "description": "File containing samtools flagstat output", + "pattern": "*.{flagstat}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115701,44 +147957,49 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] + ], + "identifier": "biotools:samtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "readgroup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] }, { - "readgroup": { - "type": "file", - "description": "File containing readgroup string(s)" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115774,52 +148035,63 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "Index for BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "idxstats": { - "type": "file", - "description": "File containing samtools idxstats output", - "pattern": "*.{idxstats}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index for BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + } + ] + ], + "output": [ + { + "idxstats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.idxstats": { + "type": "file", + "description": "File containing samtools idxstats output", + "pattern": "*.{idxstats}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -115955,59 +148227,90 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "fastq data to be converted to SAM/BAM/CRAM", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sam": { - "type": "file", - "description": "SAM file", - "pattern": "*.sam" - } - }, - { - "bam": { - "type": "file", - "description": "Unaligned BAM file", - "pattern": "*.bam" - } - }, - { - "cram": { - "type": "file", - "description": "Unaligned CRAM file", - "pattern": "*.cram" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq data to be converted to SAM/BAM/CRAM", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } + } + ] + ], + "output": [ + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "SAM file", + "pattern": "*.sam" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Unaligned BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Unaligned CRAM file", + "pattern": "*.cram" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -116040,59 +148343,89 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "crai": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "csi": { - "type": "file", - "description": "CSI index file", - "pattern": "*.{csi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "input file" + } + } + ] + ], + "output": [ + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "CSI index file", + "pattern": "*.{csi}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -116284,58 +148617,105 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "A reference genome in FASTA format", - "pattern": "*.fasta" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "output": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A reference genome in FASTA format", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*{.bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "CRAM file", + "pattern": "*{.cram}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "SAM file", + "pattern": "*{.sam}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -116368,92 +148748,137 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_files": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM was created with (optional)", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the reference file the CRAM was created with (optional)", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "CRAM file", - "pattern": "*.{cram}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csi": { - "type": "file", - "description": "BAM index file (optional)", - "pattern": "*.csi" - } - }, - { - "crai": { - "type": "file", - "description": "CRAM index file (optional)", - "pattern": "*.crai" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_files": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file the CRAM was created with (optional)", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the reference file the CRAM was created with (optional)", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "BAM index file (optional)", + "pattern": "*.csi" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "CRAM index file (optional)", + "pattern": "*.crai" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -116540,59 +148965,72 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" - } - }, - { - "intervals": { - "type": "file", - "description": "Interval FILE", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mpileup": { - "type": "file", - "description": "mpileup file", - "pattern": "*.{mpileup}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval FILE", + "pattern": "*.bed" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "mpileup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mpileup.gz": { + "type": "file", + "description": "mpileup file", + "pattern": "*.{mpileup}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -116637,45 +149075,56 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] + ], + "identifier": "biotools:samtools" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file to be reheaded", - "pattern": "*.{bam,cram}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file to be reheaded", + "pattern": "*.{bam,cram}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Reheaded BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Reheaded BAM/CRAM file", - "pattern": "*.{bam,cram}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -116724,7 +149173,8 @@ "licence": [ "MIT" ], - "args_id": "$args" + "args_id": "$args", + "identifier": "biotools:samtools" } }, { @@ -116736,7 +149186,8 @@ "licence": [ "MIT" ], - "args_id": "$args2" + "args_id": "$args2", + "identifier": "biotools:samtools" } }, { @@ -116748,7 +149199,8 @@ "licence": [ "MIT" ], - "args_id": "$args3" + "args_id": "$args3", + "identifier": "biotools:samtools" } }, { @@ -116760,7 +149212,8 @@ "licence": [ "MIT" ], - "args_id": "$args4" + "args_id": "$args4", + "identifier": "biotools:samtools" } }, { @@ -116772,86 +149225,139 @@ "licence": [ "MIT" ], - "args_id": "$args5" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM files", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file", - "pattern": "*.{fasta,fa,fna}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted and duplicate marked BAM file", - "pattern": "*.bam" - } - }, - { - "cram": { - "type": "file", - "description": "Sorted and duplicate marked CRAM file", - "pattern": "*.cram" - } - }, - { - "csi": { - "type": "file", - "description": "Sorted and duplicate marked BAM index file", - "pattern": "*.csi" - } - }, - { - "crai": { - "type": "file", - "description": "Sorted and duplicate marked CRAM index file", - "pattern": "*.crai" - } - }, - { - "metrics": { - "type": "file", - "description": "Duplicate metrics file", - "pattern": "*.metrics" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "args_id": "$args5", + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM files", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file", + "pattern": "*.{fasta,fa,fna}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted and duplicate marked BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Sorted and duplicate marked CRAM file", + "pattern": "*.cram" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "Sorted and duplicate marked BAM index file", + "pattern": "*.csi" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "Sorted and duplicate marked CRAM index file", + "pattern": "*.crai" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "Duplicate metrics file", + "pattern": "*.metrics" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -116884,80 +149390,123 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file(s)", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta,fna}", - "optional": true - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "Sorted CRAM file", - "pattern": "*.{cram}" - } - }, - { - "crai": { - "type": "file", - "description": "CRAM index file (optional)", - "pattern": "*.crai" - } - }, - { - "csi": { - "type": "file", - "description": "BAM index file (optional)", - "pattern": "*.csi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file(s)", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta,fna}", + "optional": true + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "Sorted CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "CRAM index file (optional)", + "pattern": "*.crai" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "BAM index file (optional)", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -117105,65 +149654,78 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM was created with (optional)", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "stats": { - "type": "file", - "description": "File containing samtools stats output", - "pattern": "*.{stats}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file the CRAM was created with (optional)", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "File containing samtools stats output", + "pattern": "*.{stats}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -117314,121 +149876,206 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "index": { - "type": "file", - "description": "BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)", - "pattern": "*.{.bai,.csi,.crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference file the CRAM was created with (optional)", - "pattern": "*.{fasta,fa}" - } - }, - { - "qname": { - "type": "file", - "description": "Optional file with read names to output only select alignments", - "pattern": "*.{txt,list}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "optional filtered/converted BAM file", - "pattern": "*.{bam}" - } - }, - { - "cram": { - "type": "file", - "description": "optional filtered/converted CRAM file", - "pattern": "*.{cram}" - } - }, - { - "sam": { - "type": "file", - "description": "optional filtered/converted SAM file", - "pattern": "*.{sam}" - } - }, - { - "bai": { - "type": "file", - "description": "optional BAM file index", - "pattern": "*.{bai}" - } - }, - { - "csi": { - "type": "file", - "description": "optional tabix BAM file index", - "pattern": "*.{csi}" - } - }, - { - "crai": { - "type": "file", - "description": "optional CRAM file index", - "pattern": "*.{crai}" - } - }, - { - "unselected": { - "type": "file", - "description": "optional file with unselected alignments", - "pattern": "*.unselected.{bam,cram,sam}" - } - }, - { - "unselected_index": { - "type": "file", - "description": "index for the \"unselected\" file", - "pattern": "*.unselected.{bai,csi,crai}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:samtools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "index": { + "type": "file", + "description": "BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)", + "pattern": "*.{.bai,.csi,.crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference file the CRAM was created with (optional)", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "qname": { + "type": "file", + "description": "Optional file with read names to output only select alignments", + "pattern": "*.{txt,list}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "optional filtered/converted BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.cram": { + "type": "file", + "description": "optional filtered/converted CRAM file", + "pattern": "*.{cram}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.sam": { + "type": "file", + "description": "optional filtered/converted SAM file", + "pattern": "*.{sam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${file_type}.bai": { + "type": "file", + "description": "optional BAM file index", + "pattern": "*.{bai}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${file_type}.csi": { + "type": "file", + "description": "optional tabix BAM file index", + "pattern": "*.{csi}" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${file_type}.crai": { + "type": "file", + "description": "optional CRAM file index", + "pattern": "*.{crai}" + } + } + ] + }, + { + "unselected": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.unselected.${file_type}": { + "type": "file", + "description": "optional file with unselected alignments", + "pattern": "*.unselected.{bam,cram,sam}" + } + } + ] + }, + { + "unselected_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.unselected.${file_type}.{bai,csi,crsi}": { + "type": "file", + "description": "index for the \"unselected\" file", + "pattern": "*.unselected.{bai,csi,crai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -117532,52 +150179,73 @@ "tool_dev_url": "https://github.com/labsyspharm/scimap", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cellbyfeature": { - "type": "file", - "description": "CSV file with cell by feature table", - "pattern": "*.{csv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "Sorted CSV file", - "pattern": "*.{csv}" - } - }, - { - "h5ad": { - "type": "file", - "description": "Sorted H5AD file", - "pattern": "*.{h5ad}" - } + ], + "identifier": "biotools:SCIMAP" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cellbyfeature": { + "type": "file", + "description": "CSV file with cell by feature table", + "pattern": "*.{csv}" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Sorted CSV file", + "pattern": "*.{csv}" + } + } + ] + }, + { + "h5ad": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.h5ad": { + "type": "file", + "description": "Sorted H5AD file", + "pattern": "*.{h5ad}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -117616,64 +150284,95 @@ "doi": "10.5281/zenodo.7854095", "licence": [ "MIT licence" - ] - } + ], + "identifier": "biotools:SCIMAP" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "phenotyped": { + "type": "file", + "description": "Phenotyped CSV file, it must contain the columns, sampleID, X, Y and Phenotype.", + "pattern": "*.{csv}" + } + } + ] + ], + "output": [ + { + "spatial_lda_output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "File with the motifs detected from SpatialLDA", + "pattern": "*.{csv}" + } + } + ] + }, + { + "composition_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.png": { + "type": "file", + "description": "Plot with the motif composition and the cell type composition of motifs.", + "pattern": "*.{png}" + } + } + ] + }, + { + "motif_location_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.html": { + "type": "file", + "description": "Plot with the locations of the motifs.", + "pattern": "*.{html}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "phenotyped": { - "type": "file", - "description": "Phenotyped CSV file, it must contain the columns, sampleID, X, Y and Phenotype.", - "pattern": "*.{csv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "spatial_lda_output": { - "type": "file", - "description": "File with the motifs detected from SpatialLDA", - "pattern": "*.{csv}" - } - }, - { - "composition_plot": { - "type": "file", - "description": "Plot with the motif composition and the cell type composition of motifs.", - "pattern": "*.{png}" - } - }, - { - "motif_location_plot": { - "type": "file", - "description": "Plot with the locations of the motifs.", - "pattern": "*.{html}" - } - } - ], - "authors": [ - "@migueLib", - "@chiarasch" + "authors": [ + "@migueLib", + "@chiarasch" ], "maintainers": [ "@migueLib", @@ -117703,59 +150402,72 @@ "doi": "10.1186/s13059-016-1108-8", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genes": { - "type": "file", - "description": "A presence/absence matrix of genes in the pan-genome", - "pattern": "*.csv" - } - }, - { - "traits": { - "type": "file", - "description": "A CSV file containing trait information per-sample", - "pattern": "*.csv" - } - }, - { - "tree": { - "type": "file", - "description": "A Newick formtted tree for phylogenetic analyses", - "pattern": "*.{dnd,nwk,treefile}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "Gene associations in a CSV file per trait", - "pattern": "*.csv" - } + ], + "identifier": "biotools:scoary" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genes": { + "type": "file", + "description": "A presence/absence matrix of genes in the pan-genome", + "pattern": "*.csv" + } + }, + { + "traits": { + "type": "file", + "description": "A CSV file containing trait information per-sample", + "pattern": "*.csv" + } + } + ], + [ + { + "tree": { + "type": "file", + "description": "A Newick formtted tree for phylogenetic analyses", + "pattern": "*.{dnd,nwk,treefile}" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Gene associations in a CSV file per trait", + "pattern": "*.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -117788,73 +150500,108 @@ "tool_dev_url": "https://github.com/GeneDx/scramble", "licence": [ "CC" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "clusters": { - "type": "file", - "description": "Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier", - "pattern": "*clusters.txt" - } - }, - { - "fasta": { - "type": "file", - "description": "Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions.", - "pattern": "*.{fasta,fa}" - } - }, - { - "mei_ref": { - "type": "file", - "description": "Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "meis_tab": { - "type": "file", - "description": "Tab-delimited text file containing MEI calls", - "pattern": "*_MEIs.txt" - } - }, - { - "dels_tab": { - "type": "file", - "description": "Tab-delimited text file containing predicted deletions", - "pattern": "*_PredictedDeletions.txt" - } - }, - { - "vcf": { - "type": "file", - "description": "A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)", - "pattern": "*.vcf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "clusters": { + "type": "file", + "description": "Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier", + "pattern": "*clusters.txt" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions.", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "mei_ref": { + "type": "file", + "description": "Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "meis_tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_MEIs.txt": { + "type": "file", + "description": "Tab-delimited text file containing MEI calls", + "pattern": "*_MEIs.txt" + } + } + ] + }, + { + "dels_tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_PredictedDeletions.txt": { + "type": "file", + "description": "Tab-delimited text file containing predicted deletions", + "pattern": "*_PredictedDeletions.txt" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -117886,59 +150633,72 @@ "tool_dev_url": "https://github.com/GeneDx/scramble", "licence": [ "CC" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index of the BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file (mandatory when using CRAM files)", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "clusters": { - "type": "file", - "description": "Tab-delimited file containing the soft-clipped clusters", - "pattern": "*.clusters.txt" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index of the BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference FASTA file (mandatory when using CRAM files)", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.clusters.txt": { + "type": "file", + "description": "Tab-delimited file containing the soft-clipped clusters", + "pattern": "*.clusters.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -117973,56 +150733,69 @@ "documentation": "https://github.com/FredHutch/SEACR", "licence": [ "GPL-2.0-only" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedgraph": { - "type": "file", - "description": "The target bedgraph file from which the peaks will be calculated.\n" - } - }, - { - "ctrlbedgraph": { - "type": "file", - "description": "Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.\n" - } - }, - { - "threshold": { - "type": "integer", - "description": "Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Bed file containing the calculated peaks.", - "pattern": "*.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "The target bedgraph file from which the peaks will be calculated.\n" + } + }, + { + "ctrlbedgraph": { + "type": "file", + "description": "Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.\n" + } + } + ], + [ + { + "threshold": { + "type": "integer", + "description": "Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph\n" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "Bed file containing the calculated peaks.", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118061,80 +150834,125 @@ "doi": "10.1186/gb-2014-15-2-r34", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTA or FASTQ files", - "pattern": "*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file used to construct Segemehl", - "pattern": "*.{fa,fasta}" - } - }, - { - "index": { - "type": "file", - "description": "Segemehl Index file from SEGEMEHL_INDEX", - "pattern": "*.idx" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "File containing genomic alignments in SAM format\n (please add \"-b\" flag to task.ext.args for BAM)\n", - "pattern": "*.{sam,bam}" - } - }, - { - "trans_alignments": { - "type": "file", - "description": "Custom text file containing all single split alignments predicted to be in trans\n (optional, only if -S flag is set in task.ext.args)\n", - "pattern": "*.trns.txt" - } - }, - { - "single_bed": { - "type": "file", - "description": "Bed file containing all single splice events predicted\nin the split read alignments.\n (optional, only if -S flag is set in task.ext.args)\n", - "pattern": "*.sngl.bed" - } - }, - { - "multi_bed": { - "type": "file", - "description": "Bed file containing all splice events predicted\nin the split read alignments.\n (optional, only if -S flag is set in task.ext.args)\n", - "pattern": "*.mult.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:segemehl" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTA or FASTQ files", + "pattern": "*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file used to construct Segemehl", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "index": { + "type": "file", + "description": "Segemehl Index file from SEGEMEHL_INDEX", + "pattern": "*.idx" + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.${suffix}": { + "type": "file", + "description": "File containing genomic alignments in SAM format\n (please add \"-b\" flag to task.ext.args for BAM)\n", + "pattern": "*.{sam,bam}" + } + } + ] + }, + { + "trans_alignments": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.trns.txt": { + "type": "file", + "description": "Custom text file containing all single split alignments predicted to be in trans\n (optional, only if -S flag is set in task.ext.args)\n", + "pattern": "*.trns.txt" + } + } + ] + }, + { + "multi_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.mult.bed": { + "type": "file", + "description": "Bed file containing all splice events predicted\nin the split read alignments.\n (optional, only if -S flag is set in task.ext.args)\n", + "pattern": "*.mult.bed" + } + } + ] + }, + { + "single_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.sngl.bed": { + "type": "file", + "description": "Bed file containing all single splice events predicted\nin the split read alignments.\n (optional, only if -S flag is set in task.ext.args)\n", + "pattern": "*.sngl.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118174,33 +150992,44 @@ "doi": "10.1186/gb-2014-15-2-r34", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:segemehl" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fa,fasta}" + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fa,fasta}" + } } - } + ] ], "output": [ { - "index": { - "type": "file", - "description": "Segemehl index file", - "pattern": "*.{idx}" - } + "index": [ + { + "*.idx": { + "type": "file", + "description": "Segemehl index file", + "pattern": "*.{idx}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118239,80 +151068,131 @@ "doi": "10.1038/s41467-022-29843-y", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of the assembled contigs", - "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "csv": { - "type": "file", - "description": "generated files", - "pattern": "*.csv" - } - }, - { - "h5": { - "type": "file", - "description": "trained model", - "pattern": "*.h5" - } - }, - { - "output_prerecluster_bins": { - "type": "file", - "description": "output_prerecluster_bins", - "pattern": "output_prerecluster_bins/*.fa" - } - }, - { - "output_recluster_bins": { - "type": "file", - "description": "output_recluster_bins", - "pattern": "output_recluster_bins/*.fa" - } - }, - { - "tsv": { - "type": "file", - "description": "information of bins", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:semibin" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of the assembled contigs", + "pattern": "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram}" + } + } + ] + ], + "output": [ + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "generated files", + "pattern": "*.csv" + } + } + ] + }, + { + "model": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.h5": { + "type": "file", + "description": "model file", + "pattern": "*.h5" + } + } + ] + }, + { + "output_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output_prerecluster_bins/*.fa": { + "type": "file", + "description": "precluster fasta files", + "pattern": "*.fa" + } + } + ] + }, + { + "recluster_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output_recluster_bins/*.fa": { + "type": "file", + "description": "recluster fasta files", + "pattern": "*.fa" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "information of bins", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118341,106 +151221,131 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.", - "pattern": "*.vcf" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "tabix index for the input vcf file.", - "pattern": "*.vcf.tbi" - } - }, - { - "recal": { - "type": "file", - "description": "Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.", - "pattern": "*.recal" - } - }, - { - "recal_index": { - "type": "file", - "description": "Index file for the recalibration file.", - "pattern": ".recal.idx" - } - }, - { - "tranches": { - "type": "file", - "description": "Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.", - "pattern": ".tranches" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "compressed vcf file containing the recalibrated variants.", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of recalibrated vcf file.", - "pattern": "*vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions.", - "pattern": "versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.", + "pattern": "*.vcf" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "tabix index for the input vcf file.", + "pattern": "*.vcf.tbi" + } + }, + { + "recal": { + "type": "file", + "description": "Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": "*.recal" + } + }, + { + "recal_index": { + "type": "file", + "description": "Index file for the recalibration file.", + "pattern": ".recal.idx" + } + }, + { + "tranches": { + "type": "file", + "description": "Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.", + "pattern": ".tranches" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "compressed vcf file containing the recalibrated variants.", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "Index of recalibrated vcf file.", + "pattern": "*vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions.", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118476,44 +151381,55 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" + "documentation": "https://www.sentieon.com/", + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "*.{amb,ann,bwt,pac,sa}" - } + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bwa": { + "type": "file", + "description": "BWA genome index files", + "pattern": "*.{amb,ann,bwt,pac,sa}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118553,87 +151469,111 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Genome fastq files (single-end or paired-end)" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "*.{amb,ann,bwt,pac,sa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "bam_and_bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "BAM file with corresponding index.", + "pattern": "*.{bam,bai}" + } + }, + { + "${prefix}.{bai,crai}": { + "type": "file", + "description": "BAM file with corresponding index.", + "pattern": "*.{bam,bai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Genome fastq files (single-end or paired-end)" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "*.{amb,ann,bwt,pac,sa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA reference.", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam_and_bai": { - "type": "file", - "description": "BAM file with corresponding index.", - "pattern": "*.{bam,bai}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@asp8200" + "authors": [ + "@asp8200" ], "maintainers": [ "@asp8200", @@ -118671,118 +151611,147 @@ "documentation": "https://www.sentieon.com/", "licence": [ "Commercial (requires license for use; redistribution allowed)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Sorted VCF file [required]", - "pattern": "*.vcf" - } - }, - { - "tbi": { - "type": "file", - "description": "VCF index file [required]", - "pattern": "*.vcf{,.gz}.tbi" - } - }, - { - "dbsnp": { - "type": "file", - "description": "dbsnp VCF file [required]", - "pattern": "*.vcf{,.gz}" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "dbsnp VCF index file [required]", - "pattern": "*.vcf{,.gz}.tbi" - } - }, - { - "interval": { - "type": "file", - "description": "BED file of genome regions to draw coverage from", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file [required]", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file [required]", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "metrics": { - "type": "file", - "description": "Metrics file from VCF\n", - "pattern": "*.variant_calling_detail_metrics" - } - }, - { - "summary": { - "type": "file", - "description": "Summary of VCF metrics\n", - "pattern": "*.collectvcmetrics.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Sorted VCF file [required]", + "pattern": "*.vcf" + } + }, + { + "tbi": { + "type": "file", + "description": "VCF index file [required]", + "pattern": "*.vcf{,.gz}.tbi" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "dbsnp VCF file [required]", + "pattern": "*.vcf{,.gz}" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "dbsnp VCF index file [required]", + "pattern": "*.vcf{,.gz}.tbi" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file [required]", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file [required]", + "pattern": "*.fai" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "interval": { + "type": "file", + "description": "BED file of genome regions to draw coverage from", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.variant_calling_detail_metrics": { + "type": "file", + "description": "Metrics file from VCF\n", + "pattern": "*.variant_calling_detail_metrics" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.variant_calling_summary_metrics": { + "type": "file", + "description": "Summary of VCF metrics\n", + "pattern": "*.collectvcmetrics.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118813,133 +151782,215 @@ "documentation": "https://www.sentieon.com/", "licence": [ "Commercial (requires license for use; redistribution allowed)" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM/SAM file index", - "pattern": "*.{bai,crai}" - } - }, - { - "interval": { - "type": "file", - "description": "BED file of genome regions to draw coverage from", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai" - } - }, - { - "gene_list": { - "type": "file", - "description": "RefSeq file used to aggregate the results", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "per_locus": { - "type": "file", - "description": "The per locus coverage with no partition.", - "pattern": "${sample_id}" - } - }, - { - "sample_summary": { - "type": "file", - "description": "The summary for PARTITION_GROUP sample, aggregated over all bases.", - "pattern": "${sample_id}.sample_summary" - } - }, - { - "statistics": { - "type": "file", - "description": "The statistics for PARTITION_GROUP library, aggregated by interval.", - "pattern": "${sample_id}.interval_statistics" - } - }, - { - "coverage_counts": { - "type": "file", - "description": "Contains the histogram of loci with depth larger than x.", - "pattern": "${sample_id}.interval_statistics" - } - }, - { - "coverage_proportions": { - "type": "file", - "description": "Contains the normalized histogram of loci with depth larger than x.", - "pattern": "${sample_id}.interval_statistics" - } - }, - { - "interval_summary": { - "type": "file", - "description": "The summary for PARTITION_GROUP library, aggregated by interval.", - "pattern": "${sample_id}.interval_summary" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM/SAM file index", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "interval": { + "type": "file", + "description": "BED file of genome regions to draw coverage from", + "pattern": "*.bed" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gene_list": { + "type": "file", + "description": "RefSeq file used to aggregate the results", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "per_locus": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$prefix": { + "type": "file", + "description": "The per locus coverage with no partition.", + "pattern": "${sample_id}" + } + } + ] + }, + { + "sample_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_summary": { + "type": "file", + "description": "The summary for PARTITION_GROUP sample, aggregated over all bases.", + "pattern": "${sample_id}.sample_summary" + } + } + ] + }, + { + "statistics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_interval_statistics": { + "type": "file", + "description": "The statistics for PARTITION_GROUP library, aggregated by interval.", + "pattern": "${sample_id}.interval_statistics" + } + } + ] + }, + { + "coverage_counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_cumulative_coverage_counts": { + "type": "file", + "description": "Contains the histogram of loci with depth larger than x.", + "pattern": "${sample_id}.interval_statistics" + } + } + ] + }, + { + "coverage_proportions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_cumulative_coverage_proportions": { + "type": "file", + "description": "Contains the normalized histogram of loci with depth larger than x.", + "pattern": "${sample_id}.interval_statistics" + } + } + ] + }, + { + "interval_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}.${partitions_output}_interval_summary": { + "type": "file", + "description": "The summary for PARTITION_GROUP library, aggregated by interval.", + "pattern": "${sample_id}.interval_summary" + } + }, + { + "_summary": { + "type": "file", + "description": "The summary for PARTITION_GROUP library, aggregated by interval.", + "pattern": "${sample_id}.interval_summary" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -118967,113 +152018,178 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "Index of th sorted BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "mq_metrics": { - "type": "file", - "description": "File containing the information about mean base quality score for each sequencing cycle", - "pattern": "*.txt" - } - }, - { - "qd_metrics": { - "type": "file", - "description": "File containing the information about number of bases with a specific base quality score", - "pattern": "*.txt" - } - }, - { - "gc_summary": { - "type": "file", - "description": "File containing the information about GC bias in the reference and the sample", - "pattern": "*.txt" - } - }, - { - "gc_metrics": { - "type": "file", - "description": "File containing the information about GC bias in the reference and the sample", - "pattern": "*.txt" - } - }, - { - "aln_metrics": { - "type": "file", - "description": "File containing the statistics about the alignment of the reads", - "pattern": "*.txt" - } - }, - { - "is_metrics": { - "type": "file", - "description": "File containing the information about statistical distribution of insert sizes", - "pattern": "*.txt" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index of th sorted BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "mq_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*mq_metrics.txt": { + "type": "file", + "description": "File containing the information about mean base quality score for each sequencing cycle", + "pattern": "*.txt" + } + } + ] + }, + { + "qd_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*qd_metrics.txt": { + "type": "file", + "description": "File containing the information about number of bases with a specific base quality score", + "pattern": "*.txt" + } + } + ] + }, + { + "gc_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*gc_summary.txt": { + "type": "file", + "description": "File containing the information about GC bias in the reference and the sample", + "pattern": "*.txt" + } + } + ] + }, + { + "gc_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*gc_metrics.txt": { + "type": "file", + "description": "File containing the information about GC bias in the reference and the sample", + "pattern": "*.txt" + } + } + ] + }, + { + "aln_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*aln_metrics.txt": { + "type": "file", + "description": "File containing the statistics about the alignment of the reads", + "pattern": "*.txt" + } + } + ] + }, + { + "is_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*is_metrics.txt": { + "type": "file", + "description": "File containing the information about statistical distribution of insert sizes", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -119110,120 +152226,195 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file.", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA reference.", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cram": { - "type": "file", - "description": "CRAM file", - "pattern": "*.cram" - } - }, - { - "crai": { - "type": "file", - "description": "CRAM index file", - "pattern": "*.crai" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file.", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai" - } - }, - { - "score": { - "type": "file", - "description": "The score file indicates which reads LocusCollector finds are likely duplicates.", - "pattern": "*.score" - } - }, - { - "metrics": { - "type": "file", - "description": "Output file containing Dedup metrics incl. histogram data.", - "pattern": "*.metrics" - } - }, - { - "metrics_multiqc_tsv": { - "type": "file", - "description": "Output tsv-file containing Dedup metrics excl. histogram data.", - "pattern": "*.metrics.multiqc.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file.", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.cram": { + "type": "file", + "description": "CRAM file", + "pattern": "*.cram" + } + } + ] + }, + { + "crai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.crai": { + "type": "file", + "description": "CRAM index file", + "pattern": "*.crai" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file.", + "pattern": "*.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai" + } + } + ] + }, + { + "score": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.score": { + "type": "file", + "description": "The score file indicates which reads LocusCollector finds are likely duplicates.", + "pattern": "*.score" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "Output file containing Dedup metrics incl. histogram data.", + "pattern": "*.metrics" + } + } + ] + }, + { + "metrics_multiqc_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics.multiqc.tsv": { + "type": "file", + "description": "Output tsv-file containing Dedup metrics excl. histogram data.", + "pattern": "*.metrics.multiqc.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -119262,98 +152453,125 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "INPUT VCF file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "idx": { - "type": "file", - "description": "Index of the input VCF file", - "pattern": "*.{tbi}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai" - } - }, - { - "ml_model": { - "type": "file", - "description": "machine learning model file", - "pattern": "*.model" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "INPUT VCF file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Index of the input VCF file", - "pattern": "*.{tbi}" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "INPUT VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "idx": { + "type": "file", + "description": "Index of the input VCF file", + "pattern": "*.{tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "ml_model": { + "type": "file", + "description": "machine learning model file", + "pattern": "*.model" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "INPUT VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the input VCF file", + "pattern": "*.{tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -119391,294 +152609,397 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file.", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai" + } + }, + { + "intervals": { + "type": "file", + "description": "bed or interval_list file containing interval in the reference that will be used in the analysis", + "pattern": "*.{bed,interval_list}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing meta information for fasta.\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing meta information for fasta index.\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing meta information for dbsnp.\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing meta information for dbsnp_tbi.\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing meta information for machine learning model for Dnascope.\n" + } + }, + { + "ml_model": { + "type": "file", + "description": "machine learning model file", + "pattern": "*.model" + } + } + ], + [ + { + "pcr_indel_model": { + "type": "string", + "description": "Controls the option pcr_indel_model for Dnascope.\nThe possible options are \"NONE\" (used for PCR free samples), and \"HOSTILE\", \"AGGRESSIVE\" and \"CONSERVATIVE\".\nSee Sentieons documentation for further explanation.\n" + } + } + ], + [ + { + "emit_vcf": { + "type": "string", + "description": "Controls the vcf output from Dnascope.\nPossible options are \"all\", \"confident\" and \"variant\".\nSee Sentieons documentation for further explanation.\n" + } + } + ], + [ + { + "emit_gvcf": { + "type": "boolean", + "description": "If true, the haplotyper will output a gvcf" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.unfiltered.vcf.gz" + } + } + ] + }, + { + "vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.unfiltered.vcf.gz.tbi" + } + } + ] + }, + { + "gvcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz": { + "type": "file", + "description": "Compressed GVCF file", + "pattern": "*.g.vcf.gz" + } + } + ] + }, + { + "gvcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz.tbi": { + "type": "file", + "description": "Index of GVCF file", + "pattern": "*.g.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file.", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai" - } - }, - { - "intervals": { - "type": "file", - "description": "bed or interval_list file containing interval in the reference that will be used in the analysis", - "pattern": "*.{bed,interval_list}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing meta information for fasta.\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing meta information for fasta index.\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing meta information for dbsnp.\n" - } - }, - { - "dbsnp": { - "type": "file", - "description": "Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing meta information for dbsnp_tbi.\n" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing meta information for machine learning model for Dnascope.\n" - } - }, - { - "ml_model": { - "type": "file", - "description": "machine learning model file", - "pattern": "*.model" - } - }, - { - "ml_model": { - "type": "file", - "description": "machine learning model file", - "pattern": "*.model" - } - }, - { - "pcr_indel_model": { - "type": "string", - "description": "Controls the option pcr_indel_model for Dnascope.\nThe possible options are \"NONE\" (used for PCR free samples), and \"HOSTILE\", \"AGGRESSIVE\" and \"CONSERVATIVE\".\nSee Sentieons documentation for further explanation.\n" - } - }, - { - "emit_vcf": { - "type": "string", - "description": "Controls the vcf output from Dnascope.\nPossible options are \"all\", \"confident\" and \"variant\".\nSee Sentieons documentation for further explanation.\n" - } - }, - { - "emit_gvcf": { - "type": "boolean", - "description": "If true, the haplotyper will output a gvcf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.unfiltered.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.unfiltered.vcf.gz.tbi" - } - }, - { - "gvcf": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz" - } - }, - { - "gvcf_tbi": { - "type": "file", - "description": "Index of GVCF file", - "pattern": "*.g.vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "2.2.0" - }, - { - "name": "sarek", - "version": "3.4.4" - } - ] - }, - { - "name": "sentieon_gvcftyper", - "path": "modules/nf-core/sentieon/gvcftyper/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_gvcftyper", - "description": "Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.\n", - "keywords": [ - "joint genotyping", - "genotype", - "gvcf" - ], - "tools": [ + "authors": [ + "@ramprasadn" + ], + "maintainers": [ + "@ramprasadn" + ] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "2.2.0" + }, + { + "name": "sarek", + "version": "3.4.4" + } + ] + }, + { + "name": "sentieon_gvcftyper", + "path": "modules/nf-core/sentieon/gvcftyper/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_gvcftyper", + "description": "Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.\n", + "keywords": [ + "joint genotyping", + "genotype", + "gvcf" + ], + "tools": [ { "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gvcfs": { - "type": "file", - "description": "gVCF(.gz) file\n", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "tbis": { - "type": "file", - "description": "index of gvcf file\n", - "pattern": "*.tbi" - } - }, - { - "intervals": { - "type": "file", - "description": "Interval file with the genomic regions included in the library (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Reference fasta index file", - "pattern": "*.fai" - } - }, - { - "dbsnp": { - "type": "file", - "description": "dbSNP VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "dbSNP VCF index file", - "pattern": "*.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Genotyped VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Tbi index for VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gvcfs": { + "type": "file", + "description": "gVCF(.gz) file\n", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbis": { + "type": "file", + "description": "index of gvcf file\n", + "pattern": "*.tbi" + } + }, + { + "intervals": { + "type": "file", + "description": "Interval file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference fasta index file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "dbSNP VCF file", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "dbSNP VCF index file", + "pattern": "*.tbi" + } + } + ] + ], + "output": [ + { + "vcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf_gz_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -119712,123 +153033,200 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "recal_table": { - "type": "file", - "description": "Recalibration table from sentieon/qualcal (optional)" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the FASTA reference.", - "pattern": "*.fai" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file containing known sites (optional)" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "VCF index of dbsnp (optional)" - } - }, - { - "emit_vcf": { - "type": "string", - "description": "Controls the vcf output from the haplotyper.\nIf emit_vcf is set to \"all\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"all\".\nIf emit_vcf is set to \"confident\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"confident\".\nIf emit_vcf is set to \"variant\" then the haplotyper will output a vcf generated by the haplotyper in emit_mode \"confident\".\n" - } - }, - { - "emit_gvcf": { - "type": "boolean", - "description": "If true, the haplotyper will output a gvcf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.unfiltered.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.unfiltered.vcf.gz.tbi" - } - }, - { - "gvcf": { - "type": "file", - "description": "Compressed GVCF file", - "pattern": "*.g.vcf.gz" - } - }, - { - "gvcf_tbi": { - "type": "file", - "description": "Index of GVCF file", - "pattern": "*.g.vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + }, + { + "recal_table": { + "type": "file", + "description": "Recalibration table from sentieon/qualcal (optional)" + } + } + ], + [ + { + "meta1": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file containing known sites (optional)" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "VCF index of dbsnp (optional)" + } + } + ], + [ + { + "emit_vcf": { + "type": "string", + "description": "Controls the vcf output from the haplotyper.\nIf emit_vcf is set to \"all\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"all\".\nIf emit_vcf is set to \"confident\" then the haplotyper will output a vcf generated by the haplotyper in emit-mode \"confident\".\nIf emit_vcf is set to \"variant\" then the haplotyper will output a vcf generated by the haplotyper in emit_mode \"confident\".\n" + } + } + ], + [ + { + "emit_gvcf": { + "type": "boolean", + "description": "If true, the haplotyper will output a gvcf" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.unfiltered.vcf.gz" + } + } + ] + }, + { + "vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unfiltered.vcf.gz.tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.unfiltered.vcf.gz.tbi" + } + } + ] + }, + { + "gvcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz": { + "type": "file", + "description": "Compressed GVCF file", + "pattern": "*.g.vcf.gz" + } + } + ] + }, + { + "gvcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.g.vcf.gz.tbi": { + "type": "file", + "description": "Index of GVCF file", + "pattern": "*.g.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -119862,121 +153260,214 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - }, - { - "known_sites": { - "type": "file", - "description": "VCF files with known sites for indels / snps (optional)", - "pattern": "*.vcf.gz" - } - }, - { - "known_sites_tbi": { - "type": "file", - "description": "Tabix index of the known_sites (optional)", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "recalibration_table": { - "type": "file", - "description": "File containing recalibration values (optional)", - "pattern": "*.table" - } - }, - { - "generate_recalibrated_bams": { - "type": "boolean", - "description": "If truem, writes recalibrated bams to disc" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "table": { - "type": "file", - "description": "Pre Recalibration table (optional)", - "pattern": "*.table" - } - }, - { - "table_post": { - "type": "file", - "description": "Post recalibration table (optional)", - "pattern": "*.table.post" - } - }, - { - "recal_alignment": { - "type": "file", - "description": "Recalibrated input files (optional)", - "pattern": "*.{bam,cram}" - } - }, - { - "csv": { - "type": "file", - "description": "Recalibration results output file used for plotting. (optional)", - "pattern": "*.csv" - } - }, - { - "pdf": { - "type": "file", - "description": "PDF file containing graphs (optional)", - "pattern": "*.pdf" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_sites": { + "type": "file", + "description": "VCF files with known sites for indels / snps (optional)", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "known_sites_tbi": { + "type": "file", + "description": "Tabix index of the known_sites (optional)", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "recalibration_table": { + "type": "file", + "description": "File containing recalibration values (optional)", + "pattern": "*.table" + } + } + ], + [ + { + "generate_recalibrated_bams": { + "type": "boolean", + "description": "If truem, writes recalibrated bams to disc" + } + } + ] + ], + "output": [ + { + "table": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table": { + "type": "file", + "description": "Pre Recalibration table (optional)", + "pattern": "*.table" + } + } + ] + }, + { + "table_post": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.table.post": { + "type": "file", + "description": "Post recalibration table (optional)", + "pattern": "*.table.post" + } + } + ] + }, + { + "recal_alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{cram,bam}": { + "type": "file", + "description": "Recalibrated input files (optional)", + "pattern": "*.{bam,cram}" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "Recalibration results output file used for plotting. (optional)", + "pattern": "*.csv" + } + } + ] + }, + { + "pdf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.pdf": { + "type": "file", + "description": "PDF file containing graphs (optional)", + "pattern": "*.pdf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -120005,91 +153496,132 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file.", - "pattern": "*.{bam,cram}" - } - }, - { - "index": { - "type": "file", - "description": "BAI/CRAI file.", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the FASTA reference.", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output": { - "type": "file", - "description": "BAM/CRAM file. Depends on how ext.prefix is set. BAM \"ext.prefix = .bam\", CRAM \"ext.prefix = .cram\". Defaults to cram", - "pattern": "*.{bam,cram}" - } - }, - { - "index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "output_index": { - "type": "file", - "description": "BAM/CRAM alignment and the corresponding index file" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file.", + "pattern": "*.{bam,cram}" + } + }, + { + "index": { + "type": "file", + "description": "BAI/CRAI file.", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the FASTA reference.", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "BAM/CRAM file. Depends on how ext.prefix is set. BAM \"ext.prefix = .bam\", CRAM \"ext.prefix = .cram\". Defaults to cram", + "pattern": "*.{bam,cram}" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.${index}": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ] + }, + { + "output_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "file", + "description": "BAM/CRAM alignment and the corresponding index file" + } + }, + { + "${prefix}.${index}": { + "type": "file", + "description": "BAM/CRAM alignment and the corresponding index file" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -120125,322 +153657,452 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "compressed vcf file from tnhaplotyper2", + "pattern": "*.vcf.gz" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Tabix index of vcf file", + "pattern": "*vcf.gz.tbi" + } + }, + { + "stats": { + "type": "file", + "description": "Stats file that pairs with output vcf file", + "pattern": "*vcf.gz.stats" + } + }, + { + "contamination": { + "type": "file", + "description": "the location and file name of the file containing the contamination information produced by ContaminationModel.", + "pattern": "*.contamination_data.tsv" + } + }, + { + "segments": { + "type": "file", + "description": "the location and file name of the file containing the tumor segments information produced by ContaminationModel.", + "pattern": "*.segments" + } + }, + { + "orientation_priors": { + "type": "file", + "description": "the location and file name of the file containing the orientation bias information produced by OrientationBias.", + "pattern": "*.orientation_data.tsv" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fasta.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "file containing filtered tnhaplotyper2 calls.", + "pattern": "*.vcf.gz" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "file containing filtered tnhaplotyper2 calls.", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf_tbi": [ + { + "meta": { + "type": "file", + "description": "tbi file that pairs with vcf.", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "tbi file that pairs with vcf.", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "file", + "description": "file containing statistics of the tnfilter run.", + "pattern": "*.stats" + } + }, + { + "*.vcf.gz.stats": { + "type": "file", + "description": "file containing statistics of the tnfilter run.", + "pattern": "*.stats" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "compressed vcf file from tnhaplotyper2", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Tabix index of vcf file", - "pattern": "*vcf.gz.tbi" - } - }, - { - "stats": { - "type": "file", - "description": "Stats file that pairs with output vcf file", - "pattern": "*vcf.gz.stats" - } - }, - { - "contamination": { - "type": "file", - "description": "the location and file name of the file containing the contamination information produced by ContaminationModel.", - "pattern": "*.contamination_data.tsv" - } - }, - { - "segments": { - "type": "file", - "description": "the location and file name of the file containing the tumor segments information produced by ContaminationModel.", - "pattern": "*.segments" - } - }, - { - "orientation_priors": { - "type": "file", - "description": "the location and file name of the file containing the orientation bias information produced by OrientationBias.", - "pattern": "*.orientation_data.tsv" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fasta.fai" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "file containing filtered tnhaplotyper2 calls.", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "tbi file that pairs with vcf.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "stats": { - "type": "file", - "description": "file containing statistics of the tnfilter run.", - "pattern": "*.stats" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@asp8200" - ] - } - }, - { - "name": "sentieon_tnhaplotyper2", - "path": "modules/nf-core/sentieon/tnhaplotyper2/meta.yml", - "type": "module", - "meta": { - "name": "sentieon_tnhaplotyper2", - "description": "Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.", - "keywords": [ - "tnseq", - "tnhaplotyper2", - "sentieon", - "variant_calling" - ], - "tools": [ + "authors": [ + "@asp8200" + ] + } + }, + { + "name": "sentieon_tnhaplotyper2", + "path": "modules/nf-core/sentieon/tnhaplotyper2/meta.yml", + "type": "module", + "meta": { + "name": "sentieon_tnhaplotyper2", + "description": "Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.", + "keywords": [ + "tnseq", + "tnhaplotyper2", + "sentieon", + "variant_calling" + ], + "tools": [ { "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta8": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file from alignment", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAI/CRAI file from alignment", - "pattern": "*.{bai,crai}" - } - }, - { - "intervals": { - "type": "file", - "description": "Bed file with the genomic regions included in the library (optional)" - } - }, - { - "dict": { - "type": "file", - "description": "GATK sequence dictionary", - "pattern": "*.dict" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai" - } - }, - { - "germline_resource": { - "type": "file", - "description": "Population vcf of germline sequencing, containing allele fractions.", - "pattern": "*.vcf.gz" - } - }, - { - "germline_resource_tbi": { - "type": "file", - "description": "Index file for the germline resource.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "panel_of_normals": { - "type": "file", - "description": "vcf file to be used as a panel of normals.", - "pattern": "*.vcf.gz" - } - }, - { - "panel_of_normals_tbi": { - "type": "file", - "description": "Index for the panel of normals.", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "emit_orientation_data": { - "type": "boolean", - "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias." - } - }, - { - "emit_contamination_data": { - "type": "boolean", - "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "orientation_data": { - "type": "file", - "description": "TSV file from Sentieon's algorithm OrientationBias", - "pattern": "*.orientation_data.tsv" - } - }, - { - "contamination_data": { - "type": "file", - "description": "TSV file from Sentieon's algorithm ContaminationModel", - "pattern": "*.contamination_data.tsv" - } - }, - { - "contamination_segments": { - "type": "file", - "description": "Tumour segments file from Sentieon's algorithm ContaminationModel", - "pattern": "*.segments" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Index of the VCF file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file from alignment", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAI/CRAI file from alignment", + "pattern": "*.{bai,crai}" + } + }, + { + "intervals": { + "type": "file", + "description": "Bed file with the genomic regions included in the library (optional)" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "dict": { + "type": "file", + "description": "GATK sequence dictionary", + "pattern": "*.dict" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "germline_resource": { + "type": "file", + "description": "Population vcf of germline sequencing, containing allele fractions.", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "germline_resource_tbi": { + "type": "file", + "description": "Index file for the germline resource.", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "panel_of_normals": { + "type": "file", + "description": "vcf file to be used as a panel of normals.", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta8": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "panel_of_normals_tbi": { + "type": "file", + "description": "Index for the panel of normals.", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "emit_orientation_data": { + "type": "boolean", + "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias." + } + } + ], + [ + { + "emit_contamination_data": { + "type": "boolean", + "description": "If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel." + } + } + ] + ], + "output": [ + { + "orientation_data": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.orientation_data.tsv": { + "type": "file", + "description": "TSV file from Sentieon's algorithm OrientationBias", + "pattern": "*.orientation_data.tsv" + } + } + ] + }, + { + "contamination_data": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.contamination_data.tsv": { + "type": "file", + "description": "TSV file from Sentieon's algorithm ContaminationModel", + "pattern": "*.contamination_data.tsv" + } + } + ] + }, + { + "contamination_segments": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.segments": { + "type": "file", + "description": "Tumour segments file from Sentieon's algorithm ContaminationModel", + "pattern": "*.segments" + } + } + ] + }, + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "Stats file from Sentieon's algorithm", + "pattern": "*.stats" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -120468,158 +154130,191 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta6": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta7": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file.", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAI file", - "pattern": "*.bai" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai" - } - }, - { - "cosmic": { - "type": "file", - "description": "Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz" - } - }, - { - "cosmic_tbi": { - "type": "file", - "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "pon": { - "type": "file", - "description": "Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz" - } - }, - { - "pon_tbi": { - "type": "file", - "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "dbsnp": { - "type": "file", - "description": "Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "interval": { - "type": "file", - "description": "bed or interval_list file containing interval in the reference that will be used in the analysis", - "pattern": "*.{bed,interval_list}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Index of the VCF file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file.", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAI file", + "pattern": "*.bai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "cosmic": { + "type": "file", + "description": "Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz" + } + }, + { + "cosmic_tbi": { + "type": "file", + "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "pon": { + "type": "file", + "description": "Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz" + } + }, + { + "pon_tbi": { + "type": "file", + "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta6": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "Index of the Single Nucleotide Polymorphism database (dbSNP) file", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta7": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test' ]\n" + } + }, + { + "interval": { + "type": "file", + "description": "bed or interval_list file containing interval in the reference that will be used in the analysis", + "pattern": "*.{bed,interval_list}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing reference information.\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -120647,101 +154342,162 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "input vcf file containing the variants to be recalibrated", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "tbi file matching with -vcf", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "resource_vcf": { - "type": "file", - "description": "all resource vcf files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz" - } - }, - { - "resource_tbi": { - "type": "file", - "description": "all resource tbi files that are used with the corresponding '--resource' label", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "labels": { - "type": "string", - "description": "necessary arguments for Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "fasta.fai" - } - } - ], - "output": [ - { - "recal": { - "type": "file", - "description": "Output recal file used by ApplyVQSR", - "pattern": "*.recal" - } - }, - { - "idx": { - "type": "file", - "description": "Index file for the recal output file", - "pattern": "*.idx" - } - }, - { - "tranches": { - "type": "file", - "description": "Output tranches file used by ApplyVQSR", - "pattern": "*.tranches" - } - }, - { - "plots": { - "type": "file", - "description": "Optional output rscript file to aid in visualization of the input data and learned model.", - "pattern": "*plots.R" - } - }, - { - "version": { - "type": "file", - "description": "File containing software versions", - "pattern": "*.versions.yml" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "input vcf file containing the variants to be recalibrated", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "tbi file matching with -vcf", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "resource_vcf": { + "type": "file", + "description": "all resource vcf files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "resource_tbi": { + "type": "file", + "description": "all resource tbi files that are used with the corresponding '--resource' label", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "labels": { + "type": "string", + "description": "necessary arguments for Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.fasta" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "fasta.fai" + } + } + ] + ], + "output": [ + { + "recal": [ + { + "meta": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal" + } + }, + { + "*.recal": { + "type": "file", + "description": "Output recal file used by ApplyVQSR", + "pattern": "*.recal" + } + } + ] + }, + { + "idx": [ + { + "meta": { + "type": "file", + "description": "Index file for the recal output file", + "pattern": "*.idx" + } + }, + { + "*.idx": { + "type": "file", + "description": "Index file for the recal output file", + "pattern": "*.idx" + } + } + ] + }, + { + "tranches": [ + { + "meta": { + "type": "file", + "description": "Output tranches file used by ApplyVQSR", + "pattern": "*.tranches" + } + }, + { + "*.tranches": { + "type": "file", + "description": "Output tranches file used by ApplyVQSR", + "pattern": "*.tranches" + } + } + ] + }, + { + "plots": [ + { + "meta": { + "type": "file", + "description": "Optional output rscript file to aid in visualization of the input data and learned model.", + "pattern": "*plots.R" + } + }, + { + "*plots.R": { + "type": "file", + "description": "Optional output rscript file to aid in visualization of the input data and learned model.", + "pattern": "*plots.R" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -120775,168 +154531,195 @@ "sentieon": { "description": "Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.\nOur software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.\n", "homepage": "https://www.sentieon.com/", - "documentation": "https://www.sentieon.com/" - } + "documentation": "https://www.sentieon.com/", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index of th sorted BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of the genome fasta file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "intervals_list": { + "type": "file", + "description": "intervals" + } + } + ] + ], + "output": [ + { + "wgs_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "File containing the information about mean base quality score for each sequencing cycle", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" - } - }, + "authors": [ + "@ramprasadn" + ], + "maintainers": [ + "@ramprasadn" + ] + }, + "pipelines": [ + { + "name": "raredisease", + "version": "2.2.0" + } + ] + }, + { + "name": "seqcluster_collapse", + "path": "modules/nf-core/seqcluster/collapse/meta.yml", + "type": "module", + "meta": { + "name": "seqcluster_collapse", + "description": "Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file.", + "keywords": [ + "smrnaseq", + "cluster", + "mirna" + ], + "tools": [ { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + "seqcluster": { + "description": "Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project.", + "homepage": "https://github.com/lpantano/seqcluster", + "documentation": "https://github.com/lpantano/seqcluster", + "tool_dev_url": "https://github.com/lpantano/seqcluster", + "doi": "10.1093/bioinformatics/btr527", + "licence": [ + "MIT" + ], + "identifier": "biotools:seqcluster" } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test' ]`\n" + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file", + "pattern": "*.{fastq.gz}" + } } - }, + ] + ], + "output": [ { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "FASTQ file", + "pattern": "*.{fastq.gz}" + } + } + ] }, { - "bai": { - "type": "file", - "description": "Index of th sorted BAM/CRAM/SAM file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of the genome fasta file", - "pattern": "*.fai" - } - }, - { - "interval_list": { - "type": "file", - "description": "bed or interval_list file containing interval in the reference that will be used in the analysis", - "pattern": "*.{bed,interval_list}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "wgs_metrics": { - "type": "file", - "description": "File containing the information about mean base quality score for each sequencing cycle", - "pattern": "*.txt" - } - } - ], - "authors": [ - "@ramprasadn" - ], - "maintainers": [ - "@ramprasadn" - ] - }, - "pipelines": [ - { - "name": "raredisease", - "version": "2.2.0" - } - ] - }, - { - "name": "seqcluster_collapse", - "path": "modules/nf-core/seqcluster/collapse/meta.yml", - "type": "module", - "meta": { - "name": "seqcluster_collapse", - "description": "Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file.", - "keywords": [ - "smrnaseq", - "cluster", - "mirna" - ], - "tools": [ - { - "seqcluster": { - "description": "Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project.", - "homepage": "https://github.com/lpantano/seqcluster", - "documentation": "https://github.com/lpantano/seqcluster", - "tool_dev_url": "https://github.com/lpantano/seqcluster", - "doi": "10.1093/bioinformatics/btr527", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fastq.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -120969,45 +154752,56 @@ "doi": "10.3390/bioengineering8050059", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:seqfu" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastas": { - "type": "file", - "description": "Input files (mainly FASTA, FASTQ supported)", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastas": { + "type": "file", + "description": "Input files (mainly FASTA, FASTQ supported)", + "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_derep.fasta.gz": { + "type": "file", + "description": "dereplicated file (FASTA format)", + "pattern": "*.{fasta.gz}" + } + } + ] }, { - "fasta": { - "type": "file", - "description": "dereplicated file (FASTA format)", - "pattern": "*.{fasta.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121040,52 +154834,73 @@ "doi": "10.3390/bioengineering8050059", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "files": { - "type": "file", - "description": "One or more FASTA or FASTQ files", - "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "stats": { - "type": "file", - "description": "Tab-separated output file with basic sequence statistics.", - "pattern": "*.{tsv}" - } - }, - { - "multiqc": { - "type": "file", - "description": "MultiQC ready table", - "pattern": "*.{_mqc.txt}" - } + ], + "identifier": "biotools:seqfu" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "files": { + "type": "file", + "description": "One or more FASTA or FASTQ files", + "pattern": "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}" + } + } + ] + ], + "output": [ + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-separated output file with basic sequence statistics.", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "multiqc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_mqc.txt": { + "type": "file", + "description": "MultiQC ready table", + "pattern": "*.{_mqc.txt}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121119,45 +154934,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "input": { - "type": "file", - "description": "Sequence file in fasta/q format", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Sequence file in fasta/q format", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "A concatenated sequence file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}" - } + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{fasta,fastq,fa,fq,fas,fna,faa}": { + "type": "file", + "description": "A concatenated sequence file", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121189,45 +155015,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Sequence file in fastq format", + "pattern": "*.{fastq,fq}.gz" + } } - }, - { - "fastq": { - "type": "file", - "description": "Sequence file in fastq format", - "pattern": "*.{fastq,fq}.gz" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "Sequence file in fasta format", + "pattern": "*.{fasta,fa}.gz" + } + } + ] }, { - "fasta": { - "type": "file", - "description": "Sequence file in fasta format", - "pattern": "*.{fasta,fa}.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121258,45 +155095,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Sequence file in fasta/q format", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Sequence file in fasta/q format", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "text": { - "type": "file", - "description": "Text file in tabular format", - "pattern": "*.txt[.gz,.zstd,.zst]" - } + "text": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt*": { + "type": "file", + "description": "Text file in tabular format", + "pattern": "*.txt[.gz,.zstd,.zst]" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121330,52 +155178,65 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sequence": { - "type": "file", - "description": "Fasta or fastq file containing sequences to be filtered\n", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" - } - }, - { - "pattern": { - "type": "file", - "description": "pattern file (one record per line). If no pattern is given, a string can be specificied within the args using '-p pattern_string'\n", - "pattern": "*.{txt,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "filter": { - "type": "file", - "description": "Fasta or fastq file containing the filtered sequences\n", - "pattern": "*.{fa,fq}[.gz]" - } + ], + "identifier": "biotools:seqkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequence": { + "type": "file", + "description": "Fasta or fastq file containing sequences to be filtered\n", + "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + } + } + ], + [ + { + "pattern": { + "type": "file", + "description": "pattern file (one record per line). If no pattern is given, a string can be specificied within the args using '-p pattern_string'\n", + "pattern": "*.{txt,tsv}" + } + } + ] + ], + "output": [ + { + "filter": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{fa,fq}.gz": { + "type": "file", + "description": "Fasta or fastq file containing the filtered sequences\n", + "pattern": "*.{fa,fq}[.gz]" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121408,51 +155269,72 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input paired-end FastQ files.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Paired fastq reads", - "pattern": "*.paired.fastq.gz" - } - }, - { - "unpaired_reads": { - "type": "file", - "description": "Unpaired reads (optional)", - "pattern": "*.unpaired.fastq.gz" - } + ], + "identifier": "biotools:seqkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired-end FastQ files.\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paired.fastq.gz": { + "type": "file", + "description": "Paired fastq reads", + "pattern": "*.paired.fastq.gz" + } + } + ] + }, + { + "unpaired_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unpaired.fastq.gz": { + "type": "file", + "description": "Unpaired reads (optional)", + "pattern": "*.unpaired.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121488,45 +155370,56 @@ "homepage": "https://bioinf.shenwei.me/seqkit/usage/", "documentation": "https://bioinf.shenwei.me/seqkit/usage/", "tool_dev_url": "https://github.com/shenwei356/seqkit/", - "doi": "10.1371/journal.pone.016396" + "doi": "10.1371/journal.pone.016396", + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastx": { + "type": "file", + "description": "fasta/q file", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + } } - }, - { - "fastx": { - "type": "file", - "description": "fasta/q file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fast*": { + "type": "file", + "description": "fasta/q file with replaced values", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + } + } + ] }, { - "fastx": { - "type": "file", - "description": "fasta/q file with replaced values", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121561,52 +155454,73 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Input fasta/fastq file", - "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Output fasta/fastq file", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}" - } - }, - { - "log": { - "type": "file", - "description": "Log containing information regarding removed duplicates", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:seqkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Input fasta/fastq file", + "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + } + } + ] + ], + "output": [ + { + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.${extension}": { + "type": "file", + "description": "Output fasta/fastq file", + "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log containing information regarding removed duplicates", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121643,45 +155557,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Input fasta/fastq file", - "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Input fasta/fastq file", + "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Output fasta/fastq file", - "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}" - } + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Output fasta/fastq file", + "pattern": "*.{fasta,fasta.gz,fastq,fastq.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121717,45 +155642,56 @@ "homepage": "https://bioinf.shenwei.me/seqkit/usage/", "documentation": "https://bioinf.shenwei.me/seqkit/usage/", "tool_dev_url": "https://github.com/shenwei356/seqkit/", - "doi": "10.1371/journal.pone.016396" + "doi": "10.1371/journal.pone.016396", + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "fasta/q file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastx": { + "type": "file", + "description": "fasta/q file", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "fasta/q window file", - "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" - } + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fast*": { + "type": "file", + "description": "fasta/q window file", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121795,45 +155731,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Input fasta/fastq file", - "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "Input fasta/fastq file", + "pattern": "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Output fasta/fastq file", - "pattern": "*.{fasta.gz,fastq.gz}" - } + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "${prefix}.*": { + "type": "file", + "description": "Output fasta/fastq file", + "pattern": "*.{fasta.gz,fastq.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121865,45 +155812,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FastQ files", + "pattern": "*.{fq.gz/fastq.gz}" + } } - }, - { - "reads": { - "type": "file", - "description": "FastQ files", - "pattern": "*.{fq.gz/fastq.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Split fastq files", - "pattern": "*.{fq.gz/fastq.gz}" - } + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "**/*.gz": { + "type": "file", + "description": "Split fastq files", + "pattern": "*.{fq.gz/fastq.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -121942,45 +155900,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Either FASTA or FASTQ files.\n", + "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + } } + ] + ], + "output": [ + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-separated output file with basic sequence statistics.\n", + "pattern": "*.tsv" + } + } + ] }, { - "reads": { - "type": "file", - "description": "Either FASTA or FASTQ files.\n", - "pattern": "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "stats": { - "type": "file", - "description": "Tab-separated output file with basic sequence statistics.\n", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122014,45 +155983,56 @@ "doi": "10.1371/journal.pone.0163962", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqkit" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "text": { - "type": "file", - "description": "Text file in tabular format", - "pattern": "*.txt[.gz,.zst]" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "text": { + "type": "file", + "description": "Text file in tabular format", + "pattern": "*.txt[.gz,.zst]" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "Sequence file in fasta/q format", - "pattern": "*.{fa,fq}[.gz,.zst]" - } + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.f*": { + "type": "file", + "description": "Sequence file in fasta/q format", + "pattern": "*.{fa,fq}[.gz,.zst]" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122086,59 +156066,90 @@ "doi": "10.1128/AEM.01746-19", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "FASTQ or FASTA formated sequences", - "pattern": "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "A log of serotype antigen results", - "pattern": "*_log.txt" - } - }, - { - "tsv": { - "type": "file", - "description": "Tab-delimited summary of the SeqSero2 results", - "pattern": "*_result.tsv" - } - }, - { - "txt": { - "type": "file", - "description": "Detailed summary of the SeqSero2 results", - "pattern": "*_result.txt" - } + ], + "identifier": "biotools:SeqSero2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "FASTQ or FASTA formated sequences", + "pattern": "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*_log.txt": { + "type": "file", + "description": "A log of serotype antigen results", + "pattern": "*_log.txt" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*_result.tsv": { + "type": "file", + "description": "Tab-delimited summary of the SeqSero2 results", + "pattern": "*_result.tsv" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*_result.txt": { + "type": "file", + "description": "Detailed summary of the SeqSero2 results", + "pattern": "*_result.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122170,45 +156181,56 @@ "tool_dev_url": "https://github.com/lh3/seqtk", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqtk" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A single fasta file to be split.", + "pattern": "*.{fasta}" + } } - }, - { - "fasta": { - "type": "file", - "description": "A single fasta file to be split.", - "pattern": "*.{fasta}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "The output bed which summarised locations of cuts", - "pattern": "*.{bed}" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "The output bed which summarised locations of cuts", + "pattern": "*.{bed}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122246,45 +156268,56 @@ "tool_dev_url": "https://github.com/lh3/seqtk", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqtk" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,respectively.", - "pattern": "*.{fastq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,respectively.", + "pattern": "*.{fastq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair.", + "pattern": "*.{fastq.gz}" + } + } + ] }, { - "reads": { - "type": "file", - "description": "If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair.", - "pattern": "*.{fastq.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122326,45 +156359,56 @@ "tool_dev_url": "https://github.com/lh3/seqtk", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqtk" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "A FASTQ or FASTA file", + "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + } } - }, - { - "sequences": { - "type": "file", - "description": "A FASTQ or FASTA file", - "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "sequences": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "FASTQ/FASTA file containing renamed sequences", + "pattern": "*.{fastq.gz, fasta.gz}" + } + } + ] }, { - "sequences": { - "type": "file", - "description": "FASTQ/FASTA file containing renamed sequences", - "pattern": "*.{fastq.gz, fasta.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122400,51 +156444,62 @@ "tool_dev_url": "https://github.com/lh3/seqtk", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files", - "pattern": "*.{fastq.gz}" - } - }, - { - "sample_size": { - "type": "integer", - "description": "Number of reads to sample." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Subsampled FastQ files", - "pattern": "*.{fastq.gz}" - } + ], + "identifier": "biotools:seqtk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files", + "pattern": "*.{fastq.gz}" + } + }, + { + "sample_size": { + "type": "integer", + "description": "Number of reads to sample." + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Subsampled FastQ files", + "pattern": "*.{fastq.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122490,45 +156545,56 @@ "tool_dev_url": "https://github.com/lh3/seqtk", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqtk" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fastx": { - "type": "file", - "description": "A FASTQ or FASTA file", - "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fastx": { + "type": "file", + "description": "A FASTQ or FASTA file", + "pattern": "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fastx": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "FASTQ/FASTA file containing renamed sequences", + "pattern": "*.{fastq.gz, fasta.gz}" + } + } + ] }, { - "fastx": { - "type": "file", - "description": "FASTQ/FASTA file containing renamed sequences", - "pattern": "*.{fastq.gz, fasta.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122578,46 +156644,66 @@ "tool_dev_url": "https://github.com/lh3/seqtk", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "sequences": { - "type": "file", - "description": "FASTQ/FASTA file", - "pattern": "*.{fq,fq.gz,fa,fa.gz}" - } - }, - { - "filter_list": { - "type": "file", - "description": "BED file or a text file with a list of sequence names", - "pattern": "*.{bed,lst}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sequences": { - "type": "file", - "description": "FASTQ/FASTA file", - "pattern": "*.{fq.gz,fa.gz}" - } + ], + "identifier": "biotools:seqtk" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "sequences": { + "type": "file", + "description": "FASTQ/FASTA file", + "pattern": "*.{fq,fq.gz,fa,fa.gz}" + } + } + ], + [ + { + "filter_list": { + "type": "file", + "description": "BED file or a text file with a list of sequence names", + "pattern": "*.{bed,lst}" + } + } + ] + ], + "output": [ + { + "sequences": [ + { + "meta": { + "type": "file", + "description": "FASTQ/FASTA file", + "pattern": "*.{fq.gz,fa.gz}" + } + }, + { + "*.gz": { + "type": "file", + "description": "FASTQ/FASTA file", + "pattern": "*.{fq.gz,fa.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122649,45 +156735,56 @@ "tool_dev_url": "https://github.com/lh3/seqtk", "licence": [ "MIT" - ] + ], + "identifier": "biotools:seqtk" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files", - "pattern": "*.{fastq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files", + "pattern": "*.{fastq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Filtered FastQ files", + "pattern": "*.{fastq.gz}" + } + } + ] }, { - "reads": { - "type": "file", - "description": "Filtered FastQ files", - "pattern": "*.{fastq.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122728,76 +156825,133 @@ "tool_dev_url": "https://github.com/stschiff/sequenceTools", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mpileup": { - "type": "file", - "description": "samtools mpileup output." - } - }, - { - "snpfile": { - "type": "file", - "description": "Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on.\nOnly alleles matching the Ref and Alt alleles of the provided snp file will be called.\n" - } - }, - { - "calling_method": { - "type": "string", - "description": "The desired calling method for pileupcaller. One of 'randomHaploid', 'randomDiploid', or 'majorityCall'." - } - }, - { - "output_format": { - "type": "string", - "description": "The desired output format. One of 'PLINK', 'EIGENSTRAT', or 'FREQSUM'." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "eigenstrat": { - "type": "file", - "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", - "pattern": "*.{geno,snp,ind}.txt" - } - }, - { - "plink": { - "type": "file", - "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", - "pattern": "*.{bed,bim,fam}" - } - }, - { - "freqsum": { - "type": "file", - "description": "The output freqsum-formatted file.", - "pattern": "*.freqsum.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "mpileup": { + "type": "file", + "description": "samtools mpileup output." + } + } + ], + [ + { + "snpfile": { + "type": "file", + "description": "Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on.\nOnly alleles matching the Ref and Alt alleles of the provided snp file will be called.\n" + } + } + ], + [ + { + "sample_names_fn": { + "type": "file", + "description": "File containing the sample names" + } + } + ] + ], + "output": [ + { + "eigenstrat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.geno": { + "type": "file", + "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", + "pattern": "*.{geno,snp,ind}.txt" + } + }, + { + "*.snp": { + "type": "file", + "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", + "pattern": "*.{geno,snp,ind}.txt" + } + }, + { + "*.ind": { + "type": "file", + "description": "A tuple containing the output Eigenstrat-formatted geno, snp and ind files.", + "pattern": "*.{geno,snp,ind}.txt" + } + } + ] + }, + { + "plink": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", + "pattern": "*.{bed,bim,fam}" + } + }, + { + "*.bim": { + "type": "file", + "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", + "pattern": "*.{bed,bim,fam}" + } + }, + { + "*.fam": { + "type": "file", + "description": "A tuple containing the output Plink-formatted bed, bim and fam files.", + "pattern": "*.{bed,bim,fam}" + } + } + ] + }, + { + "freqsum": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.freqsum.gz": { + "type": "file", + "description": "The output freqsum-formatted file.", + "pattern": "*.freqsum.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122829,66 +156983,81 @@ "doi": "10.1093/annonc/mdu479", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normalbam": { - "type": "file", - "description": "BAM file from the reference/normal sample", - "pattern": "*.{bam}" - } - }, - { - "tumourbam": { - "type": "file", - "description": "BAM file from the tumour sample", - "pattern": "*.{bam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference FASTA file", - "pattern": "*.{fasta}" - } - }, - { - "wigfile": { - "type": "file", - "description": "GC content wiggle file", - "pattern": "*.{wig.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "seqz": { - "type": "file", - "description": "Seqz file", - "pattern": "*.{seqz.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normalbam": { + "type": "file", + "description": "BAM file from the reference/normal sample", + "pattern": "*.{bam}" + } + }, + { + "tumourbam": { + "type": "file", + "description": "BAM file from the tumour sample", + "pattern": "*.{bam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference FASTA file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "wigfile": { + "type": "file", + "description": "GC content wiggle file", + "pattern": "*.{wig.gz}" + } + } + ] + ], + "output": [ + { + "seqz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "Seqz file", + "pattern": "*.{seqz.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122920,45 +157089,56 @@ "doi": "10.1093/annonc/mdu479", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig.gz": { + "type": "file", + "description": "GC Wiggle track file", + "pattern": "*.{wig.gz}" + } + } + ] }, { - "wig": { - "type": "file", - "description": "GC Wiggle track file", - "pattern": "*.{wig.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -122991,52 +157171,63 @@ "documentation": "https://github.com/ekg/seqwish", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "paf": { - "type": "list", - "description": "comma-separated PAF file(s) of alignments, single entry allowed", - "pattern": "[*.{paf,paf.gz},*.{paf,paf.gz},...]" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file used to generate alignments", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Variation graph in GFA 1.0 format", - "pattern": "*.{gfa}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "paf": { + "type": "list", + "description": "comma-separated PAF file(s) of alignments, single entry allowed", + "pattern": "[*.{paf,paf.gz},*.{paf,paf.gz},...]" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file used to generate alignments", + "pattern": "*.{fa,fa.gz,fasta,fasta.gz}" + } + } + ] + ], + "output": [ + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gfa": { + "type": "file", + "description": "Variation graph in GFA 1.0 format", + "pattern": "*.{gfa}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -123075,77 +157266,98 @@ "doi": "10.1099/mgen.0.000186", "licence": [ "GPL v3" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input Illunina paired-end FASTQ files", + "pattern": "*.{fq.gz,fastq.gz}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.tsv": { + "type": "file", + "description": "The predicted serotype in tab-delimited format", + "pattern": "*.tsv" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/detailed_serogroup_info.txt": { + "type": "file", + "description": "A detailed description of the predicted serotype", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input Illunina paired-end FASTQ files", - "pattern": "*.{fq.gz,fastq.gz}" - } - } + "authors": [ + "@rpetit3" ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "The predicted serotype in tab-delimited format", - "pattern": "*.tsv" - } - }, - { - "txt": { - "type": "file", - "description": "A detailed description of the predicted serotype", - "pattern": "*.txt" - } - } - ], - "authors": [ - "@rpetit3" - ], - "maintainers": [ - "@rpetit3" - ] - } - }, - { - "name": "severus", - "path": "modules/nf-core/severus/meta.yml", - "type": "module", - "meta": { - "name": "severus", - "description": "Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)", - "keywords": [ - "structural", - "variation", - "somatic", - "germline", - "long-read" - ], - "tools": [ + "maintainers": [ + "@rpetit3" + ] + } + }, + { + "name": "severus", + "path": "modules/nf-core/severus/meta.yml", + "type": "module", + "meta": { + "name": "severus", + "description": "Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)", + "keywords": [ + "structural", + "variation", + "somatic", + "germline", + "long-read" + ], + "tools": [ { "severus": { "description": "A tool for somatic structural variant calling using long reads", @@ -123155,184 +157367,337 @@ "doi": "10.1101/2024.03.22.24304756", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "target_input": { - "type": "file", - "description": "path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed)", - "pattern": "*.{bam,cram}" - } - }, - { - "target_index": { - "type": "file", - "description": "path to one or multiple target BAM/CRAM index files", - "pattern": "*.{bai,crai,csi}" - } - }, - { - "control_input": { - "type": "file", - "description": "path to the control BAM/CRAM file (e.g. normal, must be indexed)", - "pattern": "*.{bam,cram}" - } - }, - { - "control_index": { - "type": "file", - "description": "path to the control BAM/CRAM file index", - "pattern": "*.{bai,crai,csi}" - } - }, - { - "vcf": { - "type": "file", - "description": "path to vcf file used for phasing (if using haplotype specific SV calling", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tandem repeat regions information\ne.g. `[ id:'hg38']`\n" - } - }, - { - "bed": { - "type": "file", - "description": "path to bed file for tandem repeat regions (must be ordered)", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "Severus log file", - "pattern": "${prefix}/severus.log" - } - }, - { - "read_qual": { - "type": "file", - "description": "Severus read_qual file", - "pattern": "${prefix}/read_qual.txt" - } - }, - { - "breakpoints_double": { - "type": "file", - "description": "Severus breakpoints_double file", - "pattern": "${prefix}/breakpoints_double.csv" - } - }, - { - "read_alignments": { - "type": "file", - "description": "read alignments file", - "pattern": "${prefix}/read_alignments" - } - }, - { - "read_ids": { - "type": "file", - "description": "read IDs for support reads", - "pattern": "${prefix}/read_ids" - } - }, - { - "collapsed_dup": { - "type": "file", - "description": "a bed file with identified collapsed duplication regions", - "pattern": "${prefix}/severus_collaped_dup" - } - }, - { - "loh": { - "type": "file", - "description": "a bed file with predicted LOH regions", - "pattern": "${prefix}/severus_LOH.bed" - } - }, - { - "all_vcf": { - "type": "file", - "description": "VCF file with all SVs (somatic + germline)", - "pattern": "${prefix}/all_SVs/severus_all.vcf" - } - }, - { - "all_breakpoints_clusters_list": { - "type": "file", - "description": "Severus breakpoints clusters list file", - "pattern": "${prefix}/all_SVs/breakpoints_clusters_list.tsv" - } - }, - { - "all_breakpoints_clusters": { - "type": "file", - "description": "Severus breakpoints clusters file", - "pattern": "${prefix}/all_SVs/breakpoints_clusters.tsv" - } - }, - { - "all_plots": { - "type": "file", - "description": "Severus plots", - "pattern": "${prefix}/all_SVs/plots/*.html" - } - }, - { - "somatic_vcf": { - "type": "file", - "description": "VCF file with somatic SVs", - "pattern": "${prefix}/somatic_SVs/severus_all.vcf" - } - }, - { - "somatic_breakpoints_clusters_list": { - "type": "file", - "description": "Severus somatic breakpoints clusters list file", - "pattern": "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" - } - }, - { - "somatic_breakpoints_clusters": { - "type": "file", - "description": "Severus somatic breakpoints clusters file", - "pattern": "${prefix}/somatic_SVs/breakpoints_clusters.tsv" - } - }, - { - "somatic_plots": { - "type": "file", - "description": "Severus somatic plots", - "pattern": "${prefix}/somatic_SVs/plots/*.html" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "target_input": { + "type": "file", + "description": "path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed)", + "pattern": "*.{bam,cram}" + } + }, + { + "target_index": { + "type": "file", + "description": "path to one or multiple target BAM/CRAM index files", + "pattern": "*.{bai,crai,csi}" + } + }, + { + "control_input": { + "type": "file", + "description": "path to the control BAM/CRAM file (e.g. normal, must be indexed)", + "pattern": "*.{bam,cram}" + } + }, + { + "control_index": { + "type": "file", + "description": "path to the control BAM/CRAM file index", + "pattern": "*.{bai,crai,csi}" + } + }, + { + "vcf": { + "type": "file", + "description": "path to vcf file used for phasing (if using haplotype specific SV calling", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tandem repeat regions information\ne.g. `[ id:'hg38']`\n" + } + }, + { + "bed": { + "type": "file", + "description": "path to bed file for tandem repeat regions (must be ordered)", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/severus.log": { + "type": "file", + "description": "Severus log file", + "pattern": "${prefix}/severus.log" + } + } + ] + }, + { + "read_qual": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/read_qual.txt": { + "type": "file", + "description": "Severus read_qual file", + "pattern": "${prefix}/read_qual.txt" + } + } + ] + }, + { + "breakpoints_double": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/breakpoints_double.csv": { + "type": "file", + "description": "Severus breakpoints_double file", + "pattern": "${prefix}/breakpoints_double.csv" + } + } + ] + }, + { + "read_alignments": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/read_alignments": { + "type": "file", + "description": "read alignments file", + "pattern": "${prefix}/read_alignments" + } + } + ] + }, + { + "read_ids": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/read_ids.csv": { + "type": "file", + "description": "read IDs for support reads", + "pattern": "${prefix}/read_ids" + } + } + ] + }, + { + "collapsed_dup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/severus_collaped_dup.bed": { + "type": "file", + "description": "a bed file with identified collapsed duplication regions", + "pattern": "${prefix}/severus_collaped_dup" + } + } + ] + }, + { + "loh": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/severus_LOH.bed": { + "type": "file", + "description": "a bed file with predicted LOH regions", + "pattern": "${prefix}/severus_LOH.bed" + } + } + ] + }, + { + "all_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/all_SVs/severus_all.vcf": { + "type": "file", + "description": "VCF file with all SVs (somatic + germline)", + "pattern": "${prefix}/all_SVs/severus_all.vcf" + } + } + ] + }, + { + "all_breakpoints_clusters_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/all_SVs/breakpoints_clusters_list.tsv": { + "type": "file", + "description": "Severus breakpoints clusters list file", + "pattern": "${prefix}/all_SVs/breakpoints_clusters_list.tsv" + } + } + ] + }, + { + "all_breakpoints_clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/all_SVs/breakpoints_clusters.tsv": { + "type": "file", + "description": "Severus breakpoints clusters file", + "pattern": "${prefix}/all_SVs/breakpoints_clusters.tsv" + } + } + ] + }, + { + "all_plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/all_SVs/plots/severus_*.html": { + "type": "file", + "description": "Severus plots", + "pattern": "${prefix}/all_SVs/plots/*.html" + } + } + ] + }, + { + "somatic_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/somatic_SVs/severus_all.vcf": { + "type": "file", + "description": "VCF file with somatic SVs", + "pattern": "${prefix}/somatic_SVs/severus_all.vcf" + } + } + ] + }, + { + "somatic_breakpoints_clusters_list": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv": { + "type": "file", + "description": "Severus somatic breakpoints clusters list file", + "pattern": "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" + } + } + ] + }, + { + "somatic_breakpoints_clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/somatic_SVs/breakpoints_clusters.tsv": { + "type": "file", + "description": "Severus somatic breakpoints clusters file", + "pattern": "${prefix}/somatic_SVs/breakpoints_clusters.tsv" + } + } + ] + }, + { + "somatic_plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}/somatic_SVs/plots/severus_*.html": { + "type": "file", + "description": "Severus somatic plots", + "pattern": "${prefix}/somatic_SVs/plots/*.html" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -123366,52 +157731,81 @@ "doi": "10.1038/s41467-018-07483-5", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "depth": { - "type": "file", - "description": "Output from samtools depth (with header)", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "JSON formatted table of relative coverages on the X and Y, with associated error bars.", - "pattern": "*.json" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV table of relative coverages on the X and Y, with associated error bars.", - "pattern": "*.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "depth": { + "type": "file", + "description": "Output from samtools depth (with header)", + "pattern": "*" + } + } + ], + [ + { + "sample_list_file": { + "type": "file", + "description": "File containing the list of samples to be processed." + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON formatted table of relative coverages on the X and Y, with associated error bars.", + "pattern": "*.json" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV table of relative coverages on the X and Y, with associated error bars.", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -123442,86 +157836,147 @@ "documentation": "https://github.com/Singular-Genomics/singular-demux#sgdemux", "licence": [ "For Singular G4™ Sequencing Platform only" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sample_sheet": { - "type": "file", - "description": "sample_sheet file (either a Singular Genomics sample sheet, or a two column csv wih Sample_Barcode and Sample_ID)", - "pattern": "*.{csv}" - } - }, - { - "fastqs_dir": { - "type": "directory", - "description": "Input directory containing bgzipped (not gzip) FASTQ files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sample_fastq": { - "type": "file", - "description": "Demultiplexed per-sample FASTQ files", - "pattern": "output/*_R*.fastq.gz" - } - }, - { - "metrics": { - "type": "file", - "description": "Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates\n", - "pattern": "output/metrics.tsv" - } - }, - { - "most_frequent_unmatched": { - "type": "file", - "description": "File containing approx. counts of barcodes that did not match the expected barcodes\n", - "pattern": "output/most_frequence_unmatched.tsv" - } - }, - { - "per_project_metrics": { - "type": "file", - "description": "Summary metrics for samples in the same project", - "pattern": "output/per_project_metrics.tsv" - } - }, - { - "per_sample_metrics": { - "type": "file", - "description": "Summary metrics for each sample", - "pattern": "output/per_sample_metrics.tsv" - } - }, - { - "sample_barcode_hop_metrics": { - "type": "file", - "description": "File output for dual-indexed runs with barcodes which are unexpected combinations of\nexpected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT\n", - "pattern": "output/sample_barcode_hop_metrics/tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sample_sheet": { + "type": "file", + "description": "sample_sheet file (either a Singular Genomics sample sheet, or a two column csv wih Sample_Barcode and Sample_ID)", + "pattern": "*.{csv}" + } + }, + { + "fastqs_dir": { + "type": "directory", + "description": "Input directory containing bgzipped (not gzip) FASTQ files" + } + } + ] + ], + "output": [ + { + "sample_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/*_R*.fastq.gz": { + "type": "file", + "description": "Demultiplexed per-sample FASTQ files", + "pattern": "output/*_R*.fastq.gz" + } + } + ] + }, + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/metrics.tsv": { + "type": "file", + "description": "Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates\n", + "pattern": "output/metrics.tsv" + } + } + ] + }, + { + "most_frequent_unmatched": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/most_frequent_unmatched.tsv": { + "type": "file", + "description": "File containing approx. counts of barcodes that did not match the expected barcodes\n", + "pattern": "output/most_frequence_unmatched.tsv" + } + } + ] + }, + { + "per_project_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/per_project_metrics.tsv": { + "type": "file", + "description": "Summary metrics for samples in the same project", + "pattern": "output/per_project_metrics.tsv" + } + } + ] + }, + { + "per_sample_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/per_sample_metrics.tsv": { + "type": "file", + "description": "Summary metrics for each sample", + "pattern": "output/per_sample_metrics.tsv" + } + } + ] + }, + { + "sample_barcode_hop_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "output/sample_barcode_hop_metrics.tsv": { + "type": "file", + "description": "File output for dual-indexed runs with barcodes which are unexpected combinations of\nexpected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT\n", + "pattern": "output/sample_barcode_hop_metrics/tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -123562,52 +158017,63 @@ "doi": "10.1101/2022.10.19.512867", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_list": { - "type": "file", - "description": "VCF/BCF files containing genotype probabilities (GP field).\nThe files should be ordered by genomic position.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "input_list_index": { - "type": "file", - "description": "VCF/BCF files index.", - "pattern": "*.csi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "merged_variants": { - "type": "file", - "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } + ], + "identifier": "biotools:shapeit5" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_list": { + "type": "file", + "description": "VCF/BCF files containing genotype probabilities (GP field).\nThe files should be ordered by genomic position.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "input_list_index": { + "type": "file", + "description": "VCF/BCF files index.", + "pattern": "*.csi" + } + } + ] + ], + "output": [ + { + "merged_variants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Output VCF/BCF file for the merged regions.\nPhased information (HS field) is updated accordingly for the full region.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -123646,101 +158112,136 @@ "doi": "10.1101/2022.10.19.512867 ", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "input_index": { - "type": "file", - "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "pedigree": { - "type": "file", - "description": "Pedigree information in the following format: offspring father mother.\n", - "pattern": "*.{txt, tsv}" - } - }, - { - "region": { - "type": "string", - "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "reference": { - "type": "file", - "description": "Reference panel of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}" - } - }, - { - "reference_index": { - "type": "file", - "description": "Index file of the Reference panel file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "scaffold": { - "type": "file", - "description": "Scaffold of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}" - } - }, - { - "scaffold_index": { - "type": "file", - "description": "Index file of the scaffold file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "phased_variants": { - "type": "file", - "description": "Phased haplotypes in VCF/BCF format.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:shapeit5" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Target dataset in VCF/BCF format defined at all variable positions.\nThe file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "input_index": { + "type": "file", + "description": "Index file of the input VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "pedigree": { + "type": "file", + "description": "Pedigree information in the following format: offspring father mother.\n", + "pattern": "*.{txt, tsv}" + } + }, + { + "region": { + "type": "string", + "description": "Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference panel of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}" + } + }, + { + "reference_index": { + "type": "file", + "description": "Index file of the Reference panel file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "scaffold": { + "type": "file", + "description": "Scaffold of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}" + } + }, + { + "scaffold_index": { + "type": "file", + "description": "Index file of the scaffold file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap" + } + } + ] + ], + "output": [ + { + "phased_variant": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Phased variant dataset in VCF/BCF format.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -123780,95 +158281,122 @@ "doi": "10.1101/2022.10.19.512867 ", "licence": [ "MIT" - ] + ], + "identifier": "biotools:shapeit5" } } ], "requirement": "AVX2", "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_plain": { - "type": "file", - "description": "Genotypes to be phased in plain VCF/BCF format.\n", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "input_plain_index": { - "type": "file", - "description": "Index file of the input_plain VCF/BCF file containing genotype likelihoods.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "input_region": { - "type": "string", - "description": "Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "pedigree": { - "type": "file", - "description": "Pedigree information in the following format: offspring father mother.\n", - "pattern": "*.{txt, tsv}" - } - }, - { - "scaffold": { - "type": "file", - "description": "Scaffold of haplotypes in VCF/BCF format.", - "pattern": "*.{vcf.gz,bcf.gz}" - } - }, - { - "scaffold_index": { - "type": "file", - "description": "Index file of the scaffold file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - }, - { - "scaffold_region": { - "type": "string", - "description": "Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20).\n", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "map": { - "type": "file", - "description": "File containing the genetic map.", - "pattern": "*.gmap" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "phased_variants": { - "type": "file", - "description": "Phased haplotypes in VCF/BCF format.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_plain": { + "type": "file", + "description": "Genotypes to be phased in plain VCF/BCF format.\n", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "input_plain_index": { + "type": "file", + "description": "Index file of the input_plain VCF/BCF file containing genotype likelihoods.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "pedigree": { + "type": "file", + "description": "Pedigree information in the following format: offspring father mother.\n", + "pattern": "*.{txt, tsv}" + } + }, + { + "input_region": { + "type": "string", + "description": "Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20).\nFor chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "scaffold": { + "type": "file", + "description": "Scaffold of haplotypes in VCF/BCF format.", + "pattern": "*.{vcf.gz,bcf.gz}" + } + }, + { + "scaffold_index": { + "type": "file", + "description": "Index file of the scaffold file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + }, + { + "scaffold_region": { + "type": "string", + "description": "Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20).\n", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "map": { + "type": "file", + "description": "File containing the genetic map.", + "pattern": "*.gmap" + } + } + ] + ], + "output": [ + { + "phased_variant": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{vcf,bcf,vcf.gz,bcf.gz}": { + "type": "file", + "description": "Phased variants in VCF/BCF format.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -123902,94 +158430,121 @@ "doi": "10.1101/2022.10.19.512867 ", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "estimate": { - "type": "file", - "description": "Imputed data.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "estimate_index": { - "type": "file", - "description": "Index file of the freq VCF/BCF file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "region": { - "type": "string", - "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", - "pattern": "chrXX:leftBufferPosition-rightBufferPosition" - } - }, - { - "pedigree": { - "type": "file", - "description": "Pedigree information in the following format: offspring father mother.\n", - "pattern": "*.{txt, tsv}" - } - }, - { - "truth": { - "type": "file", - "description": "Validation dataset called at the same positions as the imputed file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "truth_index": { - "type": "file", - "description": "Index file of the truth VCF/BCF file.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "freq": { - "type": "file", - "description": "File containing allele frequencies at each site.", - "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" - } - }, - { - "freq_index": { - "type": "file", - "description": "Index file of the freq VCF/BCF file.", - "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "errors": { - "type": "file", - "description": "Estimates errors from the phased file.", - "pattern": "*.txt.gz" - } + ], + "identifier": "biotools:shapeit5" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "estimate": { + "type": "file", + "description": "Imputed data.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "estimate_index": { + "type": "file", + "description": "Index file of the freq VCF/BCF file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "region": { + "type": "string", + "description": "Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).", + "pattern": "chrXX:leftBufferPosition-rightBufferPosition" + } + }, + { + "pedigree": { + "type": "file", + "description": "Pedigree information in the following format: offspring father mother.\n", + "pattern": "*.{txt, tsv}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "truth": { + "type": "file", + "description": "Validation dataset called at the same positions as the imputed file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "truth_index": { + "type": "file", + "description": "Index file of the truth VCF/BCF file.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "freq": { + "type": "file", + "description": "File containing allele frequencies at each site.", + "pattern": "*.{vcf,bcf,vcf.gz,bcf.gz}" + } + }, + { + "freq_index": { + "type": "file", + "description": "Index file of the freq VCF/BCF file.", + "pattern": "*.{vcf.gz.csi,bcf.gz.csi}" + } + } + ] + ], + "output": [ + { + "errors": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt.gz": { + "type": "file", + "description": "Estimates errors from the phased file.", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124023,59 +158578,90 @@ "doi": "10.1038/s41587-020-0503-6", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input file in FASTQ format.", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "assembly": { - "type": "file", - "description": "Assembled FASTA file", - "pattern": "${prefix}_Assembly.fasta.gz" - } - }, - { - "gfa": { - "type": "file", - "description": "Repeat graph", - "pattern": "${prefix}_Assembly.gfa.gz" - } - }, - { - "results": { - "type": "directory", - "description": "Resulting assembly directory", - "pattern": "ShastaRun" - } + ], + "identifier": "biotools:shasta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input file in FASTQ format.", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz}" + } + } + ] + ], + "output": [ + { + "assembly": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_Assembly.fasta.gz": { + "type": "file", + "description": "Assembled FASTA file", + "pattern": "${prefix}_Assembly.fasta.gz" + } + } + ] + }, + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_Assembly.gfa.gz": { + "type": "file", + "description": "Repeat graph", + "pattern": "${prefix}_Assembly.gfa.gz" + } + } + ] + }, + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ShastaRun/": { + "type": "directory", + "description": "Resulting assembly directory", + "pattern": "ShastaRun" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124106,45 +158692,56 @@ "documentation": "https://linux.die.net/man/1/shasum", "licence": [ "GPLv3+" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "file": { - "type": "file", - "description": "Any file", - "pattern": "*.*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "file": { + "type": "file", + "description": "Any file", + "pattern": "*.*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "checksum": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sha256": { + "type": "file", + "description": "File containing checksum", + "pattern": "*.sha256" + } + } + ] }, { - "checksum": { - "type": "file", - "description": "File containing checksum", - "pattern": "*.sha256" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124177,52 +158774,73 @@ "doi": "10.1128/AEM.00165-19", "licence": [ "Public Domain" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, is_ont:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Illumina or Nanopore FASTQ file", - "pattern": "*.fastq.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "A TSV formatted file with ShigaTyper results", - "pattern": "*.tsv" - } - }, - { - "hits": { - "type": "file", - "description": "A TSV formatted file with individual gene hits", - "pattern": "*-hits.tsv" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, is_ont:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Illumina or Nanopore FASTQ file", + "pattern": "*.fastq.gz" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tsv": { + "type": "file", + "description": "A TSV formatted file with ShigaTyper results", + "pattern": "*.tsv" + } + } + ] + }, + { + "hits": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}-hits.tsv": { + "type": "file", + "description": "A TSV formatted file with individual gene hits", + "pattern": "*-hits.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124256,45 +158874,56 @@ "doi": "10.1099/mgen.0.000704", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:shigeifinder" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "Assembly or paired-end Illumina reads", - "pattern": "*.{fasta,fasta.gz,fastq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "Assembly or paired-end Illumina reads", + "pattern": "*.{fasta,fasta.gz,fastq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A TSV formatted file with ShigEiFinder results", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "A TSV formatted file with ShigEiFinder results", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124327,81 +158956,102 @@ "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", "licence": [ "AGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment, at a minimum an id.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information on experiment, at a minimum an id. To match meta.\ne.g. [ id:'test' ]\n" - } - }, - { - "sample": { - "type": "file", - "description": "CSV-format sample sheet with sample metadata\n" - } - }, - { - "feature_meta": { - "type": "file", - "description": "TSV-format feature (e.g. gene) metadata\n" - } - }, - { - "assay_files": { - "type": "file", - "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n" - } - }, - { - "contrasts": { - "type": "file", - "description": "CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.\n" - } - }, - { - "differential_results": { - "type": "file", - "description": "List of TSV-format differential analysis outputs, one per row of the contrasts file\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "data": { - "type": "file", - "description": "A shinyngs ExploratorySummarizedExperiment\nobject serialized with saveRDS().\n", - "pattern": "app/data.rds" - } - }, - { - "app": { - "type": "file", - "description": "The mini R script required build an application from data.rds.\n", - "pattern": "app/app.R" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment, at a minimum an id.\ne.g. [ id:'test' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV-format sample sheet with sample metadata\n" + } + }, + { + "feature_meta": { + "type": "file", + "description": "TSV-format feature (e.g. gene) metadata\n" + } + }, + { + "assay_files": { + "type": "file", + "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on experiment, at a minimum an id. To match meta.\ne.g. [ id:'test' ]\n" + } + }, + { + "contrasts": { + "type": "file", + "description": "CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.\n" + } + }, + { + "differential_results": { + "type": "file", + "description": "List of TSV-format differential analysis outputs, one per row of the contrasts file\n" + } + } + ], + [ + { + "contrast_stats_assay": { + "type": "file", + "description": "contrast statistics" + } + } + ] + ], + "output": [ + { + "app": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/data.rds": { + "type": "file", + "description": "The mini R script required build an application from data.rds.\n", + "pattern": "app/app.R" + } + }, + { + "*/app.R": { + "type": "file", + "description": "The mini R script required build an application from data.rds.\n", + "pattern": "app/app.R" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124440,73 +159090,96 @@ "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", "licence": [ "AGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information, to be passed as reference\nand target levels, like '--reference_level $meta.reference\n--treatment_level $meta.target'\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information on experiment represented by max,\nfeatures and samples, at a minimum an id.\ne.g. [ id:'test' ]\n" - } - }, - { - "differential_results": { - "type": "file", - "description": "CSV or TSV-format tabular file with differential analysis outputs\n" - } - }, - { - "sample": { - "type": "file", - "description": "CSV or TSV-format sample sheet with sample metadata\n" - } - }, - { - "feature_meta": { - "type": "file", - "description": "CSV or TSV-format feature (e.g. gene) metadata\n" - } - }, - { - "assay_file": { - "type": "file", - "description": "CSV or TSV matrix file to use alongside differential statistics in\ninterpretation. Usually a normalised form.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing contrast information\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" - } - }, - { - "volcanos_png": { - "type": "file", - "description": "Meta-keyed tuple containing a PNG output for a volcano plot built from\nthe differential result table.\n" - } - }, - { - "volcanos_html": { - "type": "file", - "description": "Meta-keyed tuple containing an HTML output for a volcano plot built\nfrom the differential result table.\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information, to be passed as reference\nand target levels, like '--reference_level $meta.reference\n--treatment_level $meta.target'\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "differential_result": { + "type": "file", + "description": "statistic differential results" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on experiment represented by max,\nfeatures and samples, at a minimum an id.\ne.g. [ id:'test' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV or TSV-format sample sheet with sample metadata\n" + } + }, + { + "feature_meta": { + "type": "file", + "description": "CSV or TSV-format feature (e.g. gene) metadata\n" + } + }, + { + "assay_file": { + "type": "file", + "description": "CSV or TSV matrix file to use alongside differential statistics in\ninterpretation. Usually a normalised form.\n" + } + } + ] + ], + "output": [ + { + "volcanos_png": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*/png/volcano.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for a volcano plot built from\nthe differential result table.\n" + } + } + ] + }, + { + "volcanos_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing contrast information\ne.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]\n" + } + }, + { + "*/html/volcano.html": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for a volcano plot built\nfrom the differential result table.\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124546,109 +159219,227 @@ "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", "licence": [ "AGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on variables for use in plots,\nprobably experimental information, but at a minimum an id.\ne.g. [ id:'treatment' ]\n" - } - }, - { - "sample": { - "type": "file", - "description": "CSV-format sample sheet with sample metadata\n" - } - }, - { - "feature_meta": { - "type": "file", - "description": "TSV-format feature (e.g. gene) metadata\n" - } - }, - { - "assay_files": { - "type": "file", - "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n" - } - } - ], - "output": [ - { - "boxplots_png": { - "type": "file", - "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n" - } - }, - { - "boxplots_html": { - "type": "file", - "description": "Meta-keyed tuple containing HTML output for box plots covering input\nmatrices.\n" - } - }, - { - "densities_png": { - "type": "file", - "description": "Meta-keyed tuple containing PNG output for density plots\ncovering input matrices.\n" - } - }, - { - "densities_html": { - "type": "file", - "description": "Meta-keyed tuple containing HTML output for density plots\ncovering input matrices.\n" - } - }, - { - "pca2d_png": { - "type": "file", - "description": "Meta-keyed tuple containing a PNG output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" - } - }, - { - "pca2d_html": { - "type": "file", - "description": "Meta-keyed tuple containing an HTML output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" - } - }, - { - "pca3d_png": { - "type": "file", - "description": "Meta-keyed tuple containing a PNG output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" - } - }, - { - "pca3d_html": { - "type": "file", - "description": "Meta-keyed tuple containing an HTML output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" - } - }, - { - "mad_png": { - "type": "file", - "description": "Meta-keyed tuple containing a PNG output for MAD correlation plots\ncovering specified input matrix (by default the last one in the input\nlist.\n" - } - }, - { - "mad_dendro": { - "type": "file", - "description": "Meta-keyed tuple containing an HTML output for MAD correlation plots\ncovering specified input matrix (by default the last one in the input\nlist.\n" - } - }, - { - "dendro": { - "type": "file", - "description": "Meta-keyed tuple containing a PNG, for a sample clustering\ndendrogramcovering specified input matrix (by default the last one in\nthe input list.\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on variables for use in plots,\nprobably experimental information, but at a minimum an id.\ne.g. [ id:'treatment' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV-format sample sheet with sample metadata\n" + } + }, + { + "feature_meta": { + "type": "file", + "description": "TSV-format feature (e.g. gene) metadata\n" + } + }, + { + "assay_files": { + "type": "file", + "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n" + } + } + ] + ], + "output": [ + { + "boxplots_png": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n" + } + }, + { + "*/png/boxplot.png": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for box plots covering input\nmatrices.\n" + } + } + ] + }, + { + "boxplots_html": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing HTML output for box plots covering input\nmatrices.\n" + } + }, + { + "*/html/boxplot.html": { + "type": "file", + "description": "Meta-keyed tuple containing HTML output for box plots covering input\nmatrices.\n" + } + } + ] + }, + { + "densities_png": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for density plots\ncovering input matrices.\n" + } + }, + { + "*/png/density.png": { + "type": "file", + "description": "Meta-keyed tuple containing PNG output for density plots\ncovering input matrices.\n" + } + } + ] + }, + { + "densities_html": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing HTML output for density plots\ncovering input matrices.\n" + } + }, + { + "*/html/density.html": { + "type": "file", + "description": "Meta-keyed tuple containing HTML output for density plots\ncovering input matrices.\n" + } + } + ] + }, + { + "pca2d_png": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + }, + { + "*/png/pca2d.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + } + ] + }, + { + "pca2d_html": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + }, + { + "*/html/pca2d.html": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for 2D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + } + ] + }, + { + "pca3d_png": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + }, + { + "*/png/pca3d.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + } + ] + }, + { + "pca3d_html": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + }, + { + "*/html/pca3d.html": { + "type": "file", + "description": "Meta-keyed tuple containing an HTML output for 3D PCA plots covering\nspecified input matrix (by default the last one in the input list.\n" + } + } + ] + }, + { + "mad_png": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for MAD correlation plots\ncovering specified input matrix (by default the last one in the input\nlist.\n" + } + }, + { + "*/png/mad_correlation.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG output for MAD correlation plots\ncovering specified input matrix (by default the last one in the input\nlist.\n" + } + } + ] + }, + { + "mad_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/html/mad_correlation.html": { + "type": "file", + "description": "HTML output for MAD correlation plots", + "pattern": "*{.html}" + } + } + ] + }, + { + "dendro": [ + { + "meta": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG, for a sample clustering\ndendrogramcovering specified input matrix (by default the last one in\nthe input list.\n" + } + }, + { + "*/png/sample_dendrogram.png": { + "type": "file", + "description": "Meta-keyed tuple containing a PNG, for a sample clustering\ndendrogramcovering specified input matrix (by default the last one in\nthe input list.\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124687,102 +159478,141 @@ "tool_dev_url": "https://github.com/pinin4fjords/shinyngs", "licence": [ "AGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment, at a minimum an id.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information on features.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information on contrasts.\ne.g. [ id:'test' ]\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing information on experiment, at a minimum an id. To match meta.\ne.g. [ id:'test' ]\n" - } - }, - { - "sample": { - "type": "file", - "description": "CSV-format sample sheet with sample metadata\n" - } - }, - { - "feature_meta": { - "type": "file", - "description": "TSV-format feature (e.g. gene) metadata\n" - } - }, - { - "assay_files": { - "type": "file", - "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n" - } - }, - { - "contrasts": { - "type": "file", - "description": "CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" - } - }, - { - "sample_meta": { - "type": "file", - "description": "File containing validated sample metadata", - "pattern": "/*.sample_metadata.tsv" - } - }, - { - "feature_meta": { - "type": "file", - "description": "File containing validated feature metadata", - "pattern": "/*.feature_metadata.tsv", - "optional": true - } - }, - { - "assays": { - "type": "file", - "description": "Files containing validated matrices", - "pattern": "/*.assay.tsv" - } - }, - { - "contrasts": { - "type": "file", - "description": "Files containing validated matrices", - "pattern": "/*.contrasts_file.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment, at a minimum an id.\ne.g. [ id:'test' ]\n" + } + }, + { + "sample": { + "type": "file", + "description": "CSV-format sample sheet with sample metadata\n" + } + }, + { + "assay_files": { + "type": "file", + "description": "List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on features.\ne.g. [ id:'test' ]\n" + } + }, + { + "feature_meta": { + "type": "file", + "description": "TSV-format feature (e.g. gene) metadata\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information on contrasts.\ne.g. [ id:'test' ]\n" + } + }, + { + "contrasts": { + "type": "file", + "description": "CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.\n" + } + } + ] + ], + "output": [ + { + "sample_meta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.sample_metadata.tsv": { + "type": "file", + "description": "File containing validated sample metadata", + "pattern": "/*.sample_metadata.tsv" + } + } + ] + }, + { + "feature_meta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.feature_metadata.tsv": { + "type": "file", + "description": "File containing validated feature metadata", + "pattern": "/*.feature_metadata.tsv", + "optional": true + } + } + ] + }, + { + "assays": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.assay.tsv": { + "type": "file", + "description": "Files containing validated matrices", + "pattern": "/*.assay.tsv" + } + } + ] + }, + { + "contrasts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on experiment.\ne.g. [ id:'test' ]\n" + } + }, + { + "*/*.contrasts_file.tsv": { + "type": "file", + "description": "Files containing validated matrices", + "pattern": "/*.contrasts_file.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124819,72 +159649,123 @@ "documentation": "https://github.com/tseemann/shovill/blob/master/README.md", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input paired-end FastQ files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "contigs": { - "type": "file", - "description": "The final assembly produced by Shovill", - "pattern": "contigs.fa" - } - }, - { - "corrections": { - "type": "file", - "description": "List of post-assembly corrections made by Shovill", - "pattern": "shovill.corrections" - } - }, - { - "log": { - "type": "file", - "description": "Full log file for bug reporting", - "pattern": "shovill.log" - } - }, - { - "raw_contigs": { - "type": "file", - "description": "Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)", - "pattern": "{skesa,spades,megahit,velvet}.fasta" - } - }, - { - "gfa": { - "type": "file", - "description": "Assembly graph produced by MEGAHIT, SPAdes, or Velvet", - "pattern": "contigs.{fastg,gfa,LastGraph}" - } + ], + "identifier": "biotools:shovill" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired-end FastQ files" + } + } + ] + ], + "output": [ + { + "contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contigs.fa": { + "type": "file", + "description": "The final assembly produced by Shovill", + "pattern": "contigs.fa" + } + } + ] + }, + { + "corrections": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shovill.corrections": { + "type": "file", + "description": "List of post-assembly corrections made by Shovill", + "pattern": "shovill.corrections" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shovill.log": { + "type": "file", + "description": "Full log file for bug reporting", + "pattern": "shovill.log" + } + } + ] + }, + { + "raw_contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "{skesa,spades,megahit,velvet}.fasta": { + "type": "file", + "description": "Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)", + "pattern": "{skesa,spades,megahit,velvet}.fasta" + } + } + ] + }, + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "contigs.{fastg,gfa,LastGraph}": { + "type": "file", + "description": "Assembly graph produced by MEGAHIT, SPAdes, or Velvet", + "pattern": "contigs.{fastg,gfa,LastGraph}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -124915,73 +159796,114 @@ "tool_dev_url": "https://github.com/najoshi/sickle", "licence": [ "MIT License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. File of forward reads must be supplied first and reverse reads as the second e.g. [\"read.1.fastq.gz\",\"read.2.fastq.gz\"]", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" - } - }, - { - "qual_type": { - "type": "string", - "description": "sickle needs a base quality values, which could be either illumina, solexa or sanger", - "pattern": "illumina or solexa or sanger" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" - } - }, - { - "single_trimmed": { - "type": "file", - "description": "5' or 3' trimmed (based on base quality) single-end fastq file", - "pattern": "*.se.trimmed.fastq.gz" - } - }, - { - "paired1_trimmed": { - "type": "file", - "description": "5' or 3' trimmed (based on base quality) R1 fastq file", - "pattern": "*.pe1.trimmed.fastq.gz" - } - }, - { - "paired2_trimmed": { - "type": "file", - "description": "5' or 3' trimmed (based on base quality) R2 fastq file", - "pattern": "*.pe2.trimmed.fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "log file", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:sickle" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. File of forward reads must be supplied first and reverse reads as the second e.g. [\"read.1.fastq.gz\",\"read.2.fastq.gz\"]", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" + } + }, + { + "qual_type": { + "type": "string", + "description": "sickle needs a base quality values, which could be either illumina, solexa or sanger", + "pattern": "illumina or solexa or sanger" + } + } + ] + ], + "output": [ + { + "single_trimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "${prefix}.se.trimmed.fastq.gz": { + "type": "file", + "description": "5' or 3' trimmed (based on base quality) single-end fastq file", + "pattern": "*.se.trimmed.fastq.gz" + } + } + ] + }, + { + "paired_trimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "${prefix}.pe{1,2}.trimmed.fastq.gz": { + "type": "file", + "description": "5' or 3' trimmed (based on base quality) paired-end fastq files", + "pattern": "*.pe{1,2}.trimmed.fastq.gz" + } + } + ] + }, + { + "singleton_trimmed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "${prefix}.singleton.trimmed.fastq.gz": { + "type": "file", + "description": "5' or 3' trimmed (based on base quality) singleton fastq file", + "pattern": "*.singleton.trimmed.fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false, qual:'Illumina' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "log file", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125012,82 +159934,117 @@ "homepage": "https://github.com/COMBINE-lab/simpleaf", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on genome_fasta\n" - } - }, - { - "genome_fasta": { - "type": "file", - "description": "FASTA file containing the genome sequence\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information on genome_gtf\n" - } - }, - { - "genome_gtf": { - "type": "file", - "description": "GTF file containing transcript annotations. Optional if transcript FASTA file is provided.\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information on transcript_fasta\n" - } - }, - { - "transcript_fasta": { - "type": "file", - "description": "FASTA file containing the transcript sequences. Optional if transcript GTF file is provided.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the Salmon index files\n", - "pattern": "salmon/index" - } - }, - { - "transcript_tsv": { - "type": "file", - "description": "Transcript-to-gene mapping file in 3-column TSV format\n", - "pattern": "salmon/ref/*_t2g_3col.tsv" - } - }, - { - "salmon": { - "type": "directory", - "description": "Folder containing the Salmon files\n", - "pattern": "salmon" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions\n", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on genome_fasta\n" + } + }, + { + "genome_fasta": { + "type": "file", + "description": "FASTA file containing the genome sequence\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information on genome_gtf\n" + } + }, + { + "genome_gtf": { + "type": "file", + "description": "GTF file containing transcript annotations. Optional if transcript FASTA file is provided.\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information on transcript_fasta\n" + } + }, + { + "transcript_fasta": { + "type": "file", + "description": "FASTA file containing the transcript sequences. Optional if transcript GTF file is provided.\n" + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)\n" + } + }, + { + "${prefix}/index": { + "type": "directory", + "description": "Folder containing the Salmon index files\n", + "pattern": "salmon/index" + } + } + ] + }, + { + "transcript_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)\n" + } + }, + { + "${prefix}/ref/t2g_3col.tsv": { + "type": "file", + "description": "Transcript-to-gene mapping file in 3-column TSV format\n", + "pattern": "salmon/ref/*_t2g_3col.tsv" + } + } + ] + }, + { + "salmon": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Folder containing the Salmon files\n", + "pattern": "salmon" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions\n", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125125,86 +160082,110 @@ "homepage": "https://github.com/COMBINE-lab/simpleaf", "licence": [ "BSD-3-Clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files for paired-end data.\nReads should be grouped by pairs.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing index information\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the index files" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing txp2gene information\n" - } - }, - { - "txp2gene": { - "type": "file", - "description": "File mapping transcripts to genes.\n" - } - }, - { - "chemistry": { - "type": "string", - "description": "Chemistry used for library preparation. It can be a string describing\nthe specific chemistry or the geometry of the barcode, UMI, and\nmappable read. For example, \"10xv2\" and \"10xv3\" will apply the\nappropriate settings for 10x Chromium v2 and v3 protocols,\nrespectively. Alternatively, you can provide a general geometry string\nif your chemistry is not pre-registered. For example, instead of\n\"10xv2\", you could use \"1{b[16]u[10]x:}2{r:}\", or instead of \"10xv3\",\nyou could use \"1{b[16]u[12]x:}2{r:}\".\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing whitelist information\n" - } - }, - { - "whitelist": { - "type": "file", - "description": "Whitelist file containing valid cell barcodes. Optional.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alevin_results": { - "type": "directory", - "description": "Folder containing the Alevin results for a specific sample\n", - "pattern": "*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "chemistry": { + "type": "string", + "description": "Chemistry used for library preparation. It can be a string describing\nthe specific chemistry or the geometry of the barcode, UMI, and\nmappable read. For example, \"10xv2\" and \"10xv3\" will apply the\nappropriate settings for 10x Chromium v2 and v3 protocols,\nrespectively. Alternatively, you can provide a general geometry string\nif your chemistry is not pre-registered. For example, instead of\n\"10xv2\", you could use \"1{b[16]u[10]x:}2{r:}\", or instead of \"10xv3\",\nyou could use \"1{b[16]u[12]x:}2{r:}\".\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files for paired-end data.\nReads should be grouped by pairs.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "index": { + "type": "directory", + "description": "Folder containing the index files" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing txp2gene information\n" + } + }, + { + "txp2gene": { + "type": "file", + "description": "File mapping transcripts to genes.\n" + } + } + ], + [ + { + "resolution": { + "type": "string", + "description": "Resolution for the clustering.\n" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing whitelist information\n" + } + }, + { + "whitelist": { + "type": "file", + "description": "Whitelist file containing valid cell barcodes. Optional.\n" + } + } + ] + ], + "output": [ + { + "results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}": { + "type": "directory", + "description": "Folder containing the quantification results" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125245,66 +160226,107 @@ "doi": "10.1371/journal.pone.0147101", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Nucleotide or protein sequences in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "SISTR serovar prediction", - "pattern": "*.{tsv}" - } - }, - { - "allele_json": { - "type": "file", - "description": "Allele sequences and info to JSON", - "pattern": "*.{json}" - } - }, - { - "allele_fasta": { - "type": "file", - "description": "FASTA file destination of novel cgMLST alleles", - "pattern": "*.{fasta}" - } - }, - { - "cgmlst_csv": { - "type": "file", - "description": "CSV file destination for cgMLST allelic profiles", - "pattern": "*.{csv}" - } + ], + "identifier": "biotools:SISTR" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Nucleotide or protein sequences in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "SISTR serovar prediction", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "allele_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-allele.fasta": { + "type": "file", + "description": "FASTA file destination of novel cgMLST alleles", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "allele_json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-allele.json": { + "type": "file", + "description": "Allele sequences and info to JSON", + "pattern": "*.{json}" + } + } + ] + }, + { + "cgmlst_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-cgmlst.csv": { + "type": "file", + "description": "CSV file destination for cgMLST allelic profiles", + "pattern": "*.{csv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125335,45 +160357,56 @@ "tool_dev_url": "https://github.com/Infinidat/slimfastq", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Either a single-end FASTQ file or paired-end files.", - "pattern": "*.{fq.gz,fastq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq": { + "type": "file", + "description": "Either a single-end FASTQ file or paired-end files.", + "pattern": "*.{fq.gz,fastq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "sfq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sfq": { + "type": "file", + "description": "Either one or two sequence files in slimfastq compressed format.", + "pattern": "*.{sfq}" + } + } + ] }, { - "sfq": { - "type": "file", - "description": "Either one or two sequence files in slimfastq compressed format.", - "pattern": "*.{sfq}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125408,59 +160441,80 @@ "doi": "10.1038/s41436-020-0754-0", "licence": [ "Apache License Version 2.0" - ] - } - } - ], - "input": [ - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "run_metrics": { - "type": "file", - "description": "File containing run parameters of SMNCopyNumberCaller", - "pattern": "*.{json}" - } - }, - { - "smncopynumber": { - "type": "file", - "description": "File containing the output of SMNCopyNumberCaller", - "pattern": "*.{tsv}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ] + ], + "output": [ + { + "smncopynumber": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "out/*.tsv": { + "type": "file", + "description": "File containing the output of SMNCopyNumberCaller", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "run_metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "out/*.json": { + "type": "file", + "description": "File containing run parameters of SMNCopyNumberCaller", + "pattern": "*.{json}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125499,52 +160553,67 @@ "documentation": "https://github.com/pangenome/smoothxg", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Variation graph in GFA 1.0 format", - "pattern": "*.{gfa}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Variation graph in GFA 1.0 format", + "pattern": "*.{gfa}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Linearized and simplified graph in GFA 1.0 format", - "pattern": "*.smoothxg.{gfa}" - } + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*smoothxg.gfa": { + "type": "file", + "description": "Linearized and simplified graph in GFA 1.0 format", + "pattern": "*.smoothxg.{gfa}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "maf": [ + { + "*.maf": { + "type": "file", + "description": "write the multiple sequence alignments (MSAs) in MAF format in this file (optional)", + "pattern": "*.{maf}" + } + } + ] }, { - "maf": { - "type": "file", - "description": "write the multiple sequence alignments (MSAs) in MAF format in this file (optional)", - "pattern": "*.{maf}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125583,73 +160652,100 @@ "tool_dev_url": "https://github.com/brentp/smoove", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "exclude_beds": { - "type": "file", - "description": "A BED file containing the regions to exclude from the SV calling", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "Index of reference fasta file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + }, + { + "exclude_beds": { + "type": "file", + "description": "A BED file containing the regions to exclude from the SV calling", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index of reference fasta file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125684,62 +160780,85 @@ "doi": "10.1093/bioinformatics/bty350", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "inputs": { - "type": "file", - "description": "Any input file required by Snakemake", - "pattern": "*" - } - }, - { - "meta2": { - "type": "map", - "description": "Meta information for Snakefile\ne.g. [ id: 'snakefile' ]\n" - } - }, - { - "snakefile": { - "type": "file", - "description": "Snakefile to use with Snakemake. This is required for proper execution of Snakemake.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "outputs": { - "type": "file", - "description": "Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated.\n" - } - }, - { - "snakemake_dir": { - "type": "directory", - "description": "Snakemake log directory (.snakemake). Can be used to capture logs of Snakemake execution.\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputs": { + "type": "file", + "description": "Any input file required by Snakemake", + "pattern": "*" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Meta information for Snakefile\ne.g. [ id: 'snakefile' ]\n" + } + }, + { + "snakefile": { + "type": "file", + "description": "Snakefile to use with Snakemake. This is required for proper execution of Snakemake.\n" + } + } + ] + ], + "output": [ + { + "outputs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "[!.snakemake|versions.yml]**": { + "type": "file", + "description": "Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated.\n" + } + } + ] + }, + { + "snakemake_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + ".snakemake\", type: 'dir', hidden: true": { + "type": "directory", + "description": "Snakemake log directory (.snakemake). Can be used to capture logs of Snakemake execution.\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125774,65 +160893,88 @@ "doi": "10.1101/2021.11.23.469039", "licence": [ "Apache v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq", - "pattern": "*.{fastq.gz,fq.gz,fastq,fq,bam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "file", - "description": "List of SNAP genome index files", - "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Aligned BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Optional aligned BAM file index", - "pattern": "*.{bai}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq", + "pattern": "*.{fastq.gz,fq.gz,fastq,fq,bam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "index": { + "type": "file", + "description": "List of SNAP genome index files", + "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Aligned BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "Optional aligned BAM file index", + "pattern": "*.{bai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125866,56 +161008,74 @@ "doi": "10.1101/2021.11.23.469039", "licence": [ "Apache v2" - ] - } - } - ], - "input": [ - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" - } - }, - { - "altcontigfile": { - "type": "file", - "description": "Optional file with a list of alt contig names, one per line." - } - }, - { - "nonaltcontigfile": { - "type": "file", - "description": "Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size." - } - }, - { - "altliftoverfile": { - "type": "file", - "description": "Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit." - } - } - ], - "output": [ - { - "index": { - "type": "file", - "description": "SNAP genome index files", - "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } + }, + { + "altcontigfile": { + "type": "file", + "description": "Optional file with a list of alt contig names, one per line." + } + }, + { + "nonaltcontigfile": { + "type": "file", + "description": "Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size." + } + }, + { + "altliftoverfile": { + "type": "file", + "description": "Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit." + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "file", + "description": "SNAP genome index files", + "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + } + }, + { + "snap/*": { + "type": "file", + "description": "SNAP genome index files", + "pattern": "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -125947,96 +161107,148 @@ "tool_dev_url": "https://github.com/fritzsedlazeck/Sniffles", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:sniffles" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "input": { + "type": "file", + "description": "A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input", + "pattern": "*.{bam,cram,snf,tsv}" + } + }, + { + "index": { + "type": "file", + "description": "Index of BAM/CAM file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference database in FASTA format\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing tandem repeat information\ne.g. [ id:'hg38' ]\n" + } + }, + { + "tandem_file": { + "type": "file", + "description": "Tandem repeat file", + "pattern": "*.bed" + } + } + ], + [ + { + "vcf_output": { + "type": "file", + "description": "VCF output file", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "snf_output": { + "type": "file", + "description": "SNF output file" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Compressed VCF file index", + "pattern": "*.tbi" + } + } + ] + }, + { + "snf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.snf": { + "type": "file", + "description": "SNF file", + "pattern": "*.snf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "input": { - "type": "file", - "description": "A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input", - "pattern": "*.{bam,cram,snf,tsv}" - } - }, - { - "index": { - "type": "file", - "description": "Index of BAM/CAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'fasta' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference database in FASTA format\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing tandem repeat information\ne.g. [ id:'hg38' ]\n" - } - }, - { - "tandem_file": { - "type": "file", - "description": "Tandem repeat file", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Compressed VCF file index", - "pattern": "*.tbi" - } - }, - { - "snf": { - "type": "file", - "description": "SNF file", - "pattern": "*.snf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@christopher-hakkaart", - "@yuukiiwa" + "authors": [ + "@christopher-hakkaart", + "@yuukiiwa" ], "maintainers": [ "@christopher-hakkaart", @@ -126067,87 +161279,140 @@ "tool_dev_url": "https://github.com/tseemann/snippy", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Annotated variants in VCF format", - "pattern": "*.vcf.gz" - } - }, - { - "aligned_fa": { - "type": "file", - "description": "A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)", - "pattern": "*.aligned.fa.gz" - } - }, - { - "reference": { - "type": "file", - "description": "Reference genome in GenBank (preferred) or FASTA format", - "pattern": "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "aln": { - "type": "file", - "description": "A core SNP alignment in FASTA format", - "pattern": "*.aln" - } - }, - { - "full_aln": { - "type": "file", - "description": "A whole genome SNP alignment (includes invariant sites)", - "pattern": "*.full.aln" - } - }, - { - "tab": { - "type": "file", - "description": "Tab-separated columnar list of core SNP sites with alleles but NO annotations", - "pattern": "*.tab" - } - }, - { - "vcf": { - "type": "file", - "description": "Multi-sample VCF file with genotype GT tags for all discovered alleles", - "pattern": "*.vcf" - } - }, - { - "txt": { - "type": "file", - "description": "Tab-separated columnar list of alignment/core-size statistics", - "pattern": "*.txt" - } + ], + "identifier": "biotools:snippy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Annotated variants in VCF format", + "pattern": "*.vcf.gz" + } + }, + { + "aligned_fa": { + "type": "file", + "description": "A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)", + "pattern": "*.aligned.fa.gz" + } + } + ], + [ + { + "reference": { + "type": "file", + "description": "Reference genome in GenBank (preferred) or FASTA format", + "pattern": "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}" + } + } + ] + ], + "output": [ + { + "aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.aln": { + "type": "file", + "description": "A core SNP alignment in FASTA format", + "pattern": "*.aln" + } + } + ] + }, + { + "full_aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.full.aln": { + "type": "file", + "description": "A whole genome SNP alignment (includes invariant sites)", + "pattern": "*.full.aln" + } + } + ] + }, + { + "tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.tab": { + "type": "file", + "description": "Tab-separated columnar list of core SNP sites with alleles but NO annotations", + "pattern": "*.tab" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.vcf": { + "type": "file", + "description": "Multi-sample VCF file with genotype GT tags for all discovered alleles", + "pattern": "*.vcf" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Tab-separated columnar list of alignment/core-size statistics", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126179,164 +161444,337 @@ "tool_dev_url": "https://github.com/tseemann/snippy", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" - } - }, - { - "index": { - "type": "file", - "description": "Reference genome in GenBank (preferred) or FASTA format", - "pattern": "*.{gbk,gbk.gz,fa,fa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tab": { - "type": "file", - "description": "A simple tab-separated summary of all the variants", - "pattern": "*.tab" - } - }, - { - "csv": { - "type": "file", - "description": "A comma-separated version of the .tab file", - "pattern": "*.csv" - } - }, - { - "html": { - "type": "file", - "description": "A HTML version of the .tab file", - "pattern": "*.html" - } - }, - { - "vcf": { - "type": "file", - "description": "The final annotated variants in VCF format", - "pattern": "*.vcf" - } - }, - { - "bed": { - "type": "file", - "description": "The variants in BED format", - "pattern": "*.bed" - } - }, - { - "gff": { - "type": "file", - "description": "The variants in GFF3 format", - "pattern": "*.gff" - } - }, - { - "bam": { - "type": "file", - "description": "The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "Index for the .bam file", - "pattern": "*.bam.bai" - } - }, - { - "log": { - "type": "file", - "description": "A log file with the commands run and their outputs", - "pattern": "*.log" - } - }, - { - "aligned_fa": { - "type": "file", - "description": "A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)", - "pattern": "*.aligned.fa" - } - }, - { - "consensus_fa": { - "type": "file", - "description": "A version of the reference genome with all variants instantiated", - "pattern": "*.consensus.fa" - } - }, - { - "consensus_subs_fa": { - "type": "file", - "description": "A version of the reference genome with only substitution variants instantiated", - "pattern": "*.consensus.subs.fa" - } - }, - { - "raw_vcf": { - "type": "file", - "description": "The unfiltered variant calls from Freebayes", - "pattern": "*.raw.vcf" - } - }, - { - "filt_vcf": { - "type": "file", - "description": "The filtered variant calls from Freebayes", - "pattern": "*.filt.vcf" - } - }, - { - "vcf_gz": { - "type": "file", - "description": "Compressed .vcf file via BGZIP", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_csi": { - "type": "file", - "description": "Index for the .vcf.gz via bcftools index", - "pattern": "*.vcf.gz.csi" - } - }, - { - "txt": { - "type": "file", - "description": "Tab-separated columnar list of statistics", - "pattern": "*.txt" - } + ], + "identifier": "biotools:snippy" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" + } + } + ], + [ + { + "reference": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fna,fa}" + } + } + ] + ], + "output": [ + { + "tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.tab": { + "type": "file", + "description": "A simple tab-separated summary of all the variants", + "pattern": "*.tab" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.csv": { + "type": "file", + "description": "A comma-separated version of the .tab file", + "pattern": "*.csv" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.html": { + "type": "file", + "description": "A HTML version of the .tab file", + "pattern": "*.html" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.vcf": { + "type": "file", + "description": "The final annotated variants in VCF format", + "pattern": "*.vcf" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.bed": { + "type": "file", + "description": "The variants in BED format", + "pattern": "*.bed" + } + } + ] + }, + { + "gff": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.gff": { + "type": "file", + "description": "The variants in GFF3 format", + "pattern": "*.gff" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.bam": { + "type": "file", + "description": "The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.", + "pattern": "*.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.bam.bai": { + "type": "file", + "description": "Index for the .bam file", + "pattern": "*.bam.bai" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.log": { + "type": "file", + "description": "A log file with the commands run and their outputs", + "pattern": "*.log" + } + } + ] + }, + { + "aligned_fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.aligned.fa": { + "type": "file", + "description": "A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)", + "pattern": "*.aligned.fa" + } + } + ] + }, + { + "consensus_fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.consensus.fa": { + "type": "file", + "description": "A version of the reference genome with all variants instantiated", + "pattern": "*.consensus.fa" + } + } + ] + }, + { + "consensus_subs_fa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.consensus.subs.fa": { + "type": "file", + "description": "A version of the reference genome with only substitution variants instantiated", + "pattern": "*.consensus.subs.fa" + } + } + ] + }, + { + "raw_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.raw.vcf": { + "type": "file", + "description": "The unfiltered variant calls from Freebayes", + "pattern": "*.raw.vcf" + } + } + ] + }, + { + "filt_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.filt.vcf": { + "type": "file", + "description": "The filtered variant calls from Freebayes", + "pattern": "*.filt.vcf" + } + } + ] + }, + { + "vcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.vcf.gz": { + "type": "file", + "description": "Compressed .vcf file via BGZIP", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "vcf_csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.vcf.gz.csi": { + "type": "file", + "description": "Index for the .vcf.gz via bcftools index", + "pattern": "*.vcf.gz.csi" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/${prefix}.txt": { + "type": "file", + "description": "Tab-separated columnar list of statistics", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126369,45 +161807,56 @@ "tool_dev_url": "https://github.com/tseemann/snp-dists", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment": { - "type": "file", - "description": "The input FASTA sequence alignment file", - "pattern": "*.{fasta,fasta.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "alignment": { + "type": "file", + "description": "The input FASTA sequence alignment file", + "pattern": "*.{fasta,fasta.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tsv": { - "type": "file", - "description": "The output TSV file containing SNP distance matrix", - "pattern": "*.tsv" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "The output TSV file containing SNP distance matrix", + "pattern": "*.tsv" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126440,43 +161889,61 @@ "documentation": "https://pcingola.github.io/SnpEff/se_introduction/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf to annotate\n" - } - }, - { - "db": { - "type": "string", - "description": "which db to annotate with\n" - } - } - ], - "output": [ - { - "cache": { - "type": "file", - "description": "snpEff cache\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:snpeff" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genome": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fasta,fna,fa}" + } + }, + { + "cache_version": { + "type": "string", + "description": "Version of the snpEff cache to download" + } + } + ] + ], + "output": [ + { + "cache": [ + { + "meta": { + "type": "file", + "description": "snpEff cache\n" + } + }, + { + "snpeff_cache": { + "type": "file", + "description": "snpEff cache\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126515,71 +161982,132 @@ "documentation": "https://pcingola.github.io/SnpEff/se_introduction/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf to annotate\n" - } - }, - { - "db": { - "type": "string", - "description": "which db to annotate with\n" - } - }, - { - "cache": { - "type": "file", - "description": "path to snpEff cache (optional)\n" - } - } - ], - "output": [ - { - "vcf": { - "type": "file", - "description": "annotated vcf\n", - "pattern": "*.ann.vcf" - } - }, - { - "report": { - "type": "file", - "description": "snpEff report csv file", - "pattern": "*.csv" - } - }, - { - "summary_html": { - "type": "file", - "description": "snpEff summary statistics in html file", - "pattern": "*.html" - } - }, - { - "genes_txt": { - "type": "file", - "description": "txt (tab separated) file having counts of the number of variants affecting each transcript and gene", - "pattern": "*.genes.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:snpeff" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf to annotate\n" + } + } + ], + [ + { + "db": { + "type": "string", + "description": "which db to annotate with\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "cache": { + "type": "file", + "description": "path to snpEff cache (optional)\n" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "file", + "description": "annotated vcf\n", + "pattern": "*.ann.vcf" + } + }, + { + "*.ann.vcf": { + "type": "file", + "description": "annotated vcf\n", + "pattern": "*.ann.vcf" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "file", + "description": "snpEff report csv file", + "pattern": "*.csv" + } + }, + { + "*.csv": { + "type": "file", + "description": "snpEff report csv file", + "pattern": "*.csv" + } + } + ] + }, + { + "summary_html": [ + { + "meta": { + "type": "file", + "description": "snpEff summary statistics in html file", + "pattern": "*.html" + } + }, + { + "*.html": { + "type": "file", + "description": "snpEff summary statistics in html file", + "pattern": "*.html" + } + } + ] + }, + { + "genes_txt": [ + { + "meta": { + "type": "file", + "description": "txt (tab separated) file having counts of the number of variants affecting each transcript and gene", + "pattern": "*.genes.txt" + } + }, + { + "*.genes.txt": { + "type": "file", + "description": "txt (tab separated) file having counts of the number of variants affecting each transcript and gene", + "pattern": "*.genes.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126619,72 +162147,85 @@ "doi": "10.3389/fgene.2012.00035", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information regarding vcf file provided\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf, vcf.gz}" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Tabix file for compressed vcf provided", - "pattern": "*.{tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy map containing sample information regarding database provided\n" - } - }, - { - "database": { - "type": "file", - "description": "Database for use to annotate", - "pattern": "*.{vcf/vcf.gz}" - } - }, - { - "dbs_tbi": { - "type": "file", - "description": "Tabix file for compressed database provided", - "pattern": "*.{tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant Calling File annotated", - "pattern": "*.{vcf}" - } + ], + "identifier": "biotools:snpsift" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information regarding vcf file provided\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf, vcf.gz}" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Tabix file for compressed vcf provided", + "pattern": "*.{tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing sample information regarding database provided\n" + } + }, + { + "database": { + "type": "file", + "description": "Database for use to annotate", + "pattern": "*.{vcf/vcf.gz}" + } + }, + { + "dbs_tbi": { + "type": "file", + "description": "Tabix file for compressed database provided", + "pattern": "*.{tbi}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Variant Calling File annotated", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126719,72 +162260,85 @@ "doi": "10.3389/fgene.2012.00035", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information regarding vcf file provided\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf, vcf.gz}" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "Tabix file for compressed vcf provided", - "pattern": "*.{tbi}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy map containing sample information regarding database provided\n" - } - }, - { - "database": { - "type": "file", - "description": "Database for use to annotate", - "pattern": "*.{vcf/vcf.gz}" - } - }, - { - "dbs_tbi": { - "type": "file", - "description": "Tabix file for compressed database provided", - "pattern": "*.{tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variant Calling File annotated", - "pattern": "*.{vcf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:snpsift" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information regarding vcf file provided\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf, vcf.gz}" + } + }, + { + "vcf_tbi": { + "type": "file", + "description": "Tabix file for compressed vcf provided", + "pattern": "*.{tbi}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy map containing sample information regarding database provided\n" + } + }, + { + "database": { + "type": "file", + "description": "Database for use to annotate", + "pattern": "*.{vcf/vcf.gz}" + } + }, + { + "dbs_tbi": { + "type": "file", + "description": "Tabix file for compressed database provided", + "pattern": "*.{tbi}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Variant Calling File annotated", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126817,45 +162371,56 @@ "doi": "10.3389/fgene.2012.00035", "licence": [ "MIT" - ] + ], + "identifier": "biotools:snpsift" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file(s)", - "pattern": "*.{vcf,vcf.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file(s)", + "pattern": "*.{vcf,vcf.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "out_vcfs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Split/Joined VCF file(s)", + "pattern": "*.vcf" + } + } + ] }, { - "out_vcfs": { - "type": "file", - "description": "Split/Joined VCF file(s)", - "pattern": "*.vcf" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -126888,47 +162453,66 @@ "documentation": "https://github.com/sanger-pathogens/snp-sites", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "alignment": { - "type": "file", - "description": "fasta alignment file", - "pattern": "*.{fasta,fas,fa,aln}" + [ + { + "alignment": { + "type": "file", + "description": "fasta alignment file", + "pattern": "*.{fasta,fas,fa,aln}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fasta": [ + { + "*.fas": { + "type": "file", + "description": "Variant fasta file", + "pattern": "*.{fas}" + } + } + ] }, { - "fasta": { - "type": "file", - "description": "Variant fasta file", - "pattern": "*.{fas}" - } + "constant_sites": [ + { + "*.sites.txt": { + "type": "file", + "description": "Text file containing counts of constant sites", + "pattern": "*.{sites.txt}" + } + } + ] }, { - "constant_sites": { - "type": "file", - "description": "Text file containing counts of constant sites", - "pattern": "*.{sites.txt}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] }, { - "constant_sites_string": { - "type": "integer", - "description": "Value with the number of constant sites", - "pattern": "*.{sites.txt}" - } + "constant_sites_string": [ + { + "CONSTANT_SITES": { + "type": "integer", + "description": "Value with the number of constant sites", + "pattern": "*.{sites.txt}" + } + } + ] } ], "authors": [ @@ -126969,76 +162553,99 @@ "doi": "10.1186/s13073-020-00761-2", "licence": [ "MIT" - ] - } + ], + "identifier": "biotools:somalier" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "query_somalier_files": { + "type": "file", + "description": "Set of somalier files for query samples. Obtained via somalier extract.", + "pattern": "*.{somalier}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing labelled samples information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "labels_tsv": { + "type": "file", + "description": "TSV for labelled samples. e.g. Somalier labels for 1kg https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv", + "pattern": "*.{tsv}" + } + }, + { + "labelled_somalier_files": { + "type": "file", + "description": "Set of somalier files for labelled samples. e.g. Somalier files for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1", + "pattern": "*.{somalier}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-ancestry.tsv": { + "type": "file", + "description": "TSV with ancestry information for query and labelled samples.", + "pattern": "*.{-ancestry.tsv}" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*-ancestry.html": { + "type": "file", + "description": "html file with ancestry information for query and labelled samples.", + "pattern": "*.{-ancestry.html}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "query_somalier_files": { - "type": "file", - "description": "Set of somalier files for query samples. Obtained via somalier extract.", - "pattern": "*.{somalier}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing labelled samples information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "labelled_somalier_files": { - "type": "file", - "description": "Set of somalier files for labelled samples. e.g. Somalier files for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1", - "pattern": "*.{somalier}" - } - }, - { - "labels_tsv": { - "type": "file", - "description": "TSV for labelled samples. e.g. Somalier labels for 1kg https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv", - "pattern": "*.{tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV with ancestry information for query and labelled samples.", - "pattern": "*.{-ancestry.tsv}" - } - }, - { - "html": { - "type": "file", - "description": "html file with ancestry information for query and labelled samples.", - "pattern": "*.{-ancestry.html}" - } - } - ], - "authors": [ - "@atrigila" + "authors": [ + "@atrigila" ], "maintainers": [ "@atrigila" @@ -127075,89 +162682,106 @@ "doi": "10.1186/s13073-020-00761-2", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file" - } - }, - { - "input_index": { - "type": "file", - "description": "index file of the input data, e.g., bam.bai, cram.crai" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'hg38' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fna,fas,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'hg38' ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.fai" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sites information\ne.g. [ id:'hg38' ]\n" - } - }, - { - "sites": { - "type": "file", - "description": "sites file in VCF format which can be taken from https://github.com/brentp/somalier", - "pattern": "*.vcf.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "extract": { - "type": "file", - "description": "binary output file based on extracted sites", - "pattern": "*.{somalier}" - } + ], + "identifier": "biotools:somalier" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file" + } + }, + { + "input_index": { + "type": "file", + "description": "index file of the input data, e.g., bam.bai, cram.crai" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'hg38' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fna,fas,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'hg38' ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.fai" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sites information\ne.g. [ id:'hg38' ]\n" + } + }, + { + "sites": { + "type": "file", + "description": "sites file in VCF format which can be taken from https://github.com/brentp/somalier", + "pattern": "*.vcf.gz" + } + } + ] + ], + "output": [ + { + "extract": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somalier": { + "type": "file", + "description": "binary output file based on extracted sites", + "pattern": "*.{somalier}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127200,67 +162824,109 @@ "doi": "10.1186/s13073-020-00761-2", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "extract": { - "type": "file", - "description": "extract file(s) from Somalier extract", - "pattern": "*.somalier" - } - }, - { - "ped": { - "type": "file", - "description": "optional path to a ped or fam file indicating the expected relationships among samples", - "pattern": "*.{ped,fam}" - } - }, - { - "sample_groups": { - "type": "file", - "description": "optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line", - "pattern": "*.{txt,csv}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "html": { - "type": "file", - "description": "html file", - "pattern": "*.html" - } - }, - { - "pairs_tsv": { - "type": "file", - "description": "tsv file with output stats for pairs of samples", - "pattern": "*.pairs.tsv" - } - }, - { - "samples_tsv": { - "type": "file", - "description": "tsv file with sample-level information", - "pattern": "*.samples.tsv" - } + ], + "identifier": "biotools:somalier" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "extract": { + "type": "file", + "description": "extract file(s) from Somalier extract", + "pattern": "*.somalier" + } + }, + { + "ped": { + "type": "file", + "description": "optional path to a ped or fam file indicating the expected relationships among samples", + "pattern": "*.{ped,fam}" + } + } + ], + [ + { + "sample_groups": { + "type": "file", + "description": "optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line", + "pattern": "*.{txt,csv}" + } + } + ] + ], + "output": [ + { + "html": [ + { + "meta": { + "type": "file", + "description": "html file", + "pattern": "*.html" + } + }, + { + "*.html": { + "type": "file", + "description": "html file", + "pattern": "*.html" + } + } + ] + }, + { + "pairs_tsv": [ + { + "meta": { + "type": "file", + "description": "tsv file with output stats for pairs of samples", + "pattern": "*.pairs.tsv" + } + }, + { + "*.pairs.tsv": { + "type": "file", + "description": "tsv file with output stats for pairs of samples", + "pattern": "*.pairs.tsv" + } + } + ] + }, + { + "samples_tsv": [ + { + "meta": { + "type": "file", + "description": "tsv file with sample-level information", + "pattern": "*.samples.tsv" + } + }, + { + "*.samples.tsv": { + "type": "file", + "description": "tsv file with sample-level information", + "pattern": "*.samples.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127295,87 +162961,116 @@ "documentation": "https://github.com/biocore/sortmerna/wiki/", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "fastas": { - "type": "file", - "description": "Path to reference file(s)\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing index information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Path to index directory of a previous sortmerna run\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ], or reference information from an\nindexing-only run\n" - } - }, - { - "reads": { - "type": "file", - "description": "The filtered fastq reads", - "pattern": "*fastq.gz" - } - }, - { - "log": { - "type": "file", - "description": "SortMeRNA log file", - "pattern": "*sortmerna.log" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Path to index directory generated by sortmern\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:sortmerna" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "fastas": { + "type": "file", + "description": "Path to reference file(s)\n" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "Path to index directory of a previous sortmerna run\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ], or reference information from an\nindexing-only run\n" + } + }, + { + "*non_rRNA.fastq.gz": { + "type": "file", + "description": "The filtered fastq reads", + "pattern": "*fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ], or reference information from an\nindexing-only run\n" + } + }, + { + "*.log": { + "type": "file", + "description": "SortMeRNA log file", + "pattern": "*sortmerna.log" + } + } + ] + }, + { + "index": [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "idx": { + "type": "directory", + "description": "Path to index directory generated by sortmern\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127428,77 +163123,114 @@ "doi": "10.21105/joss.00027", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "signatures": { - "type": "file", - "description": "Files containing signatures (hash sketches) of samples", - "pattern": "*.{sig}" - } - }, - { - "file_list": { - "type": "file", - "description": "An optional file specifying a list of file paths that should be appended to the input signatures.\n" - } - }, - { - "save_numpy_matrix": { - "type": "boolean", - "description": "If true, output will contain a (dis)similarity matrix numpy binary format.\nAt least one of save_numpy_matrix or save_csv is required.\n" - } - }, - { - "save_csv": { - "type": "boolean", - "description": "If true, output will contain a (dis)similarity matrix in CSV format\nAt least one of save_numpy_matrix or save_csv is required.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "matrix": { - "type": "file", - "description": "An optional (dis)similarity matrix numpy binary format", - "pattern": "*.comp" - } - }, - { - "csv": { - "type": "file", - "description": "An optional (dis)similarity matrix in CSV format", - "pattern": "*.comp.csv" - } - }, - { - "labels": { - "type": "file", - "description": "A text file that specifies the labels in the output numpy_matrix", - "pattern": "*.comp.labels.txt" - } + ], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "signatures": { + "type": "file", + "description": "Files containing signatures (hash sketches) of samples", + "pattern": "*.{sig}" + } + } + ], + [ + { + "file_list": { + "type": "file", + "description": "An optional file specifying a list of file paths that should be appended to the input signatures.\n" + } + } + ], + [ + { + "save_numpy_matrix": { + "type": "boolean", + "description": "If true, output will contain a (dis)similarity matrix numpy binary format.\nAt least one of save_numpy_matrix or save_csv is required.\n" + } + } + ], + [ + { + "save_csv": { + "type": "boolean", + "description": "If true, output will contain a (dis)similarity matrix in CSV format\nAt least one of save_numpy_matrix or save_csv is required.\n" + } + } + ] + ], + "output": [ + { + "matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*comp.npy": { + "type": "file", + "description": "An optional (dis)similarity matrix numpy binary format", + "pattern": "*.comp" + } + } + ] + }, + { + "labels": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*comp.npy.labels.txt": { + "type": "file", + "description": "A text file that specifies the labels in the output numpy_matrix", + "pattern": "*.comp.labels.txt" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*comp.csv": { + "type": "file", + "description": "An optional (dis)similarity matrix in CSV format", + "pattern": "*.comp.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127543,103 +163275,164 @@ "doi": "10.21105/joss.00027", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "signature": { - "type": "file", - "description": "File containing signatures (hash sketches) of a sample", - "pattern": "*.{sig}" - } - }, - { - "db": { - "type": "file", - "description": "Sourmash database (a list of signatures, SBTs, or signature zip files)" - } - }, - { - "save_unassigned": { - "type": "boolean", - "description": "If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query\n" - } - }, - { - "save_matches_sig": { - "type": "boolean", - "description": "If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query\n" - } - }, - { - "save_prefetch": { - "type": "boolean", - "description": "If true, output will contain a file with all prefetch-matched signatures from the database\n" - } - }, - { - "save_prefetch_csv": { - "type": "boolean", - "description": "If true, output will contain a csv file with the names of all prefetch-matched signatures\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "result": { - "type": "file", - "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s).\n", - "pattern": "*{csv.gz}" - } - }, - { - "matches": { - "type": "file", - "description": "A signature containing FracMinHash sketches of genomes\nin the sourmash database.\n", - "pattern": "*{sig.zip}" - } - }, - { - "unassigned": { - "type": "file", - "description": "A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes\nin the sourmash database(s).\n", - "pattern": "*{sig.zip}" - } - }, - { - "prefetch": { - "type": "file", - "description": "All prefetch-matched signatures from the database.\n", - "pattern": "*{sig.zip}" - } - }, - { - "prefetchcsv": { - "type": "file", - "description": "The names of all prefetch-matched signatures from the database in CSV format.\n", - "pattern": "*{csv.gz}" - } + ], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "signature": { + "type": "file", + "description": "File containing signatures (hash sketches) of a sample", + "pattern": "*.{sig}" + } + } + ], + [ + { + "database": { + "type": "file", + "description": "database" + } + } + ], + [ + { + "save_unassigned": { + "type": "boolean", + "description": "If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query\n" + } + } + ], + [ + { + "save_matches_sig": { + "type": "boolean", + "description": "If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query\n" + } + } + ], + [ + { + "save_prefetch": { + "type": "boolean", + "description": "If true, output will contain a file with all prefetch-matched signatures from the database\n" + } + } + ], + [ + { + "save_prefetch_csv": { + "type": "boolean", + "description": "If true, output will contain a csv file with the names of all prefetch-matched signatures\n" + } + } + ] + ], + "output": [ + { + "result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv.gz": { + "type": "file", + "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s).\n", + "pattern": "*{csv.gz}" + } + } + ] + }, + { + "unassigned": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_unassigned.sig.zip": { + "type": "file", + "description": "A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes\nin the sourmash database(s).\n", + "pattern": "*{sig.zip}" + } + } + ] + }, + { + "matches": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_matches.sig.zip": { + "type": "file", + "description": "A signature containing FracMinHash sketches of genomes\nin the sourmash database.\n", + "pattern": "*{sig.zip}" + } + } + ] + }, + { + "prefetch": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_prefetch.sig.zip": { + "type": "file", + "description": "All prefetch-matched signatures from the database.\n", + "pattern": "*{sig.zip}" + } + } + ] + }, + { + "prefetchcsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_prefetch.csv.gz": { + "type": "file", + "description": "The names of all prefetch-matched signatures from the database in CSV format.\n", + "pattern": "*{csv.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127683,51 +163476,64 @@ "doi": "10.21105/joss.00027", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "signatures": { - "type": "file", - "description": "Files containing signature (hash sketches) of reference genomes", - "pattern": "*.{sig}" - } - }, - { - "ksize": { - "type": "integer", - "description": "ksize value" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "signature_index": { - "type": "file", - "description": "Database of signatures", - "pattern": "*.{sbt.zip}" - } + ], + "identifier": "biotools:sourmash" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "signatures": { + "type": "file", + "description": "Files containing signature (hash sketches) of reference genomes", + "pattern": "*.{sig}" + } + } + ], + [ + { + "ksize": { + "type": "integer", + "description": "ksize value" + } + } + ] + ], + "output": [ + { + "signature_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sbt.zip": { + "type": "file", + "description": "Database of signatures", + "pattern": "*.{sbt.zip}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127770,45 +163576,56 @@ "doi": "10.21105/joss.00027", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "biotools:sourmash" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sequence": { + "type": "file", + "description": "FASTA or FASTQ file containing (genomic, transcriptomic, or proteomic) sequence data", + "pattern": "*.{fna,fa,fasta,fastq,fq,faa}.gz" + } } - }, - { - "sequence": { - "type": "file", - "description": "FASTA or FASTQ file containing (genomic, transcriptomic, or proteomic) sequence data", - "pattern": "*.{fna,fa,fasta,fastq,fq,faa}.gz" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "signatures": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sig": { + "type": "file", + "description": "FracMinHash signature of the given sequence", + "pattern": "*.{sig}" + } + } + ] }, { - "signatures": { - "type": "file", - "description": "FracMinHash signature of the given sequence", - "pattern": "*.{sig}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127857,50 +163674,63 @@ "doi": "10.21105/joss.00027", "licence": [ "BSD-3-clause" - ] + ], + "identifier": "biotools:sourmash" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gather_results": { + "type": "file", + "description": "Mandatory table with signatures classified as belonging to any of the genomes\nin the sourmash database(s), result of `sourmash gather` command.\n" + } } - }, - { - "gather_results": { - "type": "file", - "description": "Mandatory table with signatures classified as belonging to any of the genomes\nin the sourmash database(s), result of `sourmash gather` command.\n" - } - }, - { - "taxonomy": { - "type": "file", - "description": "One or more databases with lineages (in CSV format, Mandatory)" + ], + [ + { + "taxonomy": { + "type": "file", + "description": "One or more databases with lineages (in CSV format, Mandatory)" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "result": { - "type": "file", - "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s) with an additional 'lineage' column\ncontaining the taxonomic information for each database match.\n", - "pattern": "*{csv.gz}" - } + "result": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.with-lineages.csv.gz": { + "type": "file", + "description": "Table with signatures classified as belonging to any of the genomes\nin the sourmash database(s) with an additional 'lineage' column\ncontaining the taxonomic information for each database match.\n", + "pattern": "*{csv.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -127936,100 +163766,115 @@ "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", "licence": [ "10x Genomics EULA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', slide:'10L13-020', area: 'B1']\n\n`id`, `slide` and `area` are mandatory information!\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", - "pattern": "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" - } - }, - { - "image": { - "type": "file", - "description": "Brightfield tissue H&E image in JPEG or TIFF format.", - "pattern": "*.{tif,tiff,jpg,jpeg}" - } - }, - { - "cytaimage": { - "type": "file", - "description": "CytAssist instrument captured eosin stained Brightfield tissue image with fiducial\nframe in TIFF format. The size of this image is set at 3k in both dimensions and this image should\nnot be modified any way before passing it as input to either Space Ranger or Loupe Browser.\n", - "pattern": "*.{tif,tiff}" - } - }, - { - "darkimage": { - "type": "file", - "description": "Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence\nimage as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.\n", - "pattern": "*.{tif,tiff,jpg,jpeg}" - } - }, - { - "colorizedimage": { - "type": "file", - "description": "Required for color composite fluorescence microscope image input.\nA color composite of one or more fluorescence image channels saved as a single-page,\nsingle-file color TIFF or JPEG.\n", - "pattern": "*.{tif,tiff,jpg,jpeg}" - } - }, - { - "alignment": { - "type": "file", - "description": "OPTIONAL - Path to manual image alignment.", - "pattern": "*.json" - } - }, - { - "slidefile": { - "type": "file", - "description": "OPTIONAL - Path to slide specifications.", - "pattern": "*.json" - } - }, - { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Space Ranger" - } - }, - { - "probeset": { - "type": "file", - "description": "OPTIONAL - Probe set specification.", - "pattern": "*.csv" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "outs": { - "type": "file", - "description": "Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list", - "pattern": "outs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', slide:'10L13-020', area: 'B1']\n\n`id`, `slide` and `area` are mandatory information!\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n", + "pattern": "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" + } + }, + { + "image": { + "type": "file", + "description": "Brightfield tissue H&E image in JPEG or TIFF format.", + "pattern": "*.{tif,tiff,jpg,jpeg}" + } + }, + { + "cytaimage": { + "type": "file", + "description": "CytAssist instrument captured eosin stained Brightfield tissue image with fiducial\nframe in TIFF format. The size of this image is set at 3k in both dimensions and this image should\nnot be modified any way before passing it as input to either Space Ranger or Loupe Browser.\n", + "pattern": "*.{tif,tiff}" + } + }, + { + "darkimage": { + "type": "file", + "description": "Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence\nimage as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.\n", + "pattern": "*.{tif,tiff,jpg,jpeg}" + } + }, + { + "colorizedimage": { + "type": "file", + "description": "Required for color composite fluorescence microscope image input.\nA color composite of one or more fluorescence image channels saved as a single-page,\nsingle-file color TIFF or JPEG.\n", + "pattern": "*.{tif,tiff,jpg,jpeg}" + } + }, + { + "alignment": { + "type": "file", + "description": "OPTIONAL - Path to manual image alignment.", + "pattern": "*.json" + } + }, + { + "slidefile": { + "type": "file", + "description": "OPTIONAL - Path to slide specifications.", + "pattern": "*.json" + } + } + ], + [ + { + "reference": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Space Ranger" + } + } + ], + [ + { + "probeset": { + "type": "file", + "description": "OPTIONAL - Probe set specification.", + "pattern": "*.csv" + } + } + ] + ], + "output": [ + { + "outs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "outs/**": { + "type": "file", + "description": "Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list", + "pattern": "outs/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128068,33 +163913,44 @@ "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", "licence": [ "10x Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "gtf": { - "type": "file", - "description": "The reference GTF transcriptome file", - "pattern": "*.gtf" + [ + { + "gtf": { + "type": "file", + "description": "The reference GTF transcriptome file", + "pattern": "*.gtf" + } } - } + ] ], "output": [ { - "gtf": { - "type": "directory", - "description": "The filtered GTF transcriptome file", - "pattern": "*.filtered.gtf" - } + "gtf": [ + { + "*.gtf": { + "type": "directory", + "description": "The filtered GTF transcriptome file", + "pattern": "*.filtered.gtf" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128127,46 +163983,61 @@ "tool_dev_url": "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger", "licence": [ "10x Genomics EULA" - ] + ], + "identifier": "" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "Reference genome FASTA file", - "pattern": "*.{fasta,fa}" + [ + { + "fasta": { + "type": "file", + "description": "Reference genome FASTA file", + "pattern": "*.{fasta,fa}" + } } - }, - { - "gtf": { - "type": "file", - "description": "Reference transcriptome GTF file", - "pattern": "*.gtf" + ], + [ + { + "gtf": { + "type": "file", + "description": "Reference transcriptome GTF file", + "pattern": "*.gtf" + } } - }, - { - "reference_name": { - "type": "string", - "description": "The name to give the new reference folder", - "pattern": "str" + ], + [ + { + "reference_name": { + "type": "string", + "description": "The name to give the new reference folder", + "pattern": "str" + } } - } + ] ], "output": [ { - "reference": { - "type": "directory", - "description": "Folder containing all the reference indices needed by Space Ranger" - } + "reference": [ + { + "${reference_name}": { + "type": "directory", + "description": "Folder containing all the reference indices needed by Space Ranger" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128201,111 +164072,191 @@ "doi": "10.1089/cmb.2012.0021", "licence": [ "GPL v2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "illumina": { - "type": "file", - "description": "List of input FastQ (Illumina or PacBio CCS reads) files\nof size 1 and 2 for single-end and paired-end data,\nrespectively. This input data type is required.\n" - } - }, - { - "pacbio": { - "type": "file", - "description": "List of input PacBio CLR FastQ files of size 1.\n" - } - }, - { - "nanopore": { - "type": "file", - "description": "List of input FastQ files of size 1, originating from Oxford Nanopore technology.\n" - } - }, - { - "yml": { - "type": "file", - "description": "Path to yml file containing read information.\nThe raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML.\nFile entries in this yml must contain only the file name and no paths.\n", - "pattern": "*.{yml,yaml}" - } - }, - { - "hmm": { - "type": "file", - "description": "File or directory with amino acid HMMs for Spades HMM-guided mode." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "scaffolds": { - "type": "file", - "description": "Fasta file containing scaffolds\n", - "pattern": "*.fa.gz" - } - }, - { - "contigs": { - "type": "file", - "description": "Fasta file containing contigs\n", - "pattern": "*.fa.gz" - } - }, - { - "transcripts": { - "type": "file", - "description": "Fasta file containing transcripts\n", - "pattern": "*.fa.gz" - } - }, - { - "gene_clusters": { - "type": "file", - "description": "Fasta file containing gene_clusters\n", - "pattern": "*.fa.gz" - } - }, - { - "gfa": { - "type": "file", - "description": "gfa file containing assembly\n", - "pattern": "*.gfa.gz" - } - }, - { - "log": { - "type": "file", - "description": "Spades log file\n", - "pattern": "*.spades.log" - } - }, - { - "log": { - "type": "file", - "description": "Spades warning log file\n", - "pattern": "*.warning.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "illumina": { + "type": "file", + "description": "List of input FastQ (Illumina or PacBio CCS reads) files\nof size 1 and 2 for single-end and paired-end data,\nrespectively. This input data type is required.\n" + } + }, + { + "pacbio": { + "type": "file", + "description": "List of input PacBio CLR FastQ files of size 1.\n" + } + }, + { + "nanopore": { + "type": "file", + "description": "List of input FastQ files of size 1, originating from Oxford Nanopore technology.\n" + } + } + ], + [ + { + "yml": { + "type": "file", + "description": "Path to yml file containing read information.\nThe raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML.\nFile entries in this yml must contain only the file name and no paths.\n", + "pattern": "*.{yml,yaml}" + } + } + ], + [ + { + "hmm": { + "type": "file", + "description": "File or directory with amino acid HMMs for Spades HMM-guided mode." + } + } + ] + ], + "output": [ + { + "scaffolds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.scaffolds.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + }, + { + "contigs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.contigs.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + }, + { + "transcripts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.transcripts.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + }, + { + "gene_clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + }, + { + "*.gene_clusters.fa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.fa.gz" + } + } + ] + }, + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.gfa.gz" + } + }, + { + "*.assembly.gfa.gz": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.gfa.gz" + } + } + ] + }, + { + "warnings": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.warnings.log": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.spades.log" + } + }, + { + "*.spades.log": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.spades.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128360,59 +164311,74 @@ "doi": "10.5281/zenodo.4063625", "licence": [ "LGPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - }, - { - "repeats": { - "type": "file", - "description": "spa repeat sequences in FASTA format (Optional)", - "pattern": "*.{fasta}" - } - }, - { - "repeat_order": { - "type": "file", - "description": "spa types and order of repeats (Optional)", - "pattern": "*.{txt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "Tab-delimited results", - "pattern": "*.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } + } + ], + [ + { + "repeats": { + "type": "file", + "description": "spa repeat sequences in FASTA format (Optional)", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "repeat_order": { + "type": "file", + "description": "spa types and order of repeats (Optional)", + "pattern": "*.{txt}" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited results", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128444,45 +164410,56 @@ "tool_dev_url": "https://github.com/fellen31/splitubam", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "(u)BAM file", - "pattern": "*.{bam}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:true ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "(u)BAM file", + "pattern": "*.{bam}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Split (u)BAM file", + "pattern": "*.{bam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Split (u)BAM file", - "pattern": "*.{bam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128516,45 +164493,56 @@ "doi": "10.1101/2024.02.01.578426", "licence": [ "BSD-3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "image_2d": { + "type": "file", + "description": "2D TIF Image file with the spots to be detected", + "pattern": "*.{tif,tiff,png,jpg,jpeg}" + } } - }, - { - "image_2d": { - "type": "file", - "description": "2D TIF Image file with the spots to be detected", - "pattern": "*.{tif,tiff,png,jpg,jpeg}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "spots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "CSV file with the X, Y positions of the detected spots.", + "pattern": "*.{csv}" + } + } + ] }, { - "spots": { - "type": "file", - "description": "CSV file with the X, Y positions of the detected spots.", - "pattern": "*.{csv}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128587,52 +164575,63 @@ "doi": "10.1093/bioinformatics/bty1015", "licence": [ "Free for non-commercial use" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq1": { - "type": "file", - "description": "FASTQ file to compress.", - "pattern": "*.{fq.gz,fastq.gz}" - } - }, - { - "fastq2": { - "type": "file", - "description": "Parired FASTQ file fon non single-end experiments.", - "pattern": "*.{fq.gz,fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "spring": { - "type": "file", - "description": "One sequence file in spring compressed format.", - "pattern": "*.{spring}" - } + ], + "identifier": "biotools:spring" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fastq1": { + "type": "file", + "description": "FASTQ file to compress.", + "pattern": "*.{fq.gz,fastq.gz}" + } + }, + { + "fastq2": { + "type": "file", + "description": "Parired FASTQ file fon non single-end experiments.", + "pattern": "*.{fq.gz,fastq.gz}" + } + } + ] + ], + "output": [ + { + "spring": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.spring": { + "type": "file", + "description": "One sequence file in spring compressed format.", + "pattern": "*.{spring}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128665,52 +164664,65 @@ "doi": "10.1093/bioinformatics/bty1015", "licence": [ "Free for non-commercial use" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "spring": { - "type": "file", - "description": "Spring file to decompress.", - "pattern": "*.{spring}" - } - }, - { - "write_one_fastq_gz": { - "type": "boolean", - "description": "Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions\n", - "pattern": "true or false" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fastq": { - "type": "file", - "description": "Decompressed FASTQ file(s).", - "pattern": "*.{fastq.gz}" - } + ], + "identifier": "biotools:spring" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "spring": { + "type": "file", + "description": "Spring file to decompress.", + "pattern": "*.{spring}" + } + } + ], + [ + { + "write_one_fastq_gz": { + "type": "boolean", + "description": "Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions\n", + "pattern": "true or false" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Decompressed FASTQ file(s).", + "pattern": "*.{fastq.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128748,59 +164760,74 @@ "tool_dev_url": "https://github.com/ncbi/sra-tools", "licence": [ "Public Domain" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sra": { - "type": "directory", - "description": "Directory containing ETL data for the given SRA.", - "pattern": "*/*.sra" - } - }, - { - "ncbi_settings": { - "type": "file", - "description": "An NCBI user settings file.\n", - "pattern": "*.mkfg" - } - }, - { - "certificate": { - "type": "file", - "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", - "pattern": "*.cart" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Extracted FASTQ file or files if the sequencing reads are paired-end.", - "pattern": "*.fastq.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "sra": { + "type": "directory", + "description": "Directory containing ETL data for the given SRA.", + "pattern": "*/*.sra" + } + } + ], + [ + { + "ncbi_settings": { + "type": "file", + "description": "An NCBI user settings file.\n", + "pattern": "*.mkfg" + } + } + ], + [ + { + "certificate": { + "type": "file", + "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", + "pattern": "*.cart" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Extracted FASTQ file or files if the sequencing reads are paired-end.", + "pattern": "*.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128839,58 +164866,74 @@ "tool_dev_url": "https://github.com/ncbi/sra-tools", "licence": [ "Public Domain" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "id": { - "type": "string", - "description": "A string denoting an SRA id.\n" - } - }, - { - "ncbi_settings": { - "type": "file", - "description": "An NCBI user settings file.\n", - "pattern": "*.mkfg" - } - }, - { - "certificate": { - "type": "file", - "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", - "pattern": "*.cart" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sra": { - "type": "directory", - "description": "Directory containing the ETL data for the given SRA id.\n", - "pattern": "*/*.sra" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "id": { + "type": "string", + "description": "A string denoting an SRA id.\n" + } + } + ], + [ + { + "ncbi_settings": { + "type": "file", + "description": "An NCBI user settings file.\n", + "pattern": "*.mkfg" + } + } + ], + [ + { + "certificate": { + "type": "file", + "description": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit\n", + "pattern": "*.cart" + } + } + ] + ], + "output": [ + { + "sra": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n", + "pattern": "*/*.sra" + } + }, + { + "id, type: 'dir": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test', single_end:false ]\n", + "pattern": "*/*.sra" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -128930,80 +164973,131 @@ "doi": "10.1186/s13073-014-0090-6", "licence": [ "BSD" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\nid: should be the identification number or sample name\nsingle_end: should be true for single end data and false for paired in data\ndb: should be either 'gene' to use the --gene_db option or \"mlst\" to use the --mlst_db option\ne.g. [ id:'sample', single_end:false , db:'gene']\n" - } - }, - { - "fasta": { - "type": "file", - "description": "gzipped fasta file. If files are NOT in\nMiSeq format sample_S1_L001_R1_001.fastq.gz uses --forward and --reverse parameters; otherwise\ndefault is _1, i.e. expect forward reads as sample_1.fastq.gz).\n", - "pattern": "*.fastq.gz" - } - }, - { - "db": { - "type": "file", - "description": "Database in FASTA format", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "txt": { - "type": "file", - "description": "A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing", - "pattern": "*_fullgenes_*_results.txt" - } - }, - { - "txt": { - "type": "file", - "description": "A tabulated summary report of samples x genes.", - "pattern": "*_genes_*_results.txt" - } - }, - { - "txt": { - "type": "file", - "description": "A tabulated summary report of mlst subtyping.", - "pattern": "*_mlst_*_results.txt" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.sorted.bam" - } - }, - { - "pileup": { - "type": "file", - "description": "SAMtools pileup file", - "pattern": "*.pileup" - } + ], + "identifier": "biotools:srst2" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\nid: should be the identification number or sample name\nsingle_end: should be true for single end data and false for paired in data\ndb: should be either 'gene' to use the --gene_db option or \"mlst\" to use the --mlst_db option\ne.g. [ id:'sample', single_end:false , db:'gene']\n" + } + }, + { + "fastq_s": { + "type": "file", + "description": "input FastQ files", + "pattern": "*.{fq,fastq,fq.gz,fastq.gz}" + } + }, + { + "db": { + "type": "file", + "description": "Database in FASTA format", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "gene_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*_genes_*_results.txt": { + "type": "file", + "description": "SRST2 gene results", + "pattern": "*_genes_*_results.txt" + } + } + ] + }, + { + "fullgene_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*_fullgenes_*_results.txt": { + "type": "file", + "description": "SRST2 full gene results", + "pattern": "*_fullgenes_*_results.txt" + } + } + ] + }, + { + "mlst_results": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*_mlst_*_results.txt": { + "type": "file", + "description": "SRST2 MLST results", + "pattern": "*_mlst_*_results.txt" + } + } + ] + }, + { + "pileup": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*.pileup": { + "type": "file", + "description": "SAMtools pileup file", + "pattern": "*.pileup" + } + } + ] + }, + { + "sorted_bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'sample', single_end:false ]\n" + } + }, + { + "*.sorted.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.sorted.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -129035,45 +165129,56 @@ "tool_dev_url": "https://github.com/jimmyliu1326/SsuisSero", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Assembly in FASTA format", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Assembly in FASTA format", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited serotype prediction", + "pattern": "*.{tsv}" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited serotype prediction", - "pattern": "*.{tsv}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -129106,144 +165211,176 @@ "tool_dev_url": "https://github.com/jkbonfield/io_lib", "licence": [ "BSD" - ] + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference genome in FASTA format", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "FASTA index file from samtools faidx", + "pattern": "*.{fai}" + } + } + ], + [ + { + "gzi": { + "type": "file", + "description": "Optional gzip index file for BAM inputs", + "pattern": "*.gzi" + } + } + ] + ], + "output": [ + { + "cram": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{cram,bam}": { + "type": "file", + "description": "Compressed BAM/CRAM file", + "pattern": "*.{cram,bam}" + } + } + ] + }, + { + "gzi": [ + { + "*.gzi": { + "type": "file", + "description": "gzip index file for BAM outputs", + "pattern": ".{bam.gzi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@matthdsm" + ], + "maintainers": [ + "@matthdsm" + ] + } + }, + { + "name": "staphopiasccmec", + "path": "modules/nf-core/staphopiasccmec/meta.yml", + "type": "module", + "meta": { + "name": "staphopiasccmec", + "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", + "keywords": [ + "amr", + "fasta", + "sccmec" + ], + "tools": [ + { + "staphopiasccmec": { + "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", + "homepage": "https://staphopia.emory.edu", + "documentation": "https://github.com/staphopia/staphopia-sccmec", + "tool_dev_url": "https://github.com/staphopia/staphopia-sccmec", + "doi": "10.7717/peerj.5261", + "licence": [ + "MIT" + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA assembly file", + "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + } } - }, - { - "reads": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome in FASTA format", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "FASTA index file from samtools faidx", - "pattern": "*.{fai}" - } - }, - { - "gzi": { - "type": "file", - "description": "Optional gzip index file for BAM inputs", - "pattern": "*.gzi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "reads": { - "type": "file", - "description": "Converted reads", - "pattern": "*.{sam, bam, cram}" - } - }, - { - "gzi": { - "type": "file", - "description": "gzip index file for BAM outputs", - "pattern": ".{bam.gzi}" - } - } - ], - "authors": [ - "@matthdsm" - ], - "maintainers": [ - "@matthdsm" - ] - } - }, - { - "name": "staphopiasccmec", - "path": "modules/nf-core/staphopiasccmec/meta.yml", - "type": "module", - "meta": { - "name": "staphopiasccmec", - "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", - "keywords": [ - "amr", - "fasta", - "sccmec" - ], - "tools": [ - { - "staphopiasccmec": { - "description": "Predicts Staphylococcus aureus SCCmec type based on primers.", - "homepage": "https://staphopia.emory.edu", - "documentation": "https://github.com/staphopia/staphopia-sccmec", - "tool_dev_url": "https://github.com/staphopia/staphopia-sccmec", - "doi": "10.7717/peerj.5261", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA assembly file", - "pattern": "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Tab-delimited results", + "pattern": "*.{tsv}" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "Tab-delimited results", - "pattern": "*.{tsv}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -129276,159 +165413,359 @@ "doi": "10.1093/bioinformatics/bts635", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "STAR genome index", - "pattern": "star" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "Annotation GTF file", - "pattern": "*.{gtf}" - } - }, - { - "star_ignore_sjdbgtf": { - "type": "boolean", - "description": "Ignore annotation GTF file" - } - }, - { - "seq_platform": { - "type": "string", - "description": "Sequencing platform" - } - }, - { - "seq_center": { - "type": "string", - "description": "Sequencing center" - } - } - ], - "output": [ - { - "bam": { - "type": "file", - "description": "Output BAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "log_final": { - "type": "file", - "description": "STAR final log file", - "pattern": "*Log.final.out" - } - }, - { - "log_out": { - "type": "file", - "description": "STAR lot out file", - "pattern": "*Log.out" - } - }, - { - "log_progress": { - "type": "file", - "description": "STAR log progress file", - "pattern": "*Log.progress.out" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam_sorted": { - "type": "file", - "description": "Sorted BAM file of read alignments (optional)", - "pattern": "*sortedByCoord.out.bam" - } - }, - { - "bam_transcript": { - "type": "file", - "description": "Output BAM file of transcriptome alignment (optional)", - "pattern": "*toTranscriptome.out.bam" - } - }, - { - "bam_unsorted": { - "type": "file", - "description": "Unsorted BAM file of read alignments (optional)", - "pattern": "*Aligned.unsort.out.bam" - } - }, - { - "fastq": { - "type": "file", - "description": "Unmapped FastQ files (optional)", - "pattern": "*fastq.gz" - } - }, - { - "tab": { - "type": "file", - "description": "STAR output tab file(s) (optional)", - "pattern": "*.tab" - } - }, - { - "junction": { - "type": "file", - "description": "STAR chimeric junction output file (optional)", - "pattern": "*.out.junction" - } - }, - { - "wig": { - "type": "file", - "description": "STAR output wiggle format file(s) (optional)", - "pattern": "*.wig" - } - }, - { - "bedgraph": { - "type": "file", - "description": "STAR output bedGraph format file(s) (optional)", - "pattern": "*.bg" - } + ], + "identifier": "biotools:star" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "directory", + "description": "STAR genome index", + "pattern": "star" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "Annotation GTF file", + "pattern": "*.{gtf}" + } + } + ], + [ + { + "star_ignore_sjdbgtf": { + "type": "boolean", + "description": "Ignore annotation GTF file" + } + } + ], + [ + { + "seq_platform": { + "type": "string", + "description": "Sequencing platform" + } + } + ], + [ + { + "seq_center": { + "type": "string", + "description": "Sequencing center" + } + } + ] + ], + "output": [ + { + "log_final": [ + { + "meta": { + "type": "file", + "description": "STAR final log file", + "pattern": "*Log.final.out" + } + }, + { + "*Log.final.out": { + "type": "file", + "description": "STAR final log file", + "pattern": "*Log.final.out" + } + } + ] + }, + { + "log_out": [ + { + "meta": { + "type": "file", + "description": "STAR lot out file", + "pattern": "*Log.out" + } + }, + { + "*Log.out": { + "type": "file", + "description": "STAR lot out file", + "pattern": "*Log.out" + } + } + ] + }, + { + "log_progress": [ + { + "meta": { + "type": "file", + "description": "STAR log progress file", + "pattern": "*Log.progress.out" + } + }, + { + "*Log.progress.out": { + "type": "file", + "description": "STAR log progress file", + "pattern": "*Log.progress.out" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + }, + { + "*d.out.bam": { + "type": "file", + "description": "Output BAM file containing read alignments", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bam_sorted": [ + { + "meta": { + "type": "file", + "description": "Sorted BAM file of read alignments (optional)", + "pattern": "*sortedByCoord.out.bam" + } + }, + { + "*sortedByCoord.out.bam": { + "type": "file", + "description": "Sorted BAM file of read alignments (optional)", + "pattern": "*sortedByCoord.out.bam" + } + } + ] + }, + { + "bam_transcript": [ + { + "meta": { + "type": "file", + "description": "Output BAM file of transcriptome alignment (optional)", + "pattern": "*toTranscriptome.out.bam" + } + }, + { + "*toTranscriptome.out.bam": { + "type": "file", + "description": "Output BAM file of transcriptome alignment (optional)", + "pattern": "*toTranscriptome.out.bam" + } + } + ] + }, + { + "bam_unsorted": [ + { + "meta": { + "type": "file", + "description": "Unsorted BAM file of read alignments (optional)", + "pattern": "*Aligned.unsort.out.bam" + } + }, + { + "*Aligned.unsort.out.bam": { + "type": "file", + "description": "Unsorted BAM file of read alignments (optional)", + "pattern": "*Aligned.unsort.out.bam" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "file", + "description": "Unmapped FastQ files (optional)", + "pattern": "*fastq.gz" + } + }, + { + "*fastq.gz": { + "type": "file", + "description": "Unmapped FastQ files (optional)", + "pattern": "*fastq.gz" + } + } + ] + }, + { + "tab": [ + { + "meta": { + "type": "file", + "description": "STAR output tab file(s) (optional)", + "pattern": "*.tab" + } + }, + { + "*.tab": { + "type": "file", + "description": "STAR output tab file(s) (optional)", + "pattern": "*.tab" + } + } + ] + }, + { + "spl_junc_tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.SJ.out.tab": { + "type": "file", + "description": "STAR output splice junction tab file", + "pattern": "*.SJ.out.tab" + } + } + ] + }, + { + "read_per_gene_tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ReadsPerGene.out.tab": { + "type": "file", + "description": "STAR output read per gene tab file", + "pattern": "*.ReadsPerGene.out.tab" + } + } + ] + }, + { + "junction": [ + { + "meta": { + "type": "file", + "description": "STAR chimeric junction output file (optional)", + "pattern": "*.out.junction" + } + }, + { + "*.out.junction": { + "type": "file", + "description": "STAR chimeric junction output file (optional)", + "pattern": "*.out.junction" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.out.sam": { + "type": "file", + "description": "STAR output SAM file", + "pattern": "*.out.sam" + } + } + ] + }, + { + "wig": [ + { + "meta": { + "type": "file", + "description": "STAR output wiggle format file(s) (optional)", + "pattern": "*.wig" + } + }, + { + "*.wig": { + "type": "file", + "description": "STAR output wiggle format file(s) (optional)", + "pattern": "*.wig" + } + } + ] + }, + { + "bedgraph": [ + { + "meta": { + "type": "file", + "description": "STAR output bedGraph format file(s) (optional)", + "pattern": "*.bg" + } + }, + { + "*.bg": { + "type": "file", + "description": "STAR output bedGraph format file(s) (optional)", + "pattern": "*.bg" + } + } + ] } ], "authors": [ @@ -129503,56 +165840,69 @@ "doi": "10.1093/bioinformatics/bts635", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Fasta file of the reference genome" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file of the reference genome" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "index": { - "type": "directory", - "description": "Folder containing the star index files", - "pattern": "star" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:star" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Fasta file of the reference genome" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file of the reference genome" + } + } + ] + ], + "output": [ + { + "index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "star": { + "type": "directory", + "description": "Folder containing the star index files", + "pattern": "star" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -129633,84 +165983,152 @@ "doi": "10.1101/2021.05.05.442755", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "solotype": { - "type": "string", - "description": "Type of single-cell library.\nIt can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3,\nCB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing the STAR index information." - } - }, - { - "index": { - "type": "directory", - "description": "STAR genome index", - "pattern": "star" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" - } - }, - { - "log_final": { - "type": "file", - "description": "STAR final log file", - "pattern": "*Log.final.out" - } - }, - { - "log_out": { - "type": "file", - "description": "STAR lot out file", - "pattern": "*Log.out" - } - }, - { - "log_progress": { - "type": "file", - "description": "STAR log progress file", - "pattern": "*Log.progress.out" - } - }, - { - "summary": { - "type": "file", - "description": "STARSolo metrics summary CSV file.", - "pattern": "*/Gene/Summary.csv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:star" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "solotype": { + "type": "string", + "description": "Type of single-cell library.\nIt can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3,\nCB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq.\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "opt_whitelist": { + "type": "file", + "description": "Optional whitelist file" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing the STAR index information." + } + }, + { + "index": { + "type": "directory", + "description": "STAR genome index", + "pattern": "star" + } + } + ] + ], + "output": [ + { + "counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*.Solo.out": { + "type": "file", + "description": "STARSolo counts matrix", + "pattern": "*.Solo.out" + } + } + ] + }, + { + "log_final": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*Log.final.out": { + "type": "file", + "description": "STAR final log file", + "pattern": "*Log.final.out" + } + } + ] + }, + { + "log_out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*Log.out": { + "type": "file", + "description": "STAR lot out file", + "pattern": "*Log.out" + } + } + ] + }, + { + "log_progress": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*Log.progress.out": { + "type": "file", + "description": "STAR log progress file", + "pattern": "*Log.progress.out" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information.\nHere, you should add all the specific barcode/umi\ninformation for each sample.\ne.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`\n" + } + }, + { + "*/Gene/Summary.csv": { + "type": "file", + "description": "STARSolo metrics summary CSV file.", + "pattern": "*/Gene/Summary.csv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -129760,88 +166178,183 @@ "doi": "10.3390/microorganisms10020292", "licence": [ "Apache Software License" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "genome_fasta": { - "type": "file", - "description": "Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids.\n", - "pattern": "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}" - } - } - ], - "output": [ - { - "results_xlsx": { - "type": "file", - "description": "Excel spreadsheet containing summary of StarAMR results.", - "pattern": "*_results/results.xlsx" - } - }, - { - "summary_tsv": { - "type": "file", - "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", - "pattern": "*_results/summary.tsv" - } - }, - { - "detailed_summary_tsv": { - "type": "file", - "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", - "pattern": "*_results/detailed_summary.tsv" - } - }, - { - "resfinder_tsv": { - "type": "file", - "description": "A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line.", - "pattern": "*_results/resfinder.tsv" - } - }, - { - "plasmidfinder_tsv": { - "type": "file", - "description": "A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line.", - "pattern": "*_results/plasmidfinder.tsv" - } - }, - { - "mlst_tsv": { - "type": "file", - "description": "A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.", - "pattern": "*_results/mlst.tsv" - } - }, - { - "settings_txt": { - "type": "file", - "description": "The command-line, database versions, and other settings used to run staramr.", - "pattern": "*_results/settings.txt" - } - }, - { - "pointfinder_tsv": { - "type": "file", - "description": "An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line.", - "pattern": "*_results/pointfinder.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:staramr" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "genome_fasta": { + "type": "file", + "description": "Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids.\n", + "pattern": "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}" + } + } + ] + ], + "output": [ + { + "results_xlsx": [ + { + "meta": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx" + } + }, + { + "*_results/results.xlsx": { + "type": "file", + "description": "Excel spreadsheet containing summary of StarAMR results.", + "pattern": "*_results/results.xlsx" + } + } + ] + }, + { + "summary_tsv": [ + { + "meta": { + "type": "file", + "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", + "pattern": "*_results/summary.tsv" + } + }, + { + "*_results/summary.tsv": { + "type": "file", + "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", + "pattern": "*_results/summary.tsv" + } + } + ] + }, + { + "detailed_summary_tsv": [ + { + "meta": { + "type": "file", + "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", + "pattern": "*_results/detailed_summary.tsv" + } + }, + { + "*_results/detailed_summary.tsv": { + "type": "file", + "description": "A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.\nA series of descriptive statistics is also provided for each genome,\nas well as feedback for whether or not the genome passes several quality metrics and if not,\nfeedback on why the genome fails.\n", + "pattern": "*_results/detailed_summary.tsv" + } + } + ] + }, + { + "resfinder_tsv": [ + { + "meta": { + "type": "file", + "description": "A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line.", + "pattern": "*_results/resfinder.tsv" + } + }, + { + "*_results/resfinder.tsv": { + "type": "file", + "description": "A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line.", + "pattern": "*_results/resfinder.tsv" + } + } + ] + }, + { + "plasmidfinder_tsv": [ + { + "meta": { + "type": "file", + "description": "A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line.", + "pattern": "*_results/plasmidfinder.tsv" + } + }, + { + "*_results/plasmidfinder.tsv": { + "type": "file", + "description": "A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line.", + "pattern": "*_results/plasmidfinder.tsv" + } + } + ] + }, + { + "mlst_tsv": [ + { + "meta": { + "type": "file", + "description": "A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.", + "pattern": "*_results/mlst.tsv" + } + }, + { + "*_results/mlst.tsv": { + "type": "file", + "description": "A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.", + "pattern": "*_results/mlst.tsv" + } + } + ] + }, + { + "settings_txt": [ + { + "meta": { + "type": "file", + "description": "The command-line, database versions, and other settings used to run staramr.", + "pattern": "*_results/settings.txt" + } + }, + { + "*_results/settings.txt": { + "type": "file", + "description": "The command-line, database versions, and other settings used to run staramr.", + "pattern": "*_results/settings.txt" + } + } + ] + }, + { + "pointfinder_tsv": [ + { + "meta": { + "type": "file", + "description": "An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line.", + "pattern": "*_results/pointfinder.tsv" + } + }, + { + "*_results/pointfinder.tsv": { + "type": "file", + "description": "An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line.", + "pattern": "*_results/pointfinder.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -129874,45 +166387,56 @@ "doi": "10.1109/ISBIC56247.2022.9854534", "licence": [ "BSD 3-Clause" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "image": { - "type": "file", - "description": "Single channel nuclear image", - "pattern": "*.{tiff,tif}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "image": { + "type": "file", + "description": "Single channel nuclear image", + "pattern": "*.{tiff,tif}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "mask": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.stardist.tif": { + "type": "file", + "description": "labelled mask output from stardist in tif format.", + "pattern": "*.{tiff,tif}" + } + } + ] }, { - "mask": { - "type": "file", - "description": "labelled mask output from stardist in tif format.", - "pattern": "*.{tiff,tif}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -129946,45 +166470,56 @@ "doi": "10.3389/fcimb.2021.772574", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:stecfinder" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "seqs": { - "type": "file", - "description": "Illumina paired-end reads or an assembly", - "pattern": "*.{fastq.gz,fasta.gz,fna.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "seqs": { + "type": "file", + "description": "Illumina paired-end reads or an assembly", + "pattern": "*.{fastq.gz,fasta.gz,fna.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A tab-delimited report of results", + "pattern": "*.tsv" + } + } + ] }, { - "tsv": { - "type": "file", - "description": "A tab-delimited report of results", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -130021,182 +166556,245 @@ "doi": "10.1038/ng.3594", "licence": [ "GPL v3" - ] - } + ], + "identifier": "biotools:stitch-snijderlab" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information about the set of positions to run the imputation over\ne.g. `[ id:'test' ]`\n" + } + }, + { + "posfile": { + "type": "file", + "description": "Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.\n", + "pattern": "*.tsv" + } + }, + { + "input": { + "type": "directory", + "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", + "pattern": "input" + } + }, + { + "rdata": { + "type": "directory", + "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", + "pattern": "RData" + } + }, + { + "chromosome_name": { + "type": "string", + "description": "Name of the chromosome to impute. Should match a chromosome name in the reference genome." + } + }, + { + "K": { + "type": "integer", + "description": "Number of ancestral haplotypes to use for imputation. Refer to the documentation for the `--K` argument of STITCH for more information." + } + }, + { + "nGen": { + "type": "integer", + "description": "Number of generations since founding of the population to use for imputation. Refer to the documentation for the `--nGen` argument of STITCH for more information." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing information about the set of samples\ne.g. `[ id:'test' ]`\n" + } + }, + { + "collected_crams": { + "type": "file", + "description": "List of sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "collected_crais": { + "type": "file", + "description": "List of BAM/CRAM/SAM index files", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "cramlist": { + "type": "file", + "description": "Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.\n", + "pattern": "*.txt" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information about the reference genome used\ne.g. `[ id:'test' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA reference genome file", + "pattern": "*.{fa,fasta}" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "FASTA index file", + "pattern": "*.{fai}" + } + } + ], + [ + { + "seed": { + "type": "integer", + "description": "Seed for random number generation" + } + } + ] + ], + "output": [ + { + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "input\", type: \"dir": { + "type": "directory", + "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", + "pattern": "input" + } + } + ] + }, + { + "rdata": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "RData\", type: \"dir": { + "type": "directory", + "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", + "pattern": "RData" + } + } + ] + }, + { + "plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "plots\", type: \"dir": { + "type": "directory", + "description": "Folder containing plots produced by STITCH during imputation. Which plots are produced depends on the command-line arguments passed to STITCH.\n", + "pattern": "plots" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output.\n", + "pattern": ".vcf.gz" + } + } + ] + }, + { + "bgen": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "*.bgen": { + "type": "file", + "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified.\n", + "pattern": ".bgen" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information about the set of positions to run the imputation over\ne.g. `[ id:'test' ]`\n" - } - }, - { - "posfile": { - "type": "file", - "description": "Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.\n", - "pattern": "*.tsv" - } - }, - { - "input": { - "type": "directory", - "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", - "pattern": "input" - } - }, - { - "rdata": { - "type": "directory", - "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", - "pattern": "RData" - } - }, - { - "chromosome_name": { - "type": "string", - "description": "Name of the chromosome to impute. Should match a chromosome name in the reference genome." - } - }, - { - "K": { - "type": "integer", - "description": "Number of ancestral haplotypes to use for imputation. Refer to the documentation for the `--K` argument of STITCH for more information." - } - }, - { - "nGen": { - "type": "integer", - "description": "Number of generations since founding of the population to use for imputation. Refer to the documentation for the `--nGen` argument of STITCH for more information." - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about the set of samples\ne.g. `[ id:'test' ]`\n" - } - }, - { - "collected_crams": { - "type": "file", - "description": "List of sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "collected_crais": { - "type": "file", - "description": "List of BAM/CRAM/SAM index files", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "cramlist": { - "type": "file", - "description": "Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.\n", - "pattern": "*.txt" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information about the reference genome used\ne.g. `[ id:'test' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference genome file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "FASTA index file", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "input": { - "type": "directory", - "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", - "pattern": "input" - } - }, - { - "rdata": { - "type": "directory", - "description": "Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag.\n", - "pattern": "RData" - } - }, - { - "plots": { - "type": "directory", - "description": "Folder containing plots produced by STITCH during imputation. Which plots are produced depends on the command-line arguments passed to STITCH.\n", - "pattern": "plots" - } - }, - { - "vcf": { - "type": "file", - "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output.\n", - "pattern": ".vcf.gz" - } - }, - { - "bgen": { - "type": "file", - "description": "Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified.\n", - "pattern": ".bgen" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@saulpierotti" - ], - "maintainers": [ - "@saulpierotti" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "dev" - } - ] - }, - { - "name": "stranger", - "path": "modules/nf-core/stranger/meta.yml", - "type": "module", - "meta": { - "name": "stranger", - "description": "Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.", - "keywords": [ - "STR", - "repeat_expansions", - "annotate", - "vcf" - ], - "tools": [ + "authors": [ + "@saulpierotti" + ], + "maintainers": [ + "@saulpierotti" + ] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "dev" + } + ] + }, + { + "name": "stranger", + "path": "modules/nf-core/stranger/meta.yml", + "type": "module", + "meta": { + "name": "stranger", + "description": "Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.", + "keywords": [ + "STR", + "repeat_expansions", + "annotate", + "vcf" + ], + "tools": [ { "stranger": { "description": "Annotate VCF files with str variants", @@ -130206,58 +166804,71 @@ "doi": "10.5281/zenodo.4548873", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF with repeat expansions", - "pattern": "*.{vcf.gz,vcf}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" - } - }, - { - "variant_catalog": { - "type": "file", - "description": "json file with repeat expansion sites to genotype", - "pattern": "*.{json}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "annotated VCF with keys STR_STATUS, NormalMax and PathologicMin", - "pattern": "*.{vcf.gz}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF with repeat expansions", + "pattern": "*.{vcf.gz,vcf}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test' ]\n" + } + }, + { + "variant_catalog": { + "type": "file", + "description": "json file with repeat expansion sites to genotype", + "pattern": "*.{json}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "annotated VCF with keys STR_STATUS, NormalMax and PathologicMin", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -130298,101 +166909,146 @@ "doi": "10.1038/s41592-018-0051-x", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAI index file", - "pattern": "*.{bai,crai}" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - }, - { - "target_bed_index": { - "type": "file", - "description": "Index for BED file containing target regions for variant calling", - "pattern": "*.{bed.tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "vcf": { - "type": "file", - "description": "gzipped germline variant file", - "pattern": "*.{vcf.gz}" - } - }, - { - "vcf_tbi": { - "type": "file", - "description": "index file for the vcf file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "genome_vcf": { - "type": "file", - "description": "variant records and compressed non-variant blocks", - "pattern": "*_genome.vcf.gz" - } - }, - { - "genome_vcf_tbi": { - "type": "file", - "description": "index file for the genome_vcf file", - "pattern": "*_genome.vcf.gz.tbi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:strelka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAI index file", + "pattern": "*.{bai,crai}" + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + }, + { + "target_bed_index": { + "type": "file", + "description": "Index for BED file containing target regions for variant calling", + "pattern": "*.{bed.tbi}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*variants.vcf.gz": { + "type": "file", + "description": "gzipped germline variant file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*variants.vcf.gz.tbi": { + "type": "file", + "description": "index file for the vcf file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "genome_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*genome.vcf.gz": { + "type": "file", + "description": "variant records and compressed non-variant blocks", + "pattern": "*_genome.vcf.gz" + } + } + ] + }, + { + "genome_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "*genome.vcf.gz.tbi": { + "type": "file", + "description": "index file for the genome_vcf file", + "pattern": "*_genome.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -130433,129 +167089,174 @@ "doi": "10.1038/s41592-018-0051-x", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input_normal": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index_normal": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "input_tumor": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "input_index_tumor": { - "type": "file", - "description": "BAM/CRAM/SAM index file", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "manta_candidate_small_indels": { - "type": "file", - "description": "VCF.gz file", - "pattern": "*.{vcf.gz}" - } - }, - { - "manta_candidate_small_indels_tbi": { - "type": "file", - "description": "VCF.gz index file", - "pattern": "*.tbi" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome reference FASTA file", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "Genome reference FASTA index file", - "pattern": "*.{fa.fai,fasta.fai}" - } - }, - { - "target_bed": { - "type": "file", - "description": "BED file containing target regions for variant calling", - "pattern": "*.{bed}" - } - }, - { - "target_bed_index": { - "type": "file", - "description": "Index for BED file containing target regions for variant calling", - "pattern": "*.{bed.tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf_indels": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "vcf_indels_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "vcf_snvs": { - "type": "file", - "description": "Gzipped VCF file containing variants", - "pattern": "*.{vcf.gz}" - } - }, - { - "vcf_snvs_tbi": { - "type": "file", - "description": "Index for gzipped VCF file containing variants", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:strelka" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input_normal": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index_normal": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "input_tumor": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "input_index_tumor": { + "type": "file", + "description": "BAM/CRAM/SAM index file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "manta_candidate_small_indels": { + "type": "file", + "description": "VCF.gz file", + "pattern": "*.{vcf.gz}" + } + }, + { + "manta_candidate_small_indels_tbi": { + "type": "file", + "description": "VCF.gz index file", + "pattern": "*.tbi" + } + }, + { + "target_bed": { + "type": "file", + "description": "BED file containing target regions for variant calling", + "pattern": "*.{bed}" + } + }, + { + "target_bed_index": { + "type": "file", + "description": "Index for BED file containing target regions for variant calling", + "pattern": "*.{bed.tbi}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Genome reference FASTA file", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "Genome reference FASTA index file", + "pattern": "*.{fa.fai,fasta.fai}" + } + } + ] + ], + "output": [ + { + "vcf_indels": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_indels.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "vcf_indels_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_indels.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "vcf_snvs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_snvs.vcf.gz": { + "type": "file", + "description": "Gzipped VCF file containing variants", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "vcf_snvs_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.somatic_snvs.vcf.gz.tbi": { + "type": "file", + "description": "Index for gzipped VCF file containing variants", + "pattern": "*.{vcf.gz.tbi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -130596,40 +167297,53 @@ "documentation": "https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual", "licence": [ "MIT" - ] + ], + "identifier": "biotools:stringtie" } } ], "input": [ - { - "stringtie_gtf": { - "type": "file", - "description": "Stringtie transcript gtf output(s).\n", - "pattern": "*.gtf" + [ + { + "stringtie_gtf": { + "type": "file", + "description": "Stringtie transcript gtf output(s).\n", + "pattern": "*.gtf" + } } - }, - { - "annotation_gtf": { - "type": "file", - "description": "Annotation gtf file (optional).\n", - "pattern": "*.gtf" + ], + [ + { + "annotation_gtf": { + "type": "file", + "description": "Annotation gtf file (optional).\n", + "pattern": "*.gtf" + } } - } + ] ], "output": [ { - "merged_gtf": { - "type": "map", - "description": "Merged gtf from annotation and stringtie output gtfs.\n", - "pattern": "*.gtf" - } + "gtf": [ + { + "stringtie.merged.gtf": { + "type": "file", + "description": "Merged gtf file", + "pattern": "stringtie.merged.gtf" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -130671,71 +167385,114 @@ "documentation": "https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Stringtie transcript gtf output(s).\n" - } - }, - { - "annotation_gtf": { - "type": "file", - "description": "Annotation gtf file (optional).\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "transcript_gtf": { - "type": "file", - "description": "transcript gtf", - "pattern": "*.{transcripts.gtf}" - } - }, - { - "coverage_gtf": { - "type": "file", - "description": "coverage gtf", - "pattern": "*.{coverage.gtf}" - } - }, - { - "abudance": { - "type": "file", - "description": "abudance", - "pattern": "*.{abudance.txt}" - } - }, - { - "ballgown": { - "type": "file", - "description": "for running ballgown", - "pattern": "*.{ballgown}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:stringtie" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Stringtie transcript gtf output(s).\n" + } + } + ], + [ + { + "annotation_gtf": { + "type": "file", + "description": "Annotation gtf file (optional).\n" + } + } + ] + ], + "output": [ + { + "transcript_gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transcripts.gtf": { + "type": "file", + "description": "transcript gtf", + "pattern": "*.{transcripts.gtf}" + } + } + ] + }, + { + "abundance": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.abundance.txt": { + "type": "file", + "description": "abundance", + "pattern": "*.{abundance.txt}" + } + } + ] + }, + { + "coverage_gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.coverage.gtf": { + "type": "file", + "description": "coverage gtf", + "pattern": "*.{coverage.gtf}" + } + } + ] + }, + { + "ballgown": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ballgown": { + "type": "file", + "description": "for running ballgown", + "pattern": "*.{ballgown}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -130782,59 +167539,80 @@ "doi": "10.1093/bioinformatics/btt656", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file containing read alignments", - "pattern": "*.{bam}" - } - }, - { - "annotation": { - "type": "file", - "description": "Genomic features annotation in GTF or SAF", - "pattern": "*.{gtf,saf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "counts": { - "type": "file", - "description": "Counts of reads mapping to features", - "pattern": "*featureCounts.txt" - } - }, - { - "summary": { - "type": "file", - "description": "Summary log file", - "pattern": "*.featureCounts.txt.summary" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:subread" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "BAM files containing mapped reads", + "pattern": "*.bam" + } + }, + { + "annotation": { + "type": "file", + "description": "Genomic features annotation in GTF or SAF", + "pattern": "*.{gtf,saf}" + } + } + ] + ], + "output": [ + { + "counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*featureCounts.txt": { + "type": "file", + "description": "Counts of reads mapping to features", + "pattern": "*featureCounts.txt" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*featureCounts.txt.summary": { + "type": "file", + "description": "Summary log file", + "pattern": "*.featureCounts.txt.summary" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -130903,78 +167681,103 @@ "doi": "10.18129/B9.bioc.SummarizedExperiment", "licence": [ "Artistic-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "matrix_files": { - "type": "directory", - "description": "One or more paths to CSV or TSV matrix files. All files must have the\nsame rows and columns.\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information related to the species\nreference from which matrix rows are derived e.g. `[ id:'yeast' ]`\n" - } - }, - { - "rowdata": { - "type": "file", - "description": "Metadata on matrix features. One column must contain all matrix row\nIDs.\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole,\nas represented by the matrix columns and the sample sheet e.g.\n`[id:'SRP123456' ]`\n" - } - }, - { - "coldata": { - "type": "file", - "description": "Metadata on matrix columns. One column must contain all matrix column\nIDs.\n", - "pattern": "*.{csv,tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "rds": { - "type": "file", - "description": "Serialised SummarizedExperiment object", - "pattern": "*.SummarizedExperiment.rds" - } - }, - { - "log": { - "type": "file", - "description": "dump of R SessionInfo", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:summarizedexperiment" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "matrix_files": { + "type": "directory", + "description": "One or more paths to CSV or TSV matrix files. All files must have the\nsame rows and columns.\n", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information related to the species\nreference from which matrix rows are derived e.g. `[ id:'yeast' ]`\n" + } + }, + { + "rowdata": { + "type": "file", + "description": "Metadata on matrix features. One column must contain all matrix row\nIDs.\n", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole,\nas represented by the matrix columns and the sample sheet e.g.\n`[id:'SRP123456' ]`\n" + } + }, + { + "coldata": { + "type": "file", + "description": "Metadata on matrix columns. One column must contain all matrix column\nIDs.\n", + "pattern": "*.{csv,tsv}" + } + } + ] + ], + "output": [ + { + "rds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*.rds": { + "type": "file", + "description": "Serialised SummarizedExperiment object", + "pattern": "*.SummarizedExperiment.rds" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*.R_sessionInfo.log": { + "type": "file", + "description": "dump of R SessionInfo", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131018,44 +167821,55 @@ "doi": "10.1038/NCOMMS14061", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedpe": { - "type": "file", - "description": "BEDPE file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedpe": { + "type": "file", + "description": "BEDPE file" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Output VCF file", + "pattern": "*.{vcf}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Output VCF file", - "pattern": "*.{vcf}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131089,75 +167903,93 @@ "doi": "10.1038/NCOMMS14061", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to filter", - "pattern": "*.{vcf}" - } - }, - { - "bed": { - "type": "file", - "description": "BED file with regions to ignore (NA to disable)" - } - }, - { - "minsv": { - "type": "integer", - "description": "Min SV size (-1 to disable)" - } - }, - { - "maxsv": { - "type": "integer", - "description": "Max SV size (-1 to disable)" - } - }, - { - "minallelefreq": { - "type": "float", - "description": "Min allele frequency (0-1)" - } - }, - { - "minnumreads": { - "type": "integer", - "description": "Min number of reads support [RE flag (-1 to disable)]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Filtered VCF file", - "pattern": "*.{vcf}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf_file": { + "type": "file", + "description": "VCF file to filter" + } + }, + { + "bed": { + "type": "file", + "description": "BED file with regions to ignore (NA to disable)" + } + } + ], + [ + { + "minsv": { + "type": "integer", + "description": "Min SV size (-1 to disable)" + } + } + ], + [ + { + "maxsv": { + "type": "integer", + "description": "Max SV size (-1 to disable)" + } + } + ], + [ + { + "minallelefreq": { + "type": "float", + "description": "Min allele frequency (0-1)" + } + } + ], + [ + { + "minnumreads": { + "type": "integer", + "description": "Min number of reads support [RE flag (-1 to disable)]" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Filtered VCF file", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131197,81 +168029,104 @@ "doi": "10.1038/NCOMMS14061", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcfs": { - "type": "list", - "description": "The VCF files to be merged\nGzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158\n", - "pattern": "*.vcf" - } - }, - { - "max_distance_breakpoints": { - "type": "integer", - "description": "Max distance between breakpoints (0-1 percent of length, 1- number of bp)" - } - }, - { - "min_supporting_callers": { - "type": "integer", - "description": "Minimum number of supporting caller" - } - }, - { - "account_for_type": { - "type": "integer", - "description": "Take the type into account (1==yes, else no)" - } - }, - { - "account_for_sv_strands": { - "type": "integer", - "description": "Take the strands of SVs into account (1==yes, else no)" - } - }, - { - "estimate_distanced_by_sv_size": { - "type": "integer", - "description": "Estimate distance based on the size of SV (1==yes, else no)" - } - }, - { - "min_sv_size": { - "type": "integer", - "description": "Minimum size of SVs to be taken into account" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The merged VCF file", - "pattern": "*.vcf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "The VCF files to be merged\nGzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158\n", + "pattern": "*.vcf" + } + } + ], + [ + { + "max_distance_breakpoints": { + "type": "integer", + "description": "Max distance between breakpoints (0-1 percent of length, 1- number of bp)" + } + } + ], + [ + { + "min_supporting_callers": { + "type": "integer", + "description": "Minimum number of supporting caller" + } + } + ], + [ + { + "account_for_type": { + "type": "integer", + "description": "Take the type into account (1==yes, else no)" + } + } + ], + [ + { + "account_for_sv_strands": { + "type": "integer", + "description": "Take the strands of SVs into account (1==yes, else no)" + } + } + ], + [ + { + "estimate_distanced_by_sv_size": { + "type": "integer", + "description": "Estimate distance based on the size of SV (1==yes, else no)" + } + } + ], + [ + { + "min_sv_size": { + "type": "integer", + "description": "Minimum size of SVs to be taken into account" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "The merged VCF file", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131311,111 +168166,170 @@ "doi": "10.1038/NCOMMS14061", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference genome", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the reference genome", - "pattern": "*.fai" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing parameters information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "parameters": { - "type": "file", - "description": "A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied", - "pattern": "*.txt" - } - }, - { - "snp_mutation_frequency": { - "type": "float", - "description": "The SNP mutation frequency in the output VCF (0-1)" - } - }, - { - "sim_reads": { - "type": "integer", - "description": "Whether or not to simulate reads (1==yes, else no)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "parameters": { - "type": "file", - "description": "The created parameters file", - "pattern": "*.txt" - } - }, - { - "vcf": { - "type": "file", - "description": "A VCF containing the simulated variants", - "pattern": "*.vcf" - } - }, - { - "bed": { - "type": "file", - "description": "A BED file of the simulated structural variants", - "pattern": "*.bed" - } - }, - { - "fasta": { - "type": "file", - "description": "A Fasta file file containing the variants from the output VCF", - "pattern": "*.fasta" - } - }, - { - "insertions": { - "type": "file", - "description": "A Fasta file file containing insertion sequences", - "pattern": "*.insertions.fa" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference genome", + "pattern": "*.{fasta,fna,fa}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the reference genome", + "pattern": "*.fai" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing parameters information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "parameters": { + "type": "file", + "description": "A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied", + "pattern": "*.txt" + } + } + ], + [ + { + "snp_mutation_frequency": { + "type": "float", + "description": "The SNP mutation frequency in the output VCF (0-1)" + } + } + ], + [ + { + "sim_reads": { + "type": "integer", + "description": "Whether or not to simulate reads (1==yes, else no)" + } + } + ] + ], + "output": [ + { + "parameters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "The created parameters file", + "pattern": "*.txt" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "A VCF containing the simulated variants", + "pattern": "*.vcf" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "A BED file of the simulated structural variants", + "pattern": "*.bed" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "A Fasta file file containing the variants from the output VCF", + "pattern": "*.fasta" + } + } + ] + }, + { + "insertions": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.insertions.fa": { + "type": "file", + "description": "A Fasta file file containing insertion sequences", + "pattern": "*.insertions.fa" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131449,63 +168363,80 @@ "doi": "10.1038/NCOMMS14061", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file to filter", - "pattern": "*.{vcf}" - } - }, - { - "minsv": { - "type": "integer", - "description": "Min SV size (-1 to disable)" - } - }, - { - "maxsv": { - "type": "integer", - "description": "Max SV size (-1 to disable)" - } - }, - { - "minnumreads": { - "type": "integer", - "description": "Min number of reads support [RE flag (-1 to disable)]" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "stats": { - "type": "file", - "description": "File containing statistics given input VCF file", - "pattern": "*.{stats}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file to filter", + "pattern": "*.{vcf}" + } + } + ], + [ + { + "minsv": { + "type": "integer", + "description": "Min SV size (-1 to disable)" + } + } + ], + [ + { + "maxsv": { + "type": "integer", + "description": "Max SV size (-1 to disable)" + } + } + ], + [ + { + "minnumreads": { + "type": "integer", + "description": "Min number of reads support [RE flag (-1 to disable)]" + } + } + ] + ], + "output": [ + { + "stats": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.stats": { + "type": "file", + "description": "File containing statistics given input VCF file", + "pattern": "*.{stats}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131545,230 +168476,405 @@ "doi": "10.1101/gr.221028.117", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\nid: should be the identification number or sample name. If there is normal file meta should be common\ne.g. [ id:'test' ]\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing FASTA information\nid: should be the identification number for alignment file and should be the same used to create BWA index files\ne.g. [ id:'fasta' ]\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing BWA information\nid: should be the identification number same as fasta file\ne.g. [ id:'bwa' ]\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing dbSNP information\nid: should be the identification number for dbSNP files\ne.g. [ id:'test' ]\n" - } - }, - { - "meta5": { - "type": "map", - "description": "Groovy Map containing regions information\nid: should be the identification number for regions\ne.g. [ id:'test' ]\n" - } - }, - { - "tumorbam": { - "type": "file", - "description": "Tumor or metastatic sample, BAM, SAM or CRAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "tummorbai": { - "type": "file", - "description": "Index", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "normalbam": { - "type": "file", - "description": "Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "normalbai": { - "type": "file", - "description": "Index", - "pattern": "*.{bai,crai,sai}" - } - }, - { - "bwa_index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file", - "pattern": "*.{fasta|fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of FASTA file", - "pattern": "*.{fai}" - } - }, - { - "dbsnp": { - "type": "file", - "description": "VCF file including dbSNP variants", - "pattern": "*.vcf.gz" - } - }, - { - "dbsnp_tbi": { - "type": "file", - "description": "Index of VCF file including dbSNP variants", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "regions": { - "type": "file", - "description": "Targeted intervals. Accepts BED file or Samtools-style string", - "pattern": "*.bed|*.txt|*.tab" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "sv": { - "type": "file", - "description": "Filtered SVs for tumor only cases", - "pattern": "*.vcf.gz" - } - }, - { - "indel": { - "type": "file", - "description": "Filtered Indels for tumor only cases", - "pattern": "*.vcf.gz" - } - }, - { - "som_sv": { - "type": "file", - "description": "Somatic filtered SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "som_indel": { - "type": "file", - "description": "Somatic filtered Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "germ_sv": { - "type": "file", - "description": "Germline filtered SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "germ_indel": { - "type": "file", - "description": "Germline filtered Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "unfiltered_sv": { - "type": "file", - "description": "Unfiltered SVs for tumor only cases", - "pattern": "*.vcf.gz" - } - }, - { - "unfiltered_indel": { - "type": "file", - "description": "Unfiltered Indels for tumor only cases", - "pattern": "*.vcf.gz" - } - }, - { - "unfiltered_som_sv": { - "type": "file", - "description": "Unfiltered somatic SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "unfiltered_som_indel": { - "type": "file", - "description": "Unfiltered somatic Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "unfiltered_germ_sv": { - "type": "file", - "description": "Unfiltered germline SVs for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "unfiltered_germ_indel": { - "type": "file", - "description": "Unfiltered germline Indels for tumor/normal paired samples", - "pattern": "*.vcf.gz" - } - }, - { - "raw_calls": { - "type": "file", - "description": "Raw, unfiltered variants", - "pattern": "*.txt.gz" - } - }, - { - "discordants": { - "type": "file", - "description": "Information on all clusters of discordant reads identified with 2+ reads", - "pattern": "*.txt.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log file", - "pattern": "*.txt.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\nid: should be the identification number or sample name. If there is normal file meta should be common\ne.g. [ id:'test' ]\n" + } + }, + { + "tumorbam": { + "type": "file", + "description": "Tumor or metastatic sample, BAM, SAM or CRAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "tumorbai": { + "type": "file", + "description": "Index of the tumor or metastatic sample", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "normalbam": { + "type": "file", + "description": "Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "normalbai": { + "type": "file", + "description": "Index", + "pattern": "*.{bai,crai,sai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing FASTA information\nid: should be the identification number for alignment file and should be the same used to create BWA index files\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file", + "pattern": "*.{fasta|fa}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing FASTA information\nid: should be the identification number for alignment file and should be the same used to create BWA index files\ne.g. [ id:'fasta' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "Index of FASTA file", + "pattern": "*.{fai}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing BWA information\nid: should be the identification number same as fasta file\ne.g. [ id:'bwa' ]\n" + } + }, + { + "bwa_index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing dbSNP information\nid: should be the identification number for dbSNP files\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp": { + "type": "file", + "description": "VCF file including dbSNP variants", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing dbSNP information\nid: should be the identification number for dbSNP files\ne.g. [ id:'test' ]\n" + } + }, + { + "dbsnp_tbi": { + "type": "file", + "description": "Index of VCF file including dbSNP variants", + "pattern": "*.vcf.gz.tbi" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing regions information\nid: should be the identification number for regions\ne.g. [ id:'test' ]\n" + } + }, + { + "regions": { + "type": "file", + "description": "Targeted intervals. Accepts BED file or Samtools-style string", + "pattern": "*.bed|*.txt|*.tab" + } + } + ] + ], + "output": [ + { + "sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.sv.vcf.gz": { + "type": "file", + "description": "Filtered SVs for tumor only cases", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "indel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.indel.vcf.gz": { + "type": "file", + "description": "Filtered Indels for tumor only cases", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "germ_indel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.germline.indel.vcf.gz": { + "type": "file", + "description": "Germline filtered Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "germ_sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.germline.sv.vcf.gz": { + "type": "file", + "description": "Germline filtered SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "som_indel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.somatic.indel.vcf.gz": { + "type": "file", + "description": "Somatic filtered Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "som_sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.somatic.sv.vcf.gz": { + "type": "file", + "description": "Somatic filtered SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "unfiltered_sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.sv.vcf.gz": { + "type": "file", + "description": "Unfiltered SVs for tumor only cases", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "unfiltered_indel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.indel.vcf.gz": { + "type": "file", + "description": "Unfiltered Indels for tumor only cases", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "unfiltered_germ_indel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.germline.indel.vcf.gz": { + "type": "file", + "description": "Unfiltered germline Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "unfiltered_germ_sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.germline.sv.vcf.gz": { + "type": "file", + "description": "Unfiltered germline SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "unfiltered_som_indel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.somatic.indel.vcf.gz": { + "type": "file", + "description": "Unfiltered somatic Indels for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "unfiltered_som_sv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.svaba.unfiltered.somatic.sv.vcf.gz": { + "type": "file", + "description": "Unfiltered somatic SVs for tumor/normal paired samples", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "raw_calls": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bps.txt.gz": { + "type": "file", + "description": "Raw, unfiltered variants", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "discordants": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.discordants.txt.gz": { + "type": "file", + "description": "Information on all clusters of discordant reads identified with 2+ reads", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.txt.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131798,120 +168904,182 @@ "homepage": "https://svanalyzer.readthedocs.io/en/latest/index.html", "documentation": "https://svanalyzer.readthedocs.io/en/latest/index.html", "tool_dev_url": "https://github.com/nhansen/SVanalyzer", - "license": "['CC0']" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing test sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference genome information for fasta\ne.g. `[ id:'test2' ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference genome information for fai\ne.g. `[ id:'test3' ]`\n" - } - }, - { - "test": { - "type": "file", - "description": "A VCF-formatted file of structural variants to test (required)", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "test_tbi": { - "type": "file", - "description": "A VCF-formatted file index of structural variants to test only for zipped files", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "truth": { - "type": "file", - "description": "A VCF-formatted file of variants to compare against (required)", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "truth_tbi": { - "type": "file", - "description": "A VCF-formatted file of variants to compare against only for zipped files", - "pattern": "*.{vcf.gz.tbi}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file for the supplied VCF file or files (required)", - "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" - } - }, - { - "bed": { - "type": "file", - "description": "BED File of regions from which to include variants. Used to filter both test and truth variants.", - "pattern": "*.{bed}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fns": { - "type": "file", - "description": "VCF file with False Negatives", - "pattern": "*.{vcf.gz}" - } - }, - { - "fps": { - "type": "file", - "description": "VCF file with False Positives", - "pattern": "*.{vcf.gz}" - } - }, - { - "distances": { - "type": "file", - "description": "TSV file with genomic distances and size differences between structural variants compared", - "pattern": "*.{distances}" - } - }, - { - "log": { - "type": "file", - "description": "LOG file of the run", - "pattern": "*.{log}" - } - }, - { - "report": { - "type": "file", - "description": "Text file reporting RECALL, PRECISION and F1.", - "pattern": "*.{report}" - } + "license": "['CC0']", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing test sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "test": { + "type": "file", + "description": "A VCF-formatted file of structural variants to test (required)", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "test_tbi": { + "type": "file", + "description": "A VCF-formatted file index of structural variants to test only for zipped files", + "pattern": "*.{vcf.gz.tbi}" + } + }, + { + "truth": { + "type": "file", + "description": "A VCF-formatted file of variants to compare against (required)", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "truth_tbi": { + "type": "file", + "description": "A VCF-formatted file of variants to compare against only for zipped files", + "pattern": "*.{vcf.gz.tbi}" + } + }, + { + "bed": { + "type": "file", + "description": "BED File of regions from which to include variants. Used to filter both test and truth variants.", + "pattern": "*.{bed}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference genome information for fasta\ne.g. `[ id:'test2' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file for the supplied VCF file or files (required)", + "pattern": "*.{fa,fasta,fa.gz,fasta.gz}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference genome information for fai\ne.g. `[ id:'test3' ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The reference FASTA index file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "fns": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.falsenegatives.vcf.gz": { + "type": "file", + "description": "VCF file with False Negatives", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "fps": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.falsepositives.vcf.gz": { + "type": "file", + "description": "VCF file with False Positives", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "distances": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.distances": { + "type": "file", + "description": "TSV file with genomic distances and size differences between structural variants compared", + "pattern": "*.{distances}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.log": { + "type": "file", + "description": "LOG file of the run", + "pattern": "*.{log}" + } + } + ] + }, + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information inherited from test vcf\ne.g. `[ id:'test']`\n" + } + }, + { + "*.report": { + "type": "file", + "description": "Text file reporting RECALL, PRECISION and F1.", + "pattern": "*.{report}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -131945,44 +169113,63 @@ "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input VCF file(s) or folder", + "pattern": "*" + } } - }, - { - "input": { - "type": "file", - "description": "Input VCF file(s) or folder", - "pattern": "*" + ], + [ + { + "input_type": { + "type": "string", + "description": "input type" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.db": { + "type": "file", + "description": "SVDB database" + } + } + ] }, { - "db": { - "type": "file", - "description": "SVDB database" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132010,51 +169197,64 @@ "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "priority": { - "type": "list", - "description": "prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator']" - } - }, - { - "vcfs": { - "type": "list", - "description": "Two or more VCF files. Order of files should correspond to the order of tags used for priority.", - "pattern": "*.{vcf,vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "merged VCF file", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "vcfs": { + "type": "list", + "description": "Two or more VCF files. Order of files should correspond to the order of tags used for priority.", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "priority": { + "type": "list", + "description": "prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator']" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "merged VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132095,83 +169295,106 @@ "documentation": "https://github.com/J35P312/SVDB/blob/master/README.md", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "in_occs": { - "type": "list", - "description": "A list of allele count tags" - } - }, - { - "in_frqs": { - "type": "list", - "description": "A list of allele frequency tags" - } - }, - { - "vcf": { - "type": "file", - "description": "query vcf file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "vcf_dbs": { - "type": "file", - "description": "path to a database vcf, or a comma separated list of vcfs", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "bedpe_dbs": { - "type": "file", - "description": "path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files", - "pattern": "*.{bedpe}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "out_occs": { - "type": "list", - "description": "A list of allele count tags" - } - }, - { - "out_frqs": { - "type": "list", - "description": "A list of allele frequency tags" - } - }, - { - "vcf": { - "type": "file", - "description": "Annotated output VCF file", - "pattern": "*_query.vcf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "query vcf file", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "in_occs": { + "type": "list", + "description": "A list of allele count tags" + } + } + ], + [ + { + "in_frqs": { + "type": "list", + "description": "A list of allele frequency tags" + } + } + ], + [ + { + "out_occs": { + "type": "list", + "description": "A list of allele count tags" + } + } + ], + [ + { + "out_frqs": { + "type": "list", + "description": "A list of allele frequency tags" + } + } + ], + [ + { + "vcf_dbs": { + "type": "file", + "description": "path to a database vcf, or a comma separated list of vcfs", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "bedpe_dbs": { + "type": "file", + "description": "path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files", + "pattern": "*.{bedpe}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*_query.vcf": { + "type": "file", + "description": "Annotated output VCF file", + "pattern": "*_query.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132209,66 +169432,77 @@ "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "A BED file created with `svtk vcf2bed`", - "pattern": "*.bed" - } - }, - { - "baf": { - "type": "file", - "description": "A BAF file created with `gatk PrintSVEvidence`", - "pattern": "*.baf.txt.gz" - } - }, - { - "baf_index": { - "type": "file", - "description": "The index of the BAF file", - "pattern": "*.baf.txt.gz.tbi" - } - }, - { - "batch": { - "type": "file", - "description": "A text file containing information about the sample(s)", - "pattern": "*.txt" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "metrics": { - "type": "file", - "description": "The results file from the BAF test", - "pattern": "*.metrics" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "A BED file created with `svtk vcf2bed`", + "pattern": "*.bed" + } + }, + { + "baf": { + "type": "file", + "description": "A BAF file created with `gatk PrintSVEvidence`", + "pattern": "*.baf.txt.gz" + } + }, + { + "baf_index": { + "type": "file", + "description": "The index of the BAF file", + "pattern": "*.baf.txt.gz.tbi" + } + }, + { + "batch": { + "type": "file", + "description": "A text file containing information about the sample(s)", + "pattern": "*.txt" + } + } + ] + ], + "output": [ + { + "metrics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.metrics": { + "type": "file", + "description": "The results file from the BAF test", + "pattern": "*.metrics" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132302,45 +169536,56 @@ "doi": "10.1038/s41586-020-2287-8", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file containing structural variants", - "pattern": "*.vcf.gz" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file containing structural variants", + "pattern": "*.vcf.gz" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "A tab-delimited file containing the counts of the SV types", + "pattern": "*.tsv" + } + } + ] }, { - "counts": { - "type": "file", - "description": "A tab-delimited file containing the counts of the SV types", - "pattern": "*.tsv" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132375,66 +169620,89 @@ "doi": "10.1038/s41586-020-2287-8", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "An RdTest-formatted bed", - "pattern": "*.bed" - } - }, - { - "samples": { - "type": "file", - "description": "A text file containing the names of all samples that need to be added to the VCF", - "pattern": "*.txt" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The reference file of a FASTA file containing the contigs", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The converted VCF", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "The index of the converted VCF", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "An RdTest-formatted bed", + "pattern": "*.bed" + } + }, + { + "samples": { + "type": "file", + "description": "A text file containing the names of all samples that need to be added to the VCF", + "pattern": "*.txt" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "The reference file of a FASTA file containing the contigs", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The converted VCF", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "The index of the converted VCF", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132468,58 +169736,65 @@ "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "args": { - "type": "map", - "description": "Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes.\n```\n{\n [\n \"args\": \"\",\n \"caller\": \"delly\" // Should be either delly, lumpy, manta, wham or melt\n ]\n}\n```\n" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "A gzipped VCF file to be standardized", - "pattern": "*.vcf.gz" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "standardized_vcf": { - "type": "file", - "description": "A gzipped version of the standardized VCF file", - "pattern": "*.std.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "A gzipped VCF file to be standardized", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "standardized_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.std.vcf.gz": { + "type": "file", + "description": "A gzipped version of the standardized VCF file", + "pattern": "*.std.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132553,52 +169828,63 @@ "tool_dev_url": "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "A VCF file created with a structural variant caller", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "The index for the VCF file", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bed": { - "type": "file", - "description": "The created BED file", - "pattern": "*.bed" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "A VCF file created with a structural variant caller", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "The index for the VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "The created BED file", + "pattern": "*.bed" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132631,86 +169917,134 @@ "doi": "10.1038/nmeth.3505", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for FASTA file\ne.g. [ id:'fasta']\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "vcf": { - "type": "file", - "description": "Matching VCF of alignments", - "pattern": "*.vcf" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file used to generate alignments", - "pattern": "*.{fa,fasta}" - } - }, - { - "fai": { - "type": "file", - "description": "FAI file used to generate alignments", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "JSON file including Library information", - "pattern": "*.json" - } - }, - { - "gt_vcf": { - "type": "file", - "description": "Genotyped SVs", - "pattern": "*.vcf" - } - }, - { - "relevant_bam": { - "type": "file", - "description": "Relevant alignments", - "pattern": "*.bam" - } + ], + "identifier": "biotools:svtyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bam_index": { + "type": "file", + "description": "Index of the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "vcf": { + "type": "file", + "description": "Matching VCF of alignments", + "pattern": "*.vcf" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for FASTA file\ne.g. [ id:'fasta']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file used to generate alignments", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for FASTA file\ne.g. [ id:'fasta']\n" + } + }, + { + "fai": { + "type": "file", + "description": "FAI file used to generate alignments", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file including Library information", + "pattern": "*.json" + } + } + ] + }, + { + "gt_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Genotyped SVs", + "pattern": "*.vcf" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132744,79 +170078,102 @@ "doi": "10.1038/nmeth.3505", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information for reference FASTA file\ne.g. [ id:'fasta']\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM or CRAM file with alignments", - "pattern": "*.{bam,cram}" - } - }, - { - "bam_index": { - "type": "file", - "description": "BAI file matching the BAM file", - "pattern": "*.{bai}" - } - }, - { - "vcf": { - "type": "file", - "description": "Matching VCF of alignments", - "pattern": "*.vcf" - } - }, - { - "fasta": { - "type": "file", - "description": "indexed reference FASTA file (recommended for reading CRAM files)", - "pattern": "*.{fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "json": { - "type": "file", - "description": "JSON file including library information", - "pattern": "*.json" - } - }, - { - "gt_vcf": { - "type": "file", - "description": "Genotyped SVs", - "pattern": "*.vcf" - } + ], + "identifier": "biotools:svtyper" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM or CRAM file with alignments", + "pattern": "*.{bam,cram}" + } + }, + { + "bam_index": { + "type": "file", + "description": "BAI file matching the BAM file", + "pattern": "*.{bai}" + } + }, + { + "vcf": { + "type": "file", + "description": "Matching VCF of alignments", + "pattern": "*.vcf" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information for reference FASTA file\ne.g. [ id:'fasta']\n" + } + }, + { + "fasta": { + "type": "file", + "description": "indexed reference FASTA file (recommended for reading CRAM files)", + "pattern": "*.{fa,fasta}" + } + } + ] + ], + "output": [ + { + "gt_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Genotyped SVs", + "pattern": "*.vcf" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.json": { + "type": "file", + "description": "JSON file including library information", + "pattern": "*.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -132850,63 +170207,74 @@ "tool_dev_url": "https://github.com/nvnieuwk/svync", "licence": [ "MIT" - ] - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The input VCF file containing structural variants", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "The index of the input VCF file containing structural variants", + "pattern": "*.tbi" + } + }, + { + "config": { + "type": "file", + "description": "The config stating how the standardization should happen", + "pattern": "*.{yml,yaml}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The standardized VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The input VCF file containing structural variants", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "The index of the input VCF file containing structural variants", - "pattern": "*.tbi" - } - }, - { - "config": { - "type": "file", - "description": "The config stating how the standardization should happen", - "pattern": "*.{yml,yaml}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The standardized VCF file", - "pattern": "*.vcf.gz" - } - } - ], - "authors": [ - "@nvnieuwk" + "authors": [ + "@nvnieuwk" ], "maintainers": [ "@nvnieuwk" @@ -132941,51 +170309,72 @@ "doi": "10.1093/bioinformatics/btp352", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "file to compress or to decompress" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "output": { - "type": "file", - "description": "Output compressed/decompressed file", - "pattern": "*." - } - }, - { - "gzi": { - "type": "file", - "description": "Optional gzip index file for compressed inputs", - "pattern": "*.gzi" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:tabix" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "file to compress or to decompress" + } + } + ] + ], + "output": [ + { + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output}": { + "type": "file", + "description": "Output compressed/decompressed file", + "pattern": "*." + } + } + ] + }, + { + "gzi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output}.gzi": { + "type": "file", + "description": "Optional gzip index file for compressed inputs", + "pattern": "*.gzi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133059,59 +170448,86 @@ "doi": "10.1093/bioinformatics/btq671", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tab": { - "type": "file", - "description": "TAB-delimited genome position file", - "pattern": "*.{bed,gff,sam,vcf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gz": { - "type": "file", - "description": "Output compressed file", - "pattern": "*.{gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "tabix index file", - "pattern": "*.{gz.tbi}" - } - }, - { - "csi": { - "type": "file", - "description": "tabix alternate index file", - "pattern": "*.{gz.csi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:tabix" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Sorted tab-delimited genome file" + } + } + ] + ], + "output": [ + { + "gz_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "bgzipped tab-delimited genome file", + "pattern": "*.gz" + } + }, + { + "*.tbi": { + "type": "file", + "description": "tabix index file", + "pattern": "*.tbi" + } + } + ] + }, + { + "gz_csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "bgzipped tab-delimited genome file", + "pattern": "*.gz" + } + }, + { + "*.csi": { + "type": "file", + "description": "csi index file", + "pattern": "*.csi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133175,52 +170591,73 @@ "doi": "10.1093/bioinformatics/btq671", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tab": { - "type": "file", - "description": "TAB-delimited genome position file compressed with bgzip", - "pattern": "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "tbi": { - "type": "file", - "description": "tabix index file", - "pattern": "*.{tbi}" - } - }, - { - "csi": { - "type": "file", - "description": "coordinate sorted index file", - "pattern": "*.{csi}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:tabix" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "tab": { + "type": "file", + "description": "TAB-delimited genome position file compressed with bgzip", + "pattern": "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" + } + } + ] + ], + "output": [ + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tbi": { + "type": "file", + "description": "tabix index file", + "pattern": "*.{tbi}" + } + } + ] + }, + { + "csi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csi": { + "type": "file", + "description": "coordinate sorted index file", + "pattern": "*.{csi}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133303,45 +170740,56 @@ "doi": "10.1261/rna.071332.119", "licence": [ "AGPL v3" - ] + ], + "identifier": "biotools:tailfindr" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "fast5": { - "type": "file", - "description": "fast5 file", - "pattern": "*.fast5" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "fast5": { + "type": "file", + "description": "fast5 file", + "pattern": "*.fast5" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "csv_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.csv.gz": { + "type": "file", + "description": "Compressed csv file", + "pattern": "*.csv.gz" + } + } + ] }, { - "csv_gz": { - "type": "file", - "description": "Compressed csv file", - "pattern": "*.csv.gz" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133375,56 +170823,69 @@ "doi": "10.1016/j.jgg.2021.03.006", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "name": { - "type": "string", - "description": "Taxon name to look up (provide either this or names.txt, not both)" - } - }, - { - "names_txt": { - "type": "file", - "description": "File with taxon names to look up, each on their own line (provide either this or name, not both)" - } - }, - { - "taxdb": { - "type": "file", - "description": "Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsv": { - "type": "file", - "description": "TSV file of Taxon names and their taxon ID", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:taxonkit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "name": { + "type": "string", + "description": "Taxon name to look up (provide either this or names.txt, not both)" + } + }, + { + "names_txt": { + "type": "file", + "description": "File with taxon names to look up, each on their own line (provide either this or name, not both)" + } + } + ], + [ + { + "taxdb": { + "type": "file", + "description": "Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "TSV file of Taxon names and their taxon ID", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133460,73 +170921,92 @@ "tool_dev_url": "https://github.com/taxprofiler/taxpasta", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "profiles": { - "type": "file", - "description": "A list of taxonomic profiler output files (typically in text format, mandatory)", - "pattern": "*.{tsv,csv,arrow,parquet,biom}" - } - }, - { - "profiler": { - "type": "string", - "description": "Name of the profiler used to generate the profile (mandatory)", - "pattern": "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" - } - }, - { - "format": { - "type": "string", - "description": "Type of output file to be generated", - "pattern": "tsv|csv|ods|xlsx|arrow|parquet|biom" - } - }, - { - "taxonomy": { - "type": "directory", - "description": "Directory containing at a minimum nodes.dmp and names.dmp files (optional)", - "pattern": "*/" - } - }, - { - "samplesheet": { - "type": "file", - "description": "A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative from the Nextflow work directory of the executed process. The profiles must be provided even if you give a samplesheet as argument (optional)", - "pattern": "*.{tsv,csv,ods,xlsx,arrow,parquet}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "merged_profiles": { - "type": "file", - "description": "Output file with standardised multiple profiles in one go and have all profiles combined into a single table.", - "pattern": "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}" - } + ], + "identifier": "biotools:taxpasta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profiles": { + "type": "file", + "description": "A list of taxonomic profiler output files (typically in text format, mandatory)", + "pattern": "*.{tsv,csv,arrow,parquet,biom}" + } + } + ], + [ + { + "profiler": { + "type": "string", + "description": "Name of the profiler used to generate the profile (mandatory)", + "pattern": "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Type of output file to be generated", + "pattern": "tsv|csv|ods|xlsx|arrow|parquet|biom" + } + } + ], + [ + { + "taxonomy": { + "type": "directory", + "description": "Directory containing at a minimum nodes.dmp and names.dmp files (optional)", + "pattern": "*/" + } + } + ], + [ + { + "samplesheet": { + "type": "file", + "description": "A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative from the Nextflow work directory of the executed process. The profiles must be provided even if you give a samplesheet as argument (optional)", + "pattern": "*.{tsv,csv,ods,xlsx,arrow,parquet}" + } + } + ] + ], + "output": [ + { + "merged_profiles": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{tsv,csv,arrow,parquet,biom}": { + "type": "file", + "description": "Output file with standardised multiple profiles in one go and have all profiles combined into a single table.", + "pattern": "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133570,66 +171050,83 @@ "tool_dev_url": "https://github.com/taxprofiler/taxpasta", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "profile": { - "type": "file", - "description": "profiler output file (mandatory)", - "pattern": "*" - } - }, - { - "profiler": { - "type": "string", - "description": "Name of the profiler used to generate the profile (mandatory)", - "pattern": "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" - } - }, - { - "format": { - "type": "string", - "description": "Type of output file to be generated", - "pattern": "tsv|csv|ods|xlsx|arrow|parquet|biom" - } - }, - { - "taxonomy": { - "type": "directory", - "description": "Directory containing at a minimum nodes.dmp and names.dmp files (optional)", - "pattern": "*/" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "standardised_profile": { - "type": "file", - "description": "Standardised taxonomic profile", - "pattern": "*.{tsv,csv,arrow,parquet,biom}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:taxpasta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "profile": { + "type": "file", + "description": "profiler output file (mandatory)", + "pattern": "*" + } + } + ], + [ + { + "profiler": { + "type": "string", + "description": "Name of the profiler used to generate the profile (mandatory)", + "pattern": "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + } + } + ], + [ + { + "format": { + "type": "string", + "description": "Type of output file to be generated", + "pattern": "tsv|csv|ods|xlsx|arrow|parquet|biom" + } + } + ], + [ + { + "taxonomy": { + "type": "directory", + "description": "Directory containing at a minimum nodes.dmp and names.dmp files (optional)", + "pattern": "*/" + } + } + ] + ], + "output": [ + { + "standardised_profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{tsv,csv,arrow,parquet,biom}": { + "type": "file", + "description": "Standardised taxonomic profile", + "pattern": "*.{tsv,csv,arrow,parquet,biom}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133668,73 +171165,124 @@ "doi": "10.1186/s13073-019-0650-x", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ file", - "pattern": "*.{fastq.gz,fq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with alignment details", - "pattern": "*.bam" - } - }, - { - "csv": { - "type": "file", - "description": "Optional CSV formated result file of resistance and strain type", - "pattern": "*.csv" - } - }, - { - "json": { - "type": "file", - "description": "JSON formated result file of resistance and strain type", - "pattern": "*.json" - } - }, - { - "txt": { - "type": "file", - "description": "Optional text file of resistance and strain type", - "pattern": "*.txt" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF with variant info again refernce genomes", - "pattern": "*.vcf" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ file", + "pattern": "*.{fastq.gz,fq.gz}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam/*.bam": { + "type": "file", + "description": "BAM file with alignment details", + "pattern": "*.bam" + } + } + ] + }, + { + "csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.csv": { + "type": "file", + "description": "Optional CSV formated result file of resistance and strain type", + "pattern": "*.csv" + } + } + ] + }, + { + "json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.json": { + "type": "file", + "description": "JSON formated result file of resistance and strain type", + "pattern": "*.json" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "results/*.txt": { + "type": "file", + "description": "Optional text file of resistance and strain type", + "pattern": "*.txt" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf/*.vcf.gz": { + "type": "file", + "description": "VCF with variant info again refernce genomes", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133767,98 +171315,126 @@ "doi": "10.1006/jmbi.2000.4042", "licence": [ "GPL v3" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_infos']`\n" - } - }, - { - "template": { - "type": "file", - "description": "T_coffee template file that maps sequences to the accessory information files to be used.", - "pattern": "*" - } - }, - { - "accessory_informations": { - "type": "file", - "description": "Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.", - "pattern": "*" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Alignment file in FASTA format. May be gzipped.", - "pattern": "*.aln{.gz,}" - } - }, - { - "lib": { - "type": "file", - "description": "optional output, the library generated from the MSA file.", - "pattern": "*.*lib" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_infos']`\n" + } + }, + { + "template": { + "type": "file", + "description": "T_coffee template file that maps sequences to the accessory information files to be used.", + "pattern": "*" + } + }, + { + "accessory_informations": { + "type": "file", + "description": "Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.", + "pattern": "*" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file in FASTA format. May be gzipped.", + "pattern": "*.aln{.gz,}" + } + } + ] + }, + { + "lib": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.*lib": { + "type": "file", + "description": "optional output, the library generated from the MSA file.", + "pattern": "*.*lib" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133906,59 +171482,71 @@ "doi": "10.1006/jmbi.2000.4042", "licence": [ "GPL v3" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" - } - }, - { - "msa": { - "type": "file", - "description": "fasta file containing the alignment to be evaluated. Can be gzipped or uncompressed", - "pattern": "*.{aln,fa,fasta,fas}{.gz,}" - } - }, - { - "ref_msa": { - "type": "file", - "description": "fasta file containing the reference alignment used for the evaluation. Can be gzipped or uncompressed", - "pattern": "*.{aln,fa,fasta,fas}{.gz,}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "scores": { - "type": "file", - "description": "a file containing the score of the alignment", - "pattern": "*.scores" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" + } + }, + { + "msa": { + "type": "file", + "description": "fasta file containing the alignment to be evaluated. Can be gzipped or uncompressed", + "pattern": "*.{aln,fa,fasta,fas}{.gz,}" + } + }, + { + "ref_msa": { + "type": "file", + "description": "fasta file containing the reference alignment used for the evaluation. Can be gzipped or uncompressed", + "pattern": "*.{aln,fa,fasta,fas}{.gz,}" + } + } + ] + ], + "output": [ + { + "scores": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.scores": { + "type": "file", + "description": "a file containing the score of the alignment", + "pattern": "*.scores" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -133995,75 +171583,91 @@ "doi": "10.1006/jmbi.2000.4042", "licence": [ "GPL v3" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "aln": { + "type": "file", + "description": "List of multiple sequence alignments in FASTA format to be used to compute the consensus", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{aln,aln.gz}": { + "type": "file", + "description": "Consensus alignment in FASTA format", + "pattern": "*.{fa,fasta,aln}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "aln": { - "type": "file", - "description": "List of multiple sequence alignments in FASTA format to be used to compute the consensus", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "alignment": { - "type": "file", - "description": "Consensus alignment in FASTA format", - "pattern": "*.{fa,fasta,aln}" - } - } - ], - "authors": [ - "@luisas" + "authors": [ + "@luisas" ], "maintainers": [ "@luisas" @@ -134098,72 +171702,65 @@ "doi": "10.1006/jmbi.2000.4042", "licence": [ "GPL v3" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" - } - }, - { - "msa": { - "type": "file", - "description": "fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.", - "pattern": "*.{aln,fa,fasta,fas}{.gz,}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing information about the structures\ne.g. [ id:'test', ... ]\n" - } - }, - { - "template": { - "type": "file", - "description": "Template file matching the structures to the sequences in the alignment.", - "pattern": "*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" + } } - }, - { - "structures": { - "type": "directory", - "description": "Directory containing the structures file matching the sequences in the alignment in PDB format", - "pattern": "*" + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "irmsd": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.irmsd": { + "type": "file", + "description": "File containing the irmsd of the alignment", + "pattern": "*" + } + } + ] }, { - "irmsd": { - "type": "file", - "description": "File containing the irmsd of the alignment", - "pattern": "*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134199,45 +171796,55 @@ "doi": "10.1006/jmbi.2000.4042", "licence": [ "GPL v3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "infile": { - "type": "file", - "description": "Input file to be reformatted", - "pattern": "*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "infile": { + "type": "file", + "description": "Input file to be reformatted" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "formatted_file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test' ]`\n" + } + }, + { + "${prefix}.txt": { + "type": "file", + "description": "Formatted file", + "pattern": "*" + } + } + ] }, { - "formatted_file": { - "type": "file", - "description": "Formatted file", - "pattern": "*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134274,72 +171881,96 @@ "doi": "10.1006/jmbi.2000.4042", "licence": [ "GPL v3" - ] + ], + "identifier": "" } }, { "pigz": { "description": "Parallel implementation of the gzip algorithm.", "homepage": "https://zlib.net/pigz/", - "documentation": "https://zlib.net/pigz/pigz.pdf" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" - } - }, - { - "msa": { - "type": "file", - "description": "fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.", - "pattern": "*.{aln,fa,fasta,fas}{.gz,}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing library information\ne.g. [ id:'test', ... ]\n" - } - }, - { - "lib": { - "type": "file", - "description": "lib file containing the alignment library of the given msa.", - "pattern": "*{.tc_lib,*_lib}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tcs": { - "type": "file", - "description": "The msa represented in tcs format, prepended with TCS scores", - "pattern": "*.tcs" - } - }, - { - "scores": { - "type": "file", - "description": "a file containing the score of the alignment in csv format", - "pattern": "*.scores" - } + "documentation": "https://zlib.net/pigz/pigz.pdf", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', ... ]\n" + } + }, + { + "msa": { + "type": "file", + "description": "fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.", + "pattern": "*.{aln,fa,fasta,fas}{.gz,}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "lib": { + "type": "file", + "description": "lib file containing the alignment library of the given msa.", + "pattern": "*{.tc_lib,*_lib}" + } + } + ] + ], + "output": [ + { + "tcs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tcs": { + "type": "file", + "description": "The msa represented in tcs format, prepended with TCS scores", + "pattern": "*.tcs" + } + } + ] + }, + { + "scores": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.scores": { + "type": "file", + "description": "a file containing the score of the alignment in csv format", + "pattern": "*.scores" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134378,45 +172009,56 @@ "doi": "10.1021/acs.jproteome.9b00328", "licence": [ "Apache Software" - ] + ], + "identifier": "biotools:ThermoRawFileParser" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "raw": { + "type": "file", + "description": "Thermo RAW file", + "pattern": "*.{raw,RAW}" + } } - }, - { - "raw": { - "type": "file", - "description": "Thermo RAW file", - "pattern": "*.{raw,RAW}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "spectra": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}": { + "type": "file", + "description": "Mass spectra in open format", + "pattern": "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}" + } + } + ] }, { - "spectra": { - "type": "file", - "description": "Mass spectra in open format", - "pattern": "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134455,59 +172097,90 @@ "doi": "10.1093/bioinformatics/btab672", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file of assembled contigs.", - "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "classifications": { - "type": "file", - "description": "TSV file containing per-contig classification probabilities and overall classifications. Gzipped if flag --gz is set.", - "pattern": "*.{txt,txt.gz}" - } - }, - { - "log": { - "type": "file", - "description": "Log file containing tiara model parameters. Gzipped if flag --gz is set.", - "pattern": "log_*.{txt,txt.gz}" - } - }, - { - "fasta": { - "type": "file", - "description": "(optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs\n", - "pattern": "*.{fasta,fasta.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:tiara-metagenomics" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file of assembled contigs.", + "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" + } + } + ] + ], + "output": [ + { + "classifications": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.{txt,txt.gz}": { + "type": "file", + "description": "TSV file containing per-contig classification probabilities and overall classifications. Gzipped if flag --gz is set.", + "pattern": "*.{txt,txt.gz}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "log_*.{txt,txt.gz}": { + "type": "file", + "description": "Log file containing tiara model parameters. Gzipped if flag --gz is set.", + "pattern": "log_*.{txt,txt.gz}" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.{fasta,fasta.gz}": { + "type": "file", + "description": "(optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs\n", + "pattern": "*.{fasta,fasta.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134546,65 +172219,88 @@ "doi": "10.12688/f1000research.11168.1", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference genome file. Only needed when passing in CRAM instead of BAM.\nIf not using CRAM, please pass an empty file instead.\n", - "pattern": "*.fasta" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "cov": { - "type": "file", - "description": "The coverage of different regions in bed format. Optional.", - "pattern": "*.bed" - } - }, - { - "wig": { - "type": "file", - "description": "The coverage of different regions in WIG format. Optional.", - "pattern": "*.wig" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:tiddit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference genome file. Only needed when passing in CRAM instead of BAM.\nIf not using CRAM, please pass an empty file instead.\n", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "cov": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "The coverage of different regions in bed format. Optional.", + "pattern": "*.bed" + } + } + ] + }, + { + "wig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.wig": { + "type": "file", + "description": "The coverage of different regions in WIG format. Optional.", + "pattern": "*.wig" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134644,85 +172340,110 @@ "doi": "10.12688/f1000research.11168.1", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - }, - { - "input_index": { - "type": "file", - "description": "BAM/CRAM index file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test_fasta']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input FASTA file", - "pattern": "*.{fasta,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information from bwa index\ne.g. `[ id:'test_bwa-index' ]`\n" - } - }, - { - "bwa_index": { - "type": "file", - "description": "BWA genome index files", - "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf", - "pattern": "*.{vcf}" - } - }, - { - "ploidy": { - "type": "file", - "description": "tab", - "pattern": "*.{ploidies.tab}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:tiddit" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } + }, + { + "input_index": { + "type": "file", + "description": "BAM/CRAM index file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test_fasta']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input FASTA file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information from bwa index\ne.g. `[ id:'test_bwa-index' ]`\n" + } + }, + { + "bwa_index": { + "type": "file", + "description": "BWA genome index files", + "pattern": "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "vcf", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "ploidy": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ploidies.tab": { + "type": "file", + "description": "tab", + "pattern": "*.{ploidies.tab}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134765,52 +172486,73 @@ "doi": "10.5281/zenodo.10091385", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The input fasta file", - "pattern": "*.{fsa,fa,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "explore_tsv": { - "type": "file", - "description": "Telomeres and their frequencies in TSV format", - "pattern": "*.tidk.explore.tsv" - } - }, - { - "top_sequence": { - "type": "file", - "description": "The most frequent telomere sequence if one or more\nsequences are identified by the toolkit\n", - "pattern": "*.top.sequence.txt" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The input fasta file", + "pattern": "*.{fsa,fa,fasta}" + } + } + ] + ], + "output": [ + { + "explore_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tidk.explore.tsv": { + "type": "file", + "description": "Telomeres and their frequencies in TSV format", + "pattern": "*.tidk.explore.tsv" + } + } + ] + }, + { + "top_sequence": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.top.sequence.txt": { + "type": "file", + "description": "The most frequent telomere sequence if one or more\nsequences are identified by the toolkit\n", + "pattern": "*.top.sequence.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134844,45 +172586,56 @@ "doi": "10.5281/zenodo.10091385", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Search results in TSV format from `tidk search`", - "pattern": "*.tsv" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "tsv": { + "type": "file", + "description": "Search results in TSV format from `tidk search`", + "pattern": "*.tsv" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "svg": { - "type": "file", - "description": "Telomere search plot", - "pattern": "*.svg" - } + "svg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.svg": { + "type": "file", + "description": "Telomere search plot", + "pattern": "*.svg" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134915,58 +172668,81 @@ "doi": "10.5281/zenodo.10091385", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The input fasta file", - "pattern": "*.{fsa,fa,fasta}" - } - }, - { - "string": { - "type": "string", - "description": "Search string such as TTAGGG" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "tsv": { - "type": "file", - "description": "Search results in TSV format", - "pattern": "*.tsv" - } - }, - { - "bedgraph": { - "type": "file", - "description": "Search results in BEDGRAPH format", - "pattern": "*.bedgraph" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The input fasta file", + "pattern": "*.{fsa,fa,fasta}" + } + } + ], + [ + { + "string": { + "type": "string", + "description": "Search string such as TTAGGG" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Search results in TSV format", + "pattern": "*.tsv" + } + } + ] + }, + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.bedgraph": { + "type": "file", + "description": "Search results in BEDGRAPH format", + "pattern": "*.bedgraph" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -134999,93 +172775,160 @@ "doi": "10.1038/s41598-017-17723-1", "licence": [ "CC-BY" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps", - "pattern": "*.vcf.gz" - } - }, - { - "vcf_indels": { - "type": "file", - "description": "Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels", - "pattern": "*.vcf.gz" - } - }, - { - "reference": { - "type": "file", - "description": "Fasta file of reference genome", - "pattern": "*.fasta" - } - }, - { - "fai": { - "type": "file", - "description": "Optional index for the fasta file of reference genome", - "pattern": "*.fai" - } - }, - { - "vcf_output": { - "type": "boolean", - "description": "Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "Gzipped consensus fasta file with bases under threshold replaced with Ns", - "pattern": "*.fasta.gz" - } - }, - { - "vcf": { - "type": "file", - "description": "Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns", - "pattern": "*.vcf.gz" - } - }, - { - "ccf": { - "type": "file", - "description": "Statistics file containing information about the consensus calls in the fasta file", - "pattern": "*.ccf" - } - }, - { - "log": { - "type": "file", - "description": "Log file", - "pattern": "*.log" - } + ], + "identifier": "biotools:TOPAS" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf_indels": { + "type": "file", + "description": "Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels", + "pattern": "*.vcf.gz" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Fasta file of reference genome", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Optional index for the fasta file of reference genome", + "pattern": "*.fai" + } + } + ], + [ + { + "vcf_output": { + "type": "boolean", + "description": "Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta.gz": { + "type": "file", + "description": "Gzipped consensus fasta file with bases under threshold replaced with Ns", + "pattern": "*.fasta.gz" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "ccf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ccf": { + "type": "file", + "description": "Statistics file containing information about the consensus calls in the fasta file", + "pattern": "*.ccf" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log file", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135117,66 +172960,107 @@ "tool_dev_url": "https://github.com/GenomiqueENS/toulligQC", "licence": [ "CECILL-2.1" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ontfile": { - "type": "file", - "description": "Input ONT file", - "pattern": "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "report_data": { - "type": "file", - "description": "Report data emitted from toulligqc", - "pattern": "*.data" - } - }, - { - "report_html": { - "type": "file", - "description": "Report data in html format", - "pattern": "*.html" - } - }, - { - "plots_html": { - "type": "file", - "description": "Plots emitted in html format", - "pattern": "*.html" - } - }, - { - "plotly_js": { - "type": "file", - "description": "Plots emitted from toulligqc", - "pattern": "plotly.min.js" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ToulligQC" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ontfile": { + "type": "file", + "description": "Input ONT file", + "pattern": "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}" + } + } + ] + ], + "output": [ + { + "report_data": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.data": { + "type": "file", + "description": "Report data emitted from toulligqc", + "pattern": "*.data" + } + } + ] + }, + { + "report_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/*.html": { + "type": "file", + "description": "Report data in html format", + "pattern": "*.html" + } + } + ] + }, + { + "plots_html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/images/*.html": { + "type": "file", + "description": "Plots emitted in html format", + "pattern": "*.html" + } + } + ] + }, + { + "plotly_js": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*/images/plotly.min.js": { + "type": "file", + "description": "Plots emitted from toulligqc", + "pattern": "plotly.min.js" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135215,72 +173099,117 @@ "tool_dev_url": "https://github.com/TransDecoder/TransDecoder", "licence": [ "Broad Institute" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pep": { - "type": "file", - "description": "all ORFs meeting the minimum length criteria, regardless of coding potential. file", - "pattern": "*.{pep}" - } - }, - { - "gff3": { - "type": "file", - "description": "positions of all ORFs as found in the target transcripts. file", - "pattern": "*.{gff3}" - } - }, - { - "cds": { - "type": "file", - "description": "the nucleotide coding sequence for all detected ORFs. file", - "pattern": "*{cds}" - } - }, - { - "dat": { - "type": "file", - "description": "nucleotide frequencies", - "pattern": "*{dat}" - } - }, - { - "folder": { - "type": "directory", - "description": "contains all the files from the run" - } + ], + "identifier": "biotools:TransDecoder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fasta}" + } + } + ] + ], + "output": [ + { + "pep": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.pep": { + "type": "file", + "description": "all ORFs meeting the minimum length criteria, regardless of coding potential. file", + "pattern": "*.{pep}" + } + } + ] + }, + { + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.gff3": { + "type": "file", + "description": "positions of all ORFs as found in the target transcripts. file", + "pattern": "*.{gff3}" + } + } + ] + }, + { + "cds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.cds": { + "type": "file", + "description": "the nucleotide coding sequence for all detected ORFs. file", + "pattern": "*{cds}" + } + } + ] + }, + { + "dat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output_dir_name}/*.dat": { + "type": "file", + "description": "nucleotide frequencies", + "pattern": "*{dat}" + } + } + ] + }, + { + "folder": [ + { + "${output_dir_name}": { + "type": "directory", + "description": "contains all the files from the run" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135319,73 +173248,116 @@ "tool_dev_url": "https://github.com/TransDecoder/TransDecoder", "licence": [ "Broad Institute" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "fasta file", - "pattern": "*.{fasta}" - } - }, - { - "fold": { - "type": "directory", - "description": "Output from the module transdecoder_longorf", - "pattern": "*" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pep": { - "type": "file", - "description": "All ORFs meeting the minimum length criteria, regardless of coding potential", - "pattern": "*.{pep}" - } - }, - { - "gff3": { - "type": "file", - "description": "Positions of all ORFs as found in the target transcripts", - "pattern": "*.{gff3}" - } - }, - { - "cds": { - "type": "file", - "description": "the nucleotide coding sequence for all detected ORFs", - "pattern": "*{cds}" - } - }, - { - "bed": { - "type": "file", - "description": "bed file", - "pattern": "*{bed}" - } + ], + "identifier": "biotools:TransDecoder" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "fasta file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "fold": { + "type": "directory", + "description": "Output from the module transdecoder_longorf", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "pep": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.pep": { + "type": "file", + "description": "All ORFs meeting the minimum length criteria, regardless of coding potential", + "pattern": "*.{pep}" + } + } + ] + }, + { + "gff3": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.gff3": { + "type": "file", + "description": "Positions of all ORFs as found in the target transcripts", + "pattern": "*.{gff3}" + } + } + ] + }, + { + "cds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.cds": { + "type": "file", + "description": "the nucleotide coding sequence for all detected ORFs", + "pattern": "*{cds}" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.transdecoder.bed": { + "type": "file", + "description": "bed file", + "pattern": "*{bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135423,72 +173395,123 @@ "documentation": "https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - 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for\nsingle-end and paired-end data, respectively.\n", + "pattern": "*{3prime,5prime,trimmed,val}*.fq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*report.txt": { + "type": "file", + "description": "Trim Galore! trimming report", + "pattern": "*_{report.txt}" + } + } + ] + }, + { + "unpaired": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*unpaired*.fq.gz": { + "type": "file", + "description": "FastQ files containing unpaired reads from read 1 or read 2\n", + "pattern": "*unpaired*.fq.gz" + } + } + ] + }, + { + "html": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.html": { + "type": "file", + "description": "FastQC report (optional)", + "pattern": "*_{fastqc.html}" + } + } + ] + }, + { + "zip": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.zip": { + "type": "file", + "description": "FastQC report archive (optional)", + "pattern": "*_{fastqc.zip}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135574,73 +173597,124 @@ "doi": "10.1093/bioinformatics/btu170", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.\n", - "pattern": "*.fastq.gz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", 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+ } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.\n", + "pattern": "*.fastq.gz" + } + } + ] + ], + "output": [ + { + "trimmed_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paired.trim*.fastq.gz": { + "type": "file", + "description": "The trimmed/modified paired end fastq reads", + "pattern": "*.paired.trim*.fastq.gz" + } + } + ] + }, + { + "unpaired_reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unpaired.trim_*.fastq.gz": { + "type": "file", + "description": "The trimmed/modified unpaired end fastq reads", + "pattern": "*.unpaired.trim_*.fastq.gz" + } + } + ] + }, + { + "trim_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_trim.log": { + "type": "file", + "description": "trimmomatic log file, from the trim_log parameter", + "pattern": "*.log" + } + } + ] + }, + { + "out_log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_out.log": { + "type": "file", + "description": "log of output from the standard out", + "pattern": "*.log" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.summary": { + "type": "file", + "description": "trimmomatic summary file of surviving and dropped reads", + "pattern": "*.summary" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135692,52 +173766,73 @@ "doi": "10.1038/nbt.1883", "licence": [ "BSD-3-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input fasta/fastq reads to be assembled into a transcriptome.\n", - "pattern": "*.{fa|fasta|fq|fastq}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "transcript_fasta": { - "type": "file", - "description": "de novo assembled transcripts fasta file compressed", - "pattern": "*.fa.gz" - } - }, - { - "log": { - "type": "file", - "description": "Log from trinity", - "pattern": "*.log" - } + ], + "identifier": "biotools:trinity" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input fasta/fastq reads to be assembled into a transcriptome.\n", + "pattern": "*.{fa|fasta|fq|fastq}" + } + } + ] + ], + "output": [ + { + "transcript_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fa.gz": { + "type": "file", + "description": "de novo assembled transcripts fasta file compressed", + "pattern": "*.fa.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Log from trinity", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135777,98 +173872,236 @@ "tool_dev_url": "https://github.com/liulab-dfci/TRUST4", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file from bulk or single-cell RNA-seq data", - "pattern": "*.bam" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively" - } - }, - { - "fasta": { - "type": "file", - "description": "Path to the fasta file coordinate and sequence of V/D/J/C genes" - } - }, - { - "ref": { - "type": 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- "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:trust4" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file from bulk or single-cell RNA-seq data", + "pattern": "*.bam" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Path to the fasta file coordinate and sequence of V/D/J/C genes" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vdj_reference": { + "type": "file", + "description": "reference file of V/D/J genes" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "barcode_read": { + "type": "file", + "description": "barcode read file" + } + } + ], + [ + { + "meta5": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "umi_read": { + "type": "file", + "description": "umi read file" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "tsv files created by TRUST4", + "pattern": "*.tsv" + } + } + ] + }, + { + "airr_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_airr.tsv": { + "type": "file", + "description": "TRUST4 results in AIRR format", + "pattern": "*_airr.tsv" + } + } + ] + }, + { + "airr_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${meta.id}_airr.tsv": { + "type": "file", + "description": "TRUST4 results in AIRR format", + "pattern": "*_airr.tsv" + } + } + ] + }, + { + "report_tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_report.tsv": { + "type": "file", + "description": "TRUST4 report in tsv format", + "pattern": "*_report.tsv" + } + } + ] + }, + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fa": { + "type": "file", + "description": "Fasta files created by TRUST4", + "pattern": "*.fa" + } + } + ] + }, + { + "out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.out": { + "type": "file", + "description": "Further report files", + "pattern": "*.out" + } + } + ] + }, + { + "fq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.fq": { + "type": "file", + "description": "Fastq files created by TRUST4", + "pattern": "*.fq" + } + } + ] + }, + { + "outs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "**": { + "type": "file", + "description": "outputt files" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -135903,155 +174136,250 @@ "doi": "10.1186/s13059-022-02840-6", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input SV VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Input SV VCF index file", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "truth_vcf": { - "type": "file", - "description": "Input VCF file with truth SVs", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Input VCF index file with truth SVs", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "bed": { - "type": "file", - "description": "BED file containing regions to compare", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map 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} + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input SV VCF file", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "Input SV VCF index file", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "truth_vcf": { + "type": "file", + "description": "Input VCF file with truth SVs", + "pattern": "*.vcf.gz" + } + }, + { + "truth_tbi": { + "type": "file", + "description": "Input VCF index file with truth SVs", + "pattern": "*.vcf.gz.tbi" + } + }, + { + "bed": { + "type": "file", + "description": "BED file containing regions to compare", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference FASTA file", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta index information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "Reference FASTA index file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "fn_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fn.vcf.gz": { + "type": "file", + "description": "VCF file with false negatives", + "pattern": "*.fn.vcf.gz" + } + } + ] + }, + { + "fn_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fn.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file with false negatives", + "pattern": "*.fn.vcf.gz.tbi" + } + } + ] + }, + { + "fp_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fp.vcf.gz": { + "type": "file", + "description": "VCF file with false positives", + "pattern": "*.fp.vcf.gz" + } + } + ] + }, + { + "fp_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.fp.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file with false positives", + "pattern": "*.fp.vcf.gz.tbi" + } + } + ] + }, + { + "tp_base_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tp-base.vcf.gz": { + "type": "file", + "description": "VCF file with base true positives", + "pattern": "*.tp-base.vcf.gz" + } + } + ] + }, + { + "tp_base_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tp-base.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file with base true positives", + "pattern": "*.tp-base.vcf.gz.tbi" + } + } + ] + }, + { + "tp_comp_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tp-comp.vcf.gz": { + "type": "file", + "description": "VCF file with compared true positives", + "pattern": "*.tp-comp.vcf.gz" + } + } + ] + }, + { + "tp_comp_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.tp-comp.vcf.gz.tbi": { + "type": "file", + "description": "VCF index file with compared true positives", + "pattern": "*.tp-comp.vcf.gz.tbi" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.summary.json": { + "type": "file", + "description": "Summary JSON file with results from the benchmark", + "pattern": "*.summary.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136092,45 +174420,56 @@ "doi": "10.1186/s13059-022-02840-6", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "vcfs": { + "type": "file", + "description": "two or more VCF files to compare", + "pattern": "*.{vcf,gz}" + } } + ] + ], + "output": [ + { + "consistency": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.{txt,json}": { + "type": "file", + "description": "Output report in txt or json format", + "pattern": "*.{txt,json}" + } + } + ] }, { - "vcfs": { - "type": "file", - "description": "two or more VCF files to compare", - "pattern": "*.{vcf,gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "consistency": { - "type": "file", - "description": "Output report in txt or json format", - "pattern": "*.{txt,json}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136165,45 +174504,56 @@ "doi": "10.1186/s13059-022-02840-6", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Input VCF file", - "pattern": "*.{vcf,gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Input VCF file", + "pattern": "*.{vcf,gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Segmented VCF file", + "pattern": "*.{vcf}" + } + } + ] }, { - "vcf": { - "type": "file", - "description": "Segmented VCF file", - "pattern": "*.{vcf}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136237,55 +174587,60 @@ "doi": "10.1186/s13059-021-02483-z", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Long-read FASTQ file, optionally gzip compressed" - } - }, - { - "assemblies": { - "type": "file", - "description": "Input assemblies whose contigs will be clustered" - } - }, - { - "out_dir": { - "type": "directory", - "description": "Output directory for clustering results" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "cluster_dir": { - "type": "directory", - "description": "Output directory containing clustering results" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:trycycler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "contigs": { + "type": "file", + "description": "Contigs file" + } + }, + { + "reads": { + "type": "file", + "description": "Long-read FASTQ file, optionally gzip compressed" + } + } + ] + ], + "output": [ + { + "cluster_dir": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*": { + "type": "directory", + "description": "Output directory containing clustering results" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136317,50 +174672,55 @@ "doi": "10.1186/s13059-021-02483-z", "licence": [ "GPL v3" - ] + ], + "identifier": "biotools:trycycler" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "reads": { - "type": "file", - "description": "Long-read FASTQ file, optionally gzip compressed" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "Long-read FASTQ file, optionally gzip compressed" + } } - }, - { - "out_dir": { - "type": "directory", - "description": "Output directory for subsampled read sets" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "subreads": { - "type": "file", - "description": "Subsampled read sets", - "pattern": "*.{fastq.gz}" - } + "subreads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*/*.fastq.gz": { + "type": "file", + "description": "Subsampled read sets", + "pattern": "*.{fastq.gz}" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136396,73 +174756,100 @@ "doi": "10.1186/s12859-021-04482-0", "licence": [ "Artistic-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "gtfs": { - "type": "list", - "description": "List of gene prediction files in gtf", - "pattern": "*.gtf" - } - }, - { - "hints_files": { - "type": "list", - "description": "List of files containing extrinsic evidence in gff", - "pattern": "*.gff" - } - }, - { - "keep_gtfs": { - "type": "list", - "description": "List of gene prediction files in gtf. These gene sets are used the same way as other inputs, but TSEBRA ensures that all\ntranscripts from these gene sets are included in the output\n", - "pattern": "*.gtf" - } - }, - { - "config": { - "type": "file", - "description": "Configuration file that sets the parameter for TSEBRA", - "pattern": "*.cfg" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tsebra_gtf": { - "type": "file", - "description": "Output file for the combined gene predictions in gtf", - "pattern": "*.gtf" - } - }, - { - "tsebra_scores": { - "type": "file", - "description": "Transcript scores as a table", - "pattern": "*.tsv" - } + ], + "identifier": "biotools:tsebra" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "gtfs": { + "type": "list", + "description": "List of gene prediction files in gtf", + "pattern": "*.gtf" + } + } + ], + [ + { + "hints_files": { + "type": "list", + "description": "List of files containing extrinsic evidence in gff", + "pattern": "*.gff" + } + } + ], + [ + { + "keep_gtfs": { + "type": "list", + "description": "List of gene prediction files in gtf. These gene sets are used the same way as other inputs, but TSEBRA ensures that all\ntranscripts from these gene sets are included in the output\n", + "pattern": "*.gtf" + } + } + ], + [ + { + "config": { + "type": "file", + "description": "Configuration file that sets the parameter for TSEBRA", + "pattern": "*.cfg" + } + } + ] + ], + "output": [ + { + "tsebra_gtf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.gtf": { + "type": "file", + "description": "Output file for the combined gene predictions in gtf", + "pattern": "*.gtf" + } + } + ] + }, + { + "tsebra_scores": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Transcript scores as a table", + "pattern": "*.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136497,125 +174884,197 @@ "doi": "10.1371/journal.pcbi.1007664", "licence": [ "GPL-2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "quants": { - "type": "directory", - "description": "Paths to subdirectories corresponding to sample-wise runs of Salmon or Kallisto" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information related to the species\nreference e.g. `[ id:'yeast' ]`\n" - } - }, - { - "tx2gene": { - "type": "file", - "description": "A transcript to gene mapping table such as those generated by custom/tx2gene", - "pattern": "*.{csv,tsv}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "coldata": { - "type": "file", - "description": "Optional 'coldata' file equivalent to a sample sheet where the first\ncolumn corresponds to the sample names (directory names in the input\nsalmon/ kallisto results)\n", - "pattern": "*.{csv,tsv}" - } - }, - { - "quant_type": { - "type": "string", - "description": "Quantification type, 'kallisto' or 'salmon'" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" - } - }, - { - "tpm_gene": { - "type": "file", - "description": "Abundance (TPM) values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", - "pattern": "*gene_tpm.tsv" - } - }, - { - "counts_gene": { - "type": "file", - "description": "Count values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", - "pattern": "*gene_counts.tsv" - } - }, - { - "counts_gene_length_scaled": { - "type": "file", - "description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'lengthScaledTPM'\n", - "pattern": "*gene_counts_length_scaled.tsv" - } - }, - { - "counts_gene_scaled": { - "type": "file", - "description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'scaledTPM'\n", - "pattern": "*gene_counts_scaled.tsv" - } - }, - { - "lengths_gene": { - "type": "file", - "description": "Length values derived from tximport output after summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n", - "pattern": "*gene_lengths.tsv" - } - }, - { - "tpm_transcript": { - "type": "file", - "description": "Abundance (TPM) values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", - "pattern": "*transcript_tpm.tsv" - } - }, - { - "counts_transcript": { - "type": "file", - "description": "Count values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", - "pattern": "*transcript_counts.tsv" - } - }, - { - "lengths_transcript": { - "type": "file", - "description": "Length values derived from tximport output without summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n", - "pattern": "*gene_lengths.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:tximeta" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "\"quants/*\"": { + "type": "directory", + "description": "Directory containing quantification files" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information related to the species\nreference e.g. `[ id:'yeast' ]`\n" + } + }, + { + "tx2gene": { + "type": "file", + "description": "A transcript to gene mapping table such as those generated by custom/tx2gene", + "pattern": "*.{csv,tsv}" + } + } + ], + [ + { + "quant_type": { + "type": "string", + "description": "Quantification type, 'kallisto' or 'salmon'" + } + } + ] + ], + "output": [ + { + "tpm_gene": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_tpm.tsv": { + "type": "file", + "description": "Abundance (TPM) values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*gene_tpm.tsv" + } + } + ] + }, + { + "counts_gene": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_counts.tsv": { + "type": "file", + "description": "Count values derived from tximport output after\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*gene_counts.tsv" + } + } + ] + }, + { + "counts_gene_length_scaled": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_counts_length_scaled.tsv": { + "type": "file", + "description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'lengthScaledTPM'\n", + "pattern": "*gene_counts_length_scaled.tsv" + } + } + ] + }, + { + "counts_gene_scaled": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_counts_scaled.tsv": { + "type": "file", + "description": "Count values derived from tximport output after summarizeToGene(), with\na 'countsFromAbundance' specification of 'scaledTPM'\n", + "pattern": "*gene_counts_scaled.tsv" + } + } + ] + }, + { + "lengths_gene": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*gene_lengths.tsv": { + "type": "file", + "description": "Length values derived from tximport output after summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n", + "pattern": "*gene_lengths.tsv" + } + } + ] + }, + { + "tpm_transcript": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*transcript_tpm.tsv": { + "type": "file", + "description": "Abundance (TPM) values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*transcript_tpm.tsv" + } + } + ] + }, + { + "counts_transcript": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*transcript_counts.tsv": { + "type": "file", + "description": "Count values derived from tximport output without\nsummarizeToGene(), without a 'countsFromAbundance' specification\n", + "pattern": "*transcript_counts.tsv" + } + } + ] + }, + { + "lengths_transcript": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing information related to the experiment as a whole\ne.g. `[ id:'SRP123456' ]`\n" + } + }, + { + "*transcript_lengths.tsv": { + "type": "file", + "description": "Length values derived from tximport output without summarizeToGene(),\nwithout a 'countsFromAbundance' specification\n", + "pattern": "*gene_lengths.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136659,45 +175118,64 @@ "homepage": "http://hgdownload.cse.ucsc.edu/admin/exe/", "licence": [ "varies; see http://genome.ucsc.edu/license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedgraph": { - "type": "file", - "description": "bedGraph file", - "pattern": "*.{bedgraph}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bedgraph": { - "type": "file", - "description": "bedGraph file", - "pattern": "*.{bedgraph}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "bedGraph file", + "pattern": "*.{bedgraph}" + } + } + ], + [ + { + "sizes": { + "type": "file", + "description": "Chromosome sizes file" + } + } + ] + ], + "output": [ + { + "bedgraph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bedGraph": { + "type": "file", + "description": "bedGraph file", + "pattern": "*.{bedgraph}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136748,52 +175226,65 @@ "documentation": "https://genome.ucsc.edu/goldenPath/help/bigWig.html", "licence": [ "varies; see http://genome.ucsc.edu/license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bedgraph": { - "type": "file", - "description": "bedGraph file", - "pattern": "*.{bedGraph}" - } - }, - { - "sizes": { - "type": "file", - "description": "chromosome sizes file", - "pattern": "*.{sizes}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bigwig": { - "type": "file", - "description": "bigWig file", - "pattern": "*.{bigWig}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bedgraph": { + "type": "file", + "description": "bedGraph file", + "pattern": "*.{bedGraph}" + } + } + ], + [ + { + "sizes": { + "type": "file", + "description": "chromosome sizes file", + "pattern": "*.{sizes}" + } + } + ] + ], + "output": [ + { + "bigwig": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bigWig": { + "type": "file", + "description": "bigWig file", + "pattern": "*.{bigWig}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136856,59 +175347,74 @@ "documentation": "https://genome.ucsc.edu/goldenPath/help/bigBed.html", "licence": [ "varies; see http://genome.ucsc.edu/license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "bed file", - "pattern": "*.{bed}" - } - }, - { - "sizes": { - "type": "file", - "description": "chromosome sizes file", - "pattern": "*.{sizes}" - } - }, - { - "autosql": { - "type": "file", - "description": "autoSql file to describe the columns of the BED file", - "pattern": "*.{as}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bigbed": { - "type": "file", - "description": "bigBed file", - "pattern": "*.{bigBed}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "bed file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "sizes": { + "type": "file", + "description": "chromosome sizes file", + "pattern": "*.{sizes}" + } + } + ], + [ + { + "autosql": { + "type": "file", + "description": "autoSql file to describe the columns of the BED file", + "pattern": "*.{as}" + } + } + ] + ], + "output": [ + { + "bigbed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bigBed": { + "type": "file", + "description": "bigBed file", + "pattern": "*.{bigBed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -136939,52 +175445,65 @@ "documentation": "http://www.genome.ucsc.edu/goldenPath/help/bigWig.html", "licence": [ "varies; see http://genome.ucsc.edu/license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "bed file", - "pattern": "*.{bed}" - } - }, - { - "bigwig": { - "type": "file", - "description": "bigwig file", - "pattern": "*.{bigwig,bw}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "tab": { - "type": "file", - "description": "tab file", - "pattern": "*.{tab}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "bed file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "bigwig": { + "type": "file", + "description": "bigwig file", + "pattern": "*.{bigwig,bw}" + } + } + ] + ], + "output": [ + { + "tab": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tab": { + "type": "file", + "description": "tab file", + "pattern": "*.{tab}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137022,52 +175541,73 @@ "homepage": "http://hgdownload.cse.ucsc.edu/admin/exe/", "licence": [ "varies; see http://genome.ucsc.edu/license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gtf": { - "type": "file", - "description": "GTF file", - "pattern": "*.{gtf}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "genepred": { - "type": "file", - "description": "genepred file", - "pattern": "*.{genepred}" - } - }, - { - "refflat": { - "type": "file", - "description": "refflat file", - "pattern": "*.{refflat}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gtf": { + "type": "file", + "description": "GTF file", + "pattern": "*.{gtf}" + } + } + ] + ], + "output": [ + { + "genepred": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.genepred": { + "type": "file", + "description": "genepred file", + "pattern": "*.{genepred}" + } + } + ] + }, + { + "refflat": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.refflat": { + "type": "file", + "description": "refflat file", + "pattern": "*.{refflat}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137099,59 +175639,82 @@ "homepage": "http://hgdownload.cse.ucsc.edu/admin/exe/", "licence": [ "varies; see http://genome.ucsc.edu/license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bed": { - "type": "file", - "description": "Browser Extensible Data (BED) file", - "pattern": "*.{bed}" - } - }, - { - "chain": { - "type": "file", - "description": "Chain file", - "pattern": "*.{chain,chain.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } - }, - { - "lifted": { - "type": "file", - "description": "BED file containing successfully lifted variants", - "pattern": "*.{lifted.bed}" - } - }, - { - "unlifted": { - "type": "file", - "description": "BED file containing variants that couldn't be lifted", - "pattern": "*.{unlifted.bed}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bed": { + "type": "file", + "description": "Browser Extensible Data (BED) file", + "pattern": "*.{bed}" + } + } + ], + [ + { + "chain": { + "type": "file", + "description": "Chain file", + "pattern": "*.{chain,chain.gz}" + } + } + ] + ], + "output": [ + { + "lifted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lifted.bed": { + "type": "file", + "description": "BED file containing successfully lifted variants", + "pattern": "*.{lifted.bed}" + } + } + ] + }, + { + "unlifted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.unlifted.bed": { + "type": "file", + "description": "BED file containing variants that couldn't be lifted", + "pattern": "*.{unlifted.bed}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137187,45 +175750,65 @@ "homepage": "http://www.genome.ucsc.edu/goldenPath/help/bigWig.html", "licence": [ "varies; see http://genome.ucsc.edu/license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "wig": { - "type": "file", - "description": "wig file", - "pattern": "*.{wig}" - } - }, - { - "chromsizes": { - "type": "file", - "description": "chromosome sizes file" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bw": { - "type": "file", - "description": "bigwig file", - "pattern": "*.{bw}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "wig": { + "type": "file", + "description": "wig file", + "pattern": "*.{wig}" + } + } + ], + [ + { + "sizes": { + "type": "file", + "description": "Chromosome sizes file" + } + } + ] + ], + "output": [ + { + "bw": [ + { + "meta": { + "type": "file", + "description": "bigwig file", + "pattern": "*.{bw}" + } + }, + { + "*.bw": { + "type": "file", + "description": "bigwig file", + "pattern": "*.{bw}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137273,66 +175856,81 @@ "doi": "10.1093/bioinformatics/btab540", "licence": [ "GNU GPLV3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "A fasta or fastq file of reads to align", - "pattern": "*.{fa,fasta,fastq}" - } - }, - { - "genome": { - "type": "file", - "description": "A fasta file of reference genome", - "pattern": "*.{fa,fasta}" - } - }, - { - "pickle": { - "type": "file", - "description": "Pickle files generated by uLTRA index", - "pattern": "*.pickle" - } - }, - { - "db": { - "type": "file", - "description": "Database generated by uLTRA index", - "pattern": "*.db" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "The aligned reads in bam format", - "pattern": "*.bam" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "A fasta or fastq file of reads to align", + "pattern": "*.{fa,fasta,fastq}" + } + } + ], + [ + { + "genome": { + "type": "file", + "description": "A fasta file of reference genome", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "pickle": { + "type": "file", + "description": "Pickle files generated by uLTRA index", + "pattern": "*.pickle" + } + }, + { + "db": { + "type": "file", + "description": "Database generated by uLTRA index", + "pattern": "*.db" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "The aligned reads in bam format", + "pattern": "*.bam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137374,47 +175972,60 @@ "doi": "10.1093/bioinformatics/btab540", "licence": [ "GNU GPLV3" - ] + ], + "identifier": "" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "A fasta file of the genome to use as reference for mapping", - "pattern": "*.{fasta, fa}" + [ + { + "fasta": { + "type": "file", + "description": "A fasta file of the genome to use as reference for mapping", + "pattern": "*.{fasta, fa}" + } } - }, - { - "gtf": { - "type": "file", - "description": "An annotation file of the reference genome in GTF format", - "pattern": "*.gtf" + ], + [ + { + "gtf": { + "type": "file", + "description": "An annotation file of the reference genome in GTF format", + "pattern": "*.gtf" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "pickle": { - "type": "file", - "description": "Index files generated by uLTRA index", - "pattern": "*.pickle" - } + "index": [ + { + "*.pickle": { + "type": "file", + "description": "Index file", + "pattern": "*.pickle" + } + }, + { + "*.db": { + "type": "file", + "description": "Index database", + "pattern": "*.db" + } + } + ] }, { - "pickle": { - "type": "file", - "description": "database file generated by uLTRA index", - "pattern": "*.db" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137456,59 +176067,74 @@ "doi": "10.1093/bioinformatics/btab540", "licence": [ "GNU GPLV3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "A fasta or fastq file of reads to align", - "pattern": "*.{fasta,fastq}" - } - }, - { - "genome": { - "type": "file", - "description": "fasta file of reference genome", - "pattern": "*.fasta" - } - }, - { - "gtf": { - "type": "file", - "description": "A annotation of use the genome", - "pattern": "*.gtf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "sam": { - "type": "file", - "description": "The aligned reads in sam format", - "pattern": "*.sam" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "A fasta or fastq file of reads to align", + "pattern": "*.{fasta,fastq}" + } + } + ], + [ + { + "genome": { + "type": "file", + "description": "fasta file of reference genome", + "pattern": "*.fasta" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "A annotation of use the genome", + "pattern": "*.gtf" + } + } + ] + ], + "output": [ + { + "sam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sam": { + "type": "file", + "description": "The aligned reads in sam format", + "pattern": "*.sam" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137545,59 +176171,99 @@ "doi": "10.5281/zenodo.465128", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Zipped FASTQ file", - "pattern": "*.{fastq.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fastq": { - "type": "file", - "description": "Demultiplexed sample FASTQ files", - "pattern": "*[!no_match].fastq.gz" - } - }, - { - "no_match_fastq": { - "type": "file", - "description": "FASTQ file containing reads that could not be demultiplexed", - "pattern": "*no_match.fastq.gz" - } - }, - { - "report": { - "type": "file", - "description": "File containing demultiplexing log", - "pattern": "*.log" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:ultraplex" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ file(s) to demultiplex" + } + } + ], + [ + { + "barcode_file": { + "type": "file", + "description": "FASTQ file containing barcode sequences" + } + } + ], + [ + { + "adapter_seq": { + "type": "string", + "description": "adapter sequence" + } + } + ] + ], + "output": [ + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*[!no_match].fastq.gz": { + "type": "file", + "description": "Demultiplexed sample FASTQ files", + "pattern": "*[!no_match].fastq.gz" + } + } + ] + }, + { + "no_match_fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*no_match.fastq.gz": { + "type": "file", + "description": "FASTQ file containing reads that could not be demultiplexed", + "pattern": "*no_match.fastq.gz" + } + } + ] + }, + { + "report": [ + { + "*.log": { + "type": "file", + "description": "File containing demultiplexing log", + "pattern": "*.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137640,66 +176306,106 @@ "doi": "10.7717/peerj.8275", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing reads to be deduplicated via UMIs.\n", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input.\n", - "pattern": "*.{bai}" - } - }, - { - "mode": { - "type": "string", - "description": "Selects the mode of Umicollapse - either fastq or bam need to be provided.\n", - "pattern": "{fastq,bam}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with deduplicated UMIs.", - "pattern": "*.{bam}" - } - }, - { - "log": { - "type": "file", - "description": "A log file with the deduplication statistics.", - "pattern": "*_{UMICollapse.log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "file", + "description": "Input bam file", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input.\n", + "pattern": "*.{bai}" + } + } + ], + [ + { + "mode": { + "type": "string", + "description": "Selects the mode of Umicollapse - either fastq or bam need to be provided.\n", + "pattern": "{fastq,bam}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "BAM file with deduplicated UMIs.", + "pattern": "*.{bam}" + } + } + ] + }, + { + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*dedup*fastq.gz": { + "type": "file", + "description": "FASTQ file with deduplicated UMIs.", + "pattern": "*dedup*fastq.gz" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\n e.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_UMICollapse.log": { + "type": "file", + "description": "A log file with the deduplication statistics.", + "pattern": "*_{UMICollapse.log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137739,86 +176445,139 @@ "documentation": "https://umi-tools.readthedocs.io/en/latest/", "license": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing reads to be deduplicated via UMIs.\n", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index files corresponding to the input BAM file.\n", - "pattern": "*.{bai}" - } - }, - { - "get_output_stats": { - "type": "boolean", - "description": "Whether or not to generate output stats.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file with deduplicated UMIs.", - "pattern": "*.{bam}" - } - }, - { - "log": { - "type": "file", - "description": "File with logging information", - "pattern": "*.{log}" - } - }, - { - "tsv_edit_distance": { - "type": "file", - "description": "Reports the (binned) average edit distance between the UMIs at each position.", - "pattern": "*edit_distance.tsv" - } - }, - { - "tsv_per_umi": { - "type": "file", - "description": "UMI-level summary statistics.", - "pattern": "*per_umi.tsv" - } - }, - { - "tsv_umi_per_position": { - "type": "file", - "description": "Tabulates the counts for unique combinations of UMI and position.", - "pattern": "*per_position.tsv" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing reads to be deduplicated via UMIs.\n", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index files corresponding to the input BAM file.\n", + "pattern": "*.{bai}" + } + } + ], + [ + { + "get_output_stats": { + "type": "boolean", + "description": "Whether or not to generate output stats.\n" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "BAM file with deduplicated UMIs.", + "pattern": "*.{bam}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File with logging information", + "pattern": "*.{log}" + } + } + ] + }, + { + "tsv_edit_distance": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*edit_distance.tsv": { + "type": "file", + "description": "Reports the (binned) average edit distance between the UMIs at each position.", + "pattern": "*edit_distance.tsv" + } + } + ] + }, + { + "tsv_per_umi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*per_umi.tsv": { + "type": "file", + "description": "UMI-level summary statistics.", + "pattern": "*per_umi.tsv" + } + } + ] + }, + { + "tsv_umi_per_position": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*per_position.tsv": { + "type": "file", + "description": "Tabulates the counts for unique combinations of UMI and position.", + "pattern": "*per_position.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137873,51 +176632,72 @@ "umi_tools": { "description": "UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes\n", "documentation": "https://umi-tools.readthedocs.io/en/latest/", - "license": "MIT" - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "list", - "description": "List of input FASTQ files whose UMIs will be extracted.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", - "pattern": "*.{fastq.gz}" - } - }, - { - "log": { - "type": "file", - "description": "Logfile for umi_tools", - "pattern": "*.{log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "license": "MIT", + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "list", + "description": "List of input FASTQ files whose UMIs will be extracted.\n" + } + } + ] + ], + "output": [ + { + "reads": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq.gz": { + "type": "file", + "description": "Extracted FASTQ files. | For single-end reads, pattern is \\${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \\${prefix}.umi_extract_{1,2}.fastq.gz.\n", + "pattern": "*.{fastq.gz}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Logfile for umi_tools", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -137977,71 +176757,113 @@ "documentation": "https://umi-tools.readthedocs.io/en/latest/", "license": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing reads to be deduplicated via UMIs.\n", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index files corresponding to the input BAM file.\n", - "pattern": "*.{bai}" - } - }, - { - "create_bam": { - "type": "boolean", - "description": "Whether or not to create a read group tagged BAM file.\n" - } - }, - { - "get_group_info": { - "type": "boolean", - "description": "Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "a read group tagged BAM file.", - "pattern": "${prefix}.{bam}" - } - }, - { - "log": { - "type": "file", - "description": "File with logging information", - "pattern": "*.{log}" - } - }, - { - "tsv": { - "type": "file", - "description": "Flatfile describing the read groups, see docs for complete info of all columns", - "pattern": "*.{tsv}" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing reads to be deduplicated via UMIs.\n", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index files corresponding to the input BAM file.\n", + "pattern": "*.{bai}" + } + } + ], + [ + { + "create_bam": { + "type": "boolean", + "description": "Whether or not to create a read group tagged BAM file.\n" + } + } + ], + [ + { + "get_group_info": { + "type": "boolean", + "description": "Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns\n" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File with logging information", + "pattern": "*.{log}" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.bam": { + "type": "file", + "description": "a read group tagged BAM file.", + "pattern": "${prefix}.{bam}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Flatfile describing the read groups, see docs for complete info of all columns", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138072,59 +176894,80 @@ "documentation": "https://umi-tools.readthedocs.io/en/latest/", "license": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file containing reads to be deduplicated via UMIs.\n", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index files corresponding to the input BAM file.\n", - "pattern": "*.{bai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Prepared BAM file.", - "pattern": "*.{bam}" - } - }, - { - "log": { - "type": "file", - "description": "File with logging information", - "pattern": "*.{log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file containing reads to be deduplicated via UMIs.\n", + "pattern": "*.{bam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index files corresponding to the input BAM file.\n", + "pattern": "*.{bai}" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Prepared BAM file.", + "pattern": "*.{bam}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "File with logging information", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138170,77 +177013,101 @@ "doi": "10.1371/journal.pcbi.1005595", "licence": [ "GPL v3" - ] - } + ], + "identifier": "biotools:unicycler" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "shortreads": { + "type": "file", + "description": "List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + }, + { + "longreads": { + "type": "file", + "description": "List of input FastQ files of size 1, PacBio or Nanopore long reads.\n" + } + } + ] + ], + "output": [ + { + "scaffolds": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.scaffolds.fa.gz": { + "type": "file", + "description": "Fasta file containing scaffolds", + "pattern": "*.{scaffolds.fa.gz}" + } + } + ] + }, + { + "gfa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.assembly.gfa.gz": { + "type": "file", + "description": "gfa file containing assembly", + "pattern": "*.{assembly.gfa.gz}" + } + } + ] + }, + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "unicycler log file", + "pattern": "*.{log}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "shortreads": { - "type": "file", - "description": "List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "longreads": { - "type": "file", - "description": "List of input FastQ files of size 1, PacBio or Nanopore long reads.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "scaffolds": { - "type": "file", - "description": "Fasta file containing scaffolds", - "pattern": "*.{scaffolds.fa.gz}" - } - }, - { - "gfa": { - "type": "file", - "description": "gfa file containing assembly", - "pattern": "*.{assembly.gfa.gz}" - } - }, - { - "log": { - "type": "file", - "description": "unicycler log file", - "pattern": "*.{log}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@JoseEspinosa", - "@drpatelh", - "@d4straub" + "authors": [ + "@JoseEspinosa", + "@drpatelh", + "@d4straub" ], "maintainers": [ "@JoseEspinosa", @@ -138280,39 +177147,65 @@ "doi": "10.1101/2021.01.19.427209", "licence": [ "GPL-3.0-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "FASTQ or FASTQ.GZ file, list of 2 files for paired-end data", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" - } - } - ], - "output": [ - { - "outs": { - "type": "file", - "description": "Files containing the outputs of Cell Ranger", - "pattern": "sample-${meta.id}/outs/*" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software version", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:universc" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "FASTQ or FASTQ.GZ file, list of 2 files for paired-end data", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } + } + ], + [ + { + "reference": { + "type": "file", + "description": "Reference genome file" + } + } + ] + ], + "output": [ + { + "outs": [ + { + "meta": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger", + "pattern": "sample-${meta.id}/outs/*" + } + }, + { + "sample-${meta.id}/outs/*": { + "type": "file", + "description": "Files containing the outputs of Cell Ranger", + "pattern": "sample-${meta.id}/outs/*" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software version", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138350,45 +177243,56 @@ "documentation": "https://www.gnu.org/software/tar/manual/", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "archive": { - "type": "file", - "description": "File to be untar", - "pattern": "*.{tar}.{gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "archive": { + "type": "file", + "description": "File to be untar", + "pattern": "*.{tar}.{gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "untar": { - "type": "directory", - "description": "Directory containing contents of archive", - "pattern": "*/" - } + "untar": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "$prefix": { + "type": "directory", + "description": "Directory containing contents of archive", + "pattern": "*/" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138550,45 +177454,56 @@ "documentation": "https://www.gnu.org/software/tar/manual/", "licence": [ "GPL-3.0-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "archive": { - "type": "file", - "description": "File to be untar", - "pattern": "*.{tar}.{gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "archive": { + "type": "file", + "description": "File to be untar", + "pattern": "*.{tar}.{gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files": { - "type": "string", - "description": "A list containing references to individual archive files", - "pattern": "*/**" - } + "files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/**": { + "type": "string", + "description": "A list containing references to individual archive files", + "pattern": "*/**" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138635,45 +177550,56 @@ "tool_dev_url": "https://sourceforge.net/projects/p7zip\"", "licence": [ "LGPL-2.1-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "archive": { - "type": "file", - "description": "ZIP file", - "pattern": "*.zip" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "archive": { + "type": "file", + "description": "ZIP file", + "pattern": "*.zip" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "unzipped_archive": { - "type": "directory", - "description": "Directory contents of the unzipped archive", - "pattern": "${archive.baseName}/" - } + "unzipped_archive": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/": { + "type": "directory", + "description": "Directory contents of the unzipped archive", + "pattern": "${archive.baseName}/" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138724,45 +177650,56 @@ "tool_dev_url": "https://sourceforge.net/projects/p7zip\"", "licence": [ "LGPL-2.1-or-later" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "archive": { - "type": "file", - "description": "ZIP file", - "pattern": "*.zip" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "archive": { + "type": "file", + "description": "ZIP file", + "pattern": "*.zip" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files": { - "type": "list", - "description": "A list containing references to individual archive files", - "pattern": "*/**" - } + "files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}/**": { + "type": "list", + "description": "A list containing references to individual archive files", + "pattern": "*/**" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138796,45 +177733,56 @@ "tool_dev_url": "https://github.com/bjhall/upd", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": "BED file", + "pattern": "*.{bed}" + } + } + ] }, { - "bed": { - "type": "file", - "description": "BED file", - "pattern": "*.{bed}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138874,64 +177822,79 @@ "doi": "10.1093/bioinformatics/btad007", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input sequences in FASTA format", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" - } - }, - { - "tree": { - "type": "file", - "description": "Input guide tree in Newick format", - "pattern": "*.{dnd}" - } - }, - { - "compress": { - "type": "boolean", - "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" - } - }, - { - "alignment": { - "type": "file", - "description": "Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false", - "pattern": "*.aln{.gz,}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input sequences in FASTA format", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing tree information\ne.g. `[ id:'test_tree']`\n" + } + }, + { + "tree": { + "type": "file", + "description": "Input guide tree in Newick format", + "pattern": "*.{dnd}" + } + } + ], + [ + { + "compress": { + "type": "boolean", + "description": "Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression." + } + } + ] + ], + "output": [ + { + "alignment": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test']`\n" + } + }, + { + "*.aln{.gz,}": { + "type": "file", + "description": "Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false", + "pattern": "*.aln{.gz,}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -138972,85 +177935,100 @@ "doi": "10.1093/nar/gkw227 ", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bams": { - "type": "file", - "description": "One or two BAM files. Supply two BAM files to run Vardict in paired mode.", - "pattern": "*.bam" - } - }, - { - "bais": { - "type": "file", - "description": "Index/indices of the BAM file(s)", - "pattern": "*.bai" - } - }, - { - "bed": { - "type": "file", - "description": "BED with the regions of interest", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA of the reference genome", - "pattern": "*.{fa,fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the FASTA of the reference genome", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file output", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bams": { + "type": "file", + "description": "One or two BAM files. Supply two BAM files to run Vardict in paired mode.", + "pattern": "*.bam" + } + }, + { + "bais": { + "type": "file", + "description": "Index/indices of the BAM file(s)", + "pattern": "*.bai" + } + }, + { + "bed": { + "type": "file", + "description": "BED with the regions of interest", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA of the reference genome", + "pattern": "*.{fa,fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing fasta information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the FASTA of the reference genome", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "VCF file output", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139086,45 +178064,56 @@ "doi": "10.1093/bioinformatics/btw111", "licence": [ "Apache-2.0" - ] + ], + "identifier": "biotools:variantbam" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM file", + "pattern": "*.{bam,cram}" + } } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM file", - "pattern": "*.{bam,cram}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Filtered or downsampled BAM file", + "pattern": "*.{bam}" + } + } + ] }, { - "bam": { - "type": "file", - "description": "Filtered or downsampled BAM file", - "pattern": "*.{bam}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139157,87 +178146,131 @@ "doi": "10.1186/s13059-020-01993-6", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "normal_vcf": { - "type": "file", - "description": "Sorted VCF/BCF file (list)", - "pattern": "*.{bcf,vcf,vcf.gz}" - } - }, - { - "tumor_vcf": { - "type": "file", - "description": "Sorted VCF/BCF file (optional)", - "pattern": "*.{bcf,bcf.gz,vcf,vcf.gz}" - } - }, - { - "scenario": { - "type": "file", - "description": "Yaml file containing scenario information (optional)", - "pattern": "*.{yml,yaml}" - } - }, - { - "scenario_sample": { - "type": "string", - "description": "(List of) sample name(s) to be processed as named in the scenario yml (optional)", - "pattern": "*.{bcf,vcf,vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf_gz": { - "type": "file", - "description": "Compressed VCF file containing sample observations", - "pattern": "*.vcf.gz" - } - }, - { - "bcf_gz": { - "type": "file", - "description": "BCF file containing sample observations", - "pattern": "*.bcf.gz" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file containing sample observations", - "pattern": "*.vcf" - } - }, - { - "bcf": { - "type": "file", - "description": "BCF file containing sample observations", - "pattern": "*.bcf" - } + ], + "identifier": "biotools:varlociraptor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "normal_vcf": { + "type": "file", + "description": "Sorted VCF/BCF file (list)", + "pattern": "*.{bcf,vcf,vcf.gz}" + } + }, + { + "tumor_vcf": { + "type": "file", + "description": "Sorted VCF/BCF file (optional)", + "pattern": "*.{bcf,bcf.gz,vcf,vcf.gz}" + } + } + ], + [ + { + "scenario": { + "type": "file", + "description": "Yaml file containing scenario information (optional)", + "pattern": "*.{yml,yaml}" + } + } + ], + [ + { + "scenario_sample_name": { + "type": "string", + "description": "Sample name for the scenario" + } + } + ] + ], + "output": [ + { + "bcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf.gz": { + "type": "file", + "description": "BCF file containing sample observations", + "pattern": "*.bcf.gz" + } + } + ] + }, + { + "vcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file containing sample observations", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "bcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "BCF file containing sample observations", + "pattern": "*.bcf" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF file containing sample observations", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139270,71 +178303,86 @@ "doi": "10.1186/s13059-020-01993-6", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference index information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fai": { - "type": "file", - "description": "Index for reference fasta file (must be with samtools index)", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "alignment_properties_json": { - "type": "file", - "description": "File containing alignment properties", - "pattern": "*.alignment-properties.json" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:varlociraptor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference index information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index for reference fasta file (must be with samtools index)", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "alignment_properties_json": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.alignment-properties.json": { + "type": "file", + "description": "File containing alignment properties", + "pattern": "*.alignment-properties.json" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139367,221 +178415,292 @@ "doi": "10.1186/s13059-020-01993-6", "licence": [ "GPL v3" - ] - } + ], + "identifier": "biotools:varlociraptor" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "Index of the BAM/CRAM/SAM file", + "pattern": "*.{bai,crai,sai}" + } + }, + { + "candidates": { + "type": "file", + "description": "Sorted BCF/VCF file", + "pattern": "*.{bcf,vcf,vcf.gz}" + } + }, + { + "alignment_json": { + "type": "file", + "description": "File containing alignment properties obtained with varlociraptor/estimatealignmentproperties", + "pattern": "*.json" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Reference fasta file", + "pattern": "*.{fasta}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference index information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fai": { + "type": "file", + "description": "Index for reference fasta file (must be with samtools index)", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "bcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf.gz": { + "type": "file", + "description": "BCF file containing sample observations", + "pattern": "*.bcf.gz" + } + } + ] + }, + { + "vcf_gz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file containing sample observations", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "bcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "BCF file containing sample observations", + "pattern": "*.bcf" + } + } + ] + }, + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "VCF file containing sample observations", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "candidates": { - "type": "file", - "description": "Sorted BCF/VCF file", - "pattern": "*.{bcf,vcf,vcf.gz}" - } - }, - { - "alignment_json": { - "type": "file", - "description": "File containing alignment properties obtained with varlociraptor/estimatealignmentproperties", - "pattern": "*.json" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference fasta file", - "pattern": "*.{fasta}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference index information\ne.g. [ id:'test', single_end:false ]\n" - } - }, + "authors": [ + "@FriederikeHanssen" + ], + "maintainers": [ + "@FriederikeHanssen" + ] + } + }, + { + "name": "vcf2cytosure", + "path": "modules/nf-core/vcf2cytosure/meta.yml", + "type": "module", + "meta": { + "name": "vcf2cytosure", + "description": "Convert VCF with structural variations to CytoSure format", + "keywords": [ + "structural_variants", + "array_cgh", + "vcf", + "cytosure" + ], + "tools": [ { - "fai": { - "type": "file", - "description": "Index for reference fasta file (must be with samtools index)", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf_gz": { - "type": "file", - "description": "Compressed VCF file containing sample observations", - "pattern": "*.vcf.gz" - } - }, - { - "bcf_gz": { - "type": "file", - "description": "BCF file containing sample observations", - "pattern": "*.bcf.gz" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file containing sample observations", - "pattern": "*.vcf" - } - }, - { - "bcf": { - "type": "file", - "description": "BCF file containing sample observations", - "pattern": "*.bcf" - } - } - ], - "authors": [ - "@FriederikeHanssen" - ], - "maintainers": [ - "@FriederikeHanssen" - ] - } - }, - { - "name": "vcf2cytosure", - "path": "modules/nf-core/vcf2cytosure/meta.yml", - "type": "module", - "meta": { - "name": "vcf2cytosure", - "description": "Convert VCF with structural variations to CytoSure format", - "keywords": [ - "structural_variants", - "array_cgh", - "vcf", - "cytosure" - ], - "tools": [ - { - "vcf2cytosure": { - "description": "Convert VCF with structural variations to CytoSure format", - "homepage": "https://github.com/NBISweden/vcf2cytosure", - "documentation": "https://github.com/NBISweden/vcf2cytosure", - "tool_dev_url": "https://github.com/NBISweden/vcf2cytosure", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "meta4": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "sv_vcf": { - "type": "file", - "description": "VCF file with structural variants", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "coverage_bed": { - "type": "file", - "description": "Bed file with coverage data", - "pattern": "*.bed" - } - }, - { - "cns": { - "type": "file", - "description": "CN file from CNVkit, not compatible with coverage_bed file" - } - }, - { - "snv_vcf": { - "type": "file", - "description": "VCF file with SNVs to calculate probe coverage,\nnot compatible with coverage_bed\npattern: \"*.{vcf,vcf.gz}\"\n" - } - }, - { - "blacklist_bed": { - "type": "file", - "description": "Bed file with regions to exclude", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "cgh": { - "type": "file", - "description": "SV:s in CytoSure format", - "pattern": "*.cgh" - } + "vcf2cytosure": { + "description": "Convert VCF with structural variations to CytoSure format", + "homepage": "https://github.com/NBISweden/vcf2cytosure", + "documentation": "https://github.com/NBISweden/vcf2cytosure", + "tool_dev_url": "https://github.com/NBISweden/vcf2cytosure", + "licence": [ + "MIT" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "sv_vcf": { + "type": "file", + "description": "VCF file with structural variants", + "pattern": "*.{vcf,vcf.gz}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "coverage_bed": { + "type": "file", + "description": "Bed file with coverage data", + "pattern": "*.bed" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "cns": { + "type": "file", + "description": "CN file from CNVkit, not compatible with coverage_bed file" + } + } + ], + [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "snv_vcf": { + "type": "file", + "description": "VCF file with SNVs to calculate probe coverage,\nnot compatible with coverage_bed\npattern: \"*.{vcf,vcf.gz}\"\n" + } + } + ], + [ + { + "blacklist_bed": { + "type": "file", + "description": "Bed file with regions to exclude", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "cgh": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.cgh": { + "type": "file", + "description": "SV:s in CytoSure format", + "pattern": "*.cgh" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139616,52 +178735,63 @@ "tool_dev_url": "https://github.com/quinlan-lab/vcf2db", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "ped": { - "type": "file", - "description": "PED file", - "pattern": "*.ped" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "db": { - "type": "file", - "description": "Gemini-compatible database file", - "pattern": "*.db" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.vcf.gz" + } + }, + { + "ped": { + "type": "file", + "description": "PED file", + "pattern": "*.ped" + } + } + ] + ], + "output": [ + { + "db": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.db": { + "type": "file", + "description": "Gemini-compatible database file", + "pattern": "*.db" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139694,50 +178824,71 @@ "doi": "10.5281/zenodo.593251", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf to convert to MAF format. Must be uncompressed.\n" - } - }, - { - "vep_cache": { - "type": "file", - "description": "Path to VEP cache dir. Required for correct running of VEP.\n" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "maf": { - "type": "file", - "description": "MAF file produced from VCF", - "pattern": "*.maf" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "vcf to convert to MAF format. Must be uncompressed.\n" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Path to reference genome fasta file.\n" + } + } + ], + [ + { + "vep_cache": { + "type": "file", + "description": "Path to VEP cache dir. Required for correct running of VEP.\n" + } + } + ] + ], + "output": [ + { + "maf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.maf": { + "type": "file", + "description": "MAF file produced from VCF", + "pattern": "*.maf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139772,78 +178923,95 @@ "doi": "10.1186/s13059-016-0973-5", "license": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "query VCF file", - "pattern": "*.{vcf, vcf.gz}" - } - }, - { - "vcf_tabix": { - "type": "file", - "description": "tabix index of query VCF - only needed if vcf is compressed", - "pattern": "*.vcf.gz.tbi" - } - }, - { - "specific_resources": { - "type": "map", - "description": "A list of sample specific reference files defined in toml config, must also include indices if bgzipped." - } - }, - { - "toml": { - "type": "file", - "description": "configuration file with reference file basenames", - "pattern": "*.toml" - } - }, - { - "lua": { - "type": "file", - "description": "Lua file for custom annotations", - "pattern": "*.lua" - } - }, - { - "resources": { - "type": "map", - "description": "List of reference files defined in toml config, must also include indices if bgzipped." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Annotated VCF file", - "pattern": "*.vcf" - } + ], + "identifier": "biotools:vcfanno" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "query VCF file", + "pattern": "*.{vcf, vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "tabix index file for the query VCF", + "pattern": "*.tbi" + } + }, + { + "specific_resources": { + "type": "map", + "description": "A list of sample specific reference files defined in toml config, must also include indices if bgzipped." + } + } + ], + [ + { + "toml": { + "type": "file", + "description": "configuration file with reference file basenames", + "pattern": "*.toml" + } + } + ], + [ + { + "lua": { + "type": "file", + "description": "Lua file for custom annotations", + "pattern": "*.lua" + } + } + ], + [ + { + "resources": { + "type": "map", + "description": "List of reference files defined in toml config, must also include indices if bgzipped." + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Annotated VCF file", + "pattern": "*.vcf" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -139871,823 +179039,1492 @@ "description": "If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields", "keywords": [ "vcflib", - "vcfbreakmulti", - "allele-specific" - ], - "tools": [ - { - "vcflib": { - "description": "Command-line tools for manipulating VCF files", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib#USAGE", - "doi": "10.1101/2021.05.21.445151", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.{.vcf.gz,vcf}" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - } - ], - "authors": [ - "@lucpen" - ], - "maintainers": [ - "@lucpen" - ] - } - }, - { - "name": "vcflib_vcffilter", - "path": "modules/nf-core/vcflib/vcffilter/meta.yml", - "type": "module", - "meta": { - "name": "vcflib_vcffilter", - "description": "Command line tools for parsing and manipulating VCF files.", - "keywords": [ - "filter", - "variant", - "vcf", - "quality" - ], - "tools": [ - { - "vcflib": { - "description": "Command line tools for parsing and manipulating VCF files.", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib", - "tool_dev_url": "https://github.com/vcflib/vcflib", - "doi": "10.1371/journal.pcbi.1009123", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test_sample_1' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "VCF file", - "pattern": "*.{vcf,vcf.gz}" - } - }, - { - "tbi": { - "type": "file", - "description": "Index file", - "pattern": "*.{tbi}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Filtered VCF file", - "pattern": "*.{vcf.gz}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - } - ], - "authors": [ - "@zachary-foster" - ], - "maintainers": [ - "@zachary-foster" - ] - }, - "pipelines": [ - { - "name": "pathogensurveillance", - "version": "dev" - } - ] - }, - { - "name": "vcflib_vcffixup", - "path": "modules/nf-core/vcflib/vcffixup/meta.yml", - "type": "module", - "meta": { - "name": "vcflib_vcffixup", - "description": "Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.", - "keywords": [ - "vcf", - "vcflib", - "vcflib/vcffixup", - "AC/NS/AF" - ], - "tools": [ - { - "vcflib": { - "description": "Command-line tools for manipulating VCF files", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib#USAGE", - "doi": "10.1101/2021.05.21.445151", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.{.vcf.gz,vcf}" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - } - ], - "authors": [ - "@atrigila" - ], - "maintainers": [ - "@atrigila" - ] - }, - "pipelines": [ - { - "name": "phaseimpute", - "version": "dev" - } - ] - }, - { - "name": "vcflib_vcfuniq", - "path": "modules/nf-core/vcflib/vcfuniq/meta.yml", - "type": "module", - "meta": { - "name": "vcflib_vcfuniq", - "description": "List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record.", - "keywords": [ - "vcf", - "uniq", - "deduplicate" - ], - "tools": [ - { - "vcflib": { - "description": "Command-line tools for manipulating VCF files", - "homepage": "https://github.com/vcflib/vcflib", - "documentation": "https://github.com/vcflib/vcflib#USAGE", - "doi": "10.1101/2021.05.21.445151", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of VCF file", - "pattern": "*.vcf.gz.tbi" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - } - ], - "authors": [ - "@drpatelh" - ], - "maintainers": [ - "@drpatelh" - ] - }, - "pipelines": [ - { - "name": "viralrecon", - "version": "2.6.0" - } - ] - }, - { - "name": "vcftools", - "path": "modules/nf-core/vcftools/meta.yml", - "type": "module", - "meta": { - "name": "vcftools", - "description": "A set of tools written in Perl and C++ for working with VCF files", - "keywords": [ - "VCFtools", - "VCF", - "sort" - ], - "tools": [ - { - "vcftools": { - "description": "A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries", - "homepage": "http://vcftools.sourceforge.net/", - "documentation": "http://vcftools.sourceforge.net/man_latest.html", - "licence": [ - "LGPL" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "variant_file": { - "type": "file", - "description": "variant input file which can be vcf, vcf.gz, or bcf format." - } - }, - { - "bed": { - "type": "file", - "description": "bed file which can be used with different arguments in vcftools (optional)" - } - }, - { - "diff_variant_file": { - "type": "file", - "description": "secondary variant file which can be used with the 'diff' suite of tools (optional)" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "vcf file (optional)", - "pattern": "*.vcf" - } - }, - { - "bcf": { - "type": "file", - "description": "bcf file (optional)", - "pattern": "*.bcf" - } - }, - { - "frq": { - "type": "file", - "description": "Allele frequency for each site (optional)", - "pattern": "*.frq" - } - }, - { - "frq_count": { - "type": "file", - "description": "Allele counts for each site (optional)", - "pattern": "*.frq.count" - } - }, - { - "idepth": { - "type": "file", - "description": "mean depth per individual (optional)", - "pattern": "*.idepth" - } - }, - { - "ldepth": { - "type": "file", - "description": "depth per site summed across individuals (optional)", - "pattern": "*.ildepth" - } - }, - { - "ldepth_mean": { - "type": "file", - "description": "mean depth per site calculated across individuals (optional)", - "pattern": "*.ldepth.mean" - } - }, - { - "gdepth": { - "type": "file", - "description": "depth for each genotype in vcf file (optional)", - "pattern": "*.gdepth" - } - }, - { - "hap_ld": { - "type": "file", - "description": "r2, D, and D’ statistics using phased haplotypes (optional)", - "pattern": "*.hap.ld" - } - }, - { - "geno_ld": { - "type": "file", - "description": "squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional)", - "pattern": "*.geno.ld" - } - }, - { - "geno_chisq": { - "type": "file", - "description": "test for genotype independence via the chi-squared statistic (optional)", - "pattern": "*.geno.chisq" - } - }, - { - "list_hap_ld": { - "type": "file", - "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", - "pattern": "*.list.hap.ld" - } - }, - { - "list_geno_ld": { - "type": "file", - "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", - "pattern": "*.list.geno.ld" - } - }, - { - "interchrom_hap_ld": { - "type": "file", - "description": "r2 statistics for sites (haplotypes) on different chromosomes (optional)", - "pattern": "*.interchrom.hap.ld" - } - }, - { - "interchrom_geno_ld": { - "type": "file", - "description": "r2 statistics for sites (genotypes) on different chromosomes (optional)", - "pattern": "*.interchrom.geno.ld" - } - }, - { - "tstv": { - "type": "file", - "description": "Transition / Transversion ratio in bins of size defined in options (optional)", - "pattern": "*.TsTv" - } - }, - { - "tstv_summary": { - "type": "file", - "description": "Summary of all Transitions and Transversions (optional)", - "pattern": "*.TsTv.summary" - } - }, - { - "tstv_count": { - "type": "file", - "description": "Transition / Transversion ratio as a function of alternative allele count (optional)", - "pattern": "*.TsTv.count" - } - }, - { - "tstv_qual": { - "type": "file", - "description": "Transition / Transversion ratio as a function of SNP quality threshold (optional)", - "pattern": "*.TsTv.qual" - } - }, - { - "filter_summary": { - "type": "file", - "description": "Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)", - "pattern": "*.FILTER.summary" - } - }, - { - "sites_pi": { - "type": "file", - "description": "Nucleotide divergency on a per-site basis (optional)", - "pattern": "*.sites.pi" - } - }, - { - "windowed_pi": { - "type": "file", - "description": "Nucleotide diversity in windows, with window size determined by options (optional)", - "pattern": "*windowed.pi" - } - }, - { - "weir_fst": { - "type": "file", - "description": "Fst estimate from Weir and Cockerham’s 1984 paper (optional)", - "pattern": "*.weir.fst" - } - }, - { - "heterozygosity": { - "type": "file", - "description": "Heterozygosity on a per-individual basis (optional)", - "pattern": "*.het" - } - }, - { - "hwe": { - "type": "file", - "description": "Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)", - "pattern": "*.hwe" - } - }, - { - "tajima_d": { - "type": "file", - "description": "Tajima’s D statistic in bins with size of the specified number in options (optional)", - "pattern": "*.Tajima.D" - } - }, - { - "freq_burden": { - "type": "file", - "description": "Number of variants within each individual of a specific frequency in options (optional)", - "pattern": "*.ifreqburden" - } - }, - { - "lroh": { - "type": "file", - "description": "Long Runs of Homozygosity (optional)", - "pattern": "*.LROH" - } - }, - { - "relatedness": { - "type": "file", - "description": "Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)", - "pattern": "*.relatedness" - } - }, - { - "relatedness2": { - "type": "file", - "description": "Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)", - "pattern": "*.relatedness2" - } - }, - { - "lqual": { - "type": "file", - "description": "per-site SNP quality (optional)", - "pattern": "*.lqual" - } - }, - { - "missing_individual": { - "type": "file", - "description": "Missingness on a per-individual basis (optional)", - "pattern": "*.imiss" - } - }, - { - "missing_site": { - "type": "file", - "description": "Missingness on a per-site basis (optional)", - "pattern": "*.lmiss" - } - }, - { - "snp_density": { - "type": "file", - "description": "Number and density of SNPs in bins of size defined by option (optional)", - "pattern": "*.snpden" - } - }, - { - "kept_sites": { - "type": "file", - "description": "All sites that have been kept after filtering (optional)", - "pattern": "*.kept.sites" - } - }, - { - "removed_sites": { - "type": "file", - "description": "All sites that have been removed after filtering (optional)", - "pattern": "*.removed.sites" - } - }, - { - "singeltons": { - "type": "file", - "description": "Location of singletons, and the individual they occur in (optional)", - "pattern": "*.singeltons" - } - }, - { - "indel_hist": { - "type": "file", - "description": "Histogram file of the length of all indels (including SNPs) (optional)", - "pattern": "*.indel_hist" - } - }, - { - "hapcount": { - "type": "file", - "description": "Unique haplotypes within user specified bins (optional)", - "pattern": "*.hapcount" - } - }, - { - "mendel": { - "type": "file", - "description": "Mendel errors identified in trios (optional)", - "pattern": "*.mendel" - } - }, - { - "format": { - "type": "file", - "description": "Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional)", - "pattern": "*.FORMAT" - } - }, - { - "info": { - "type": "file", - "description": "Extracted information from the INFO field in the VCF file (optional)", - "pattern": "*.INFO" - } - }, - { - "genotypes_matrix": { - "type": "file", - "description": "Genotypes output as large matrix.\nGenotypes of each individual on a separate line.\nGenotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.\nMissing genotypes are represented by -1 (optional)\n", - "pattern": "*.012" - } - }, - { - "genotypes_matrix_individual": { - "type": "file", - "description": "Details the individuals included in the main genotypes_matrix file (optional)", - "pattern": "*.012.indv" - } - }, - { - "genotypes_matrix_position": { - "type": "file", - "description": "Details the site locations included in the main genotypes_matrix file (optional)", - "pattern": "*.012.pos" - } - }, - { - "impute_hap": { - "type": "file", - "description": "Phased haplotypes in IMPUTE reference-panel format (optional)", - "pattern": "*.impute.hap" - } - }, - { - "impute_hap_legend": { - "type": "file", - "description": "Impute haplotype legend file (optional)", - "pattern": "*.impute.hap.legend" - } - }, - { - "impute_hap_indv": { - "type": "file", - "description": "Impute haplotype individuals file (optional)", - "pattern": "*.impute.hap.indv" - } - }, - { - "ldhat_sites": { - "type": "file", - "description": "Output data in LDhat format, sites (optional)", - "pattern": "*.ldhat.sites" - } - }, - { - "ldhat_locs": { - "type": "file", - "description": "output data in LDhat format, locations (optional)", - "pattern": "*.ldhat.locs" - } - }, - { - "beagle_gl": { - "type": "file", - "description": "Genotype likelihoods for biallelic sites (optional)", - "pattern": "*.BEAGLE.GL" - } - }, - { - "beagle_pl": { - "type": "file", - "description": "Genotype likelihoods for biallelic sites (optional)", - "pattern": "*.BEAGLE.PL" - } - }, - { - "ped": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.ped" - } - }, - { - "map_": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.map" - } - }, - { - "tped": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.tped" - } - }, - { - "tfam": { - "type": "file", - "description": "output the genotype data in PLINK PED format (optional)", - "pattern": "*.tfam" - } - }, - { - "diff_sites_in_files": { - "type": "file", - "description": "Sites that are common / unique to each file specified in optional inputs (optional)", - "pattern": "*.diff.sites.in.files" - } - }, + "vcfbreakmulti", + "allele-specific" + ], + "tools": [ { - "diff_indv_in_files": { - "type": "file", - "description": "Individuals that are common / unique to each file specified in optional inputs (optional)", - "pattern": "*.diff.indv.in.files" - } - }, + "vcflib": { + "description": "Command-line tools for manipulating VCF files", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib#USAGE", + "doi": "10.1101/2021.05.21.445151", + "licence": [ + "MIT" + ], + "identifier": "biotools:vcflib" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.{.vcf.gz,vcf}" + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@lucpen" + ], + "maintainers": [ + "@lucpen" + ] + } + }, + { + "name": "vcflib_vcffilter", + "path": "modules/nf-core/vcflib/vcffilter/meta.yml", + "type": "module", + "meta": { + "name": "vcflib_vcffilter", + "description": "Command line tools for parsing and manipulating VCF files.", + "keywords": [ + "filter", + "variant", + "vcf", + "quality" + ], + "tools": [ { - "diff_sites": { - "type": "file", - "description": "Discordance on a site by site basis, specified in optional inputs (optional)", - "pattern": "*.diff.sites" - } - }, + "vcflib": { + "description": "Command line tools for parsing and manipulating VCF files.", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib", + "tool_dev_url": "https://github.com/vcflib/vcflib", + "doi": "10.1371/journal.pcbi.1009123", + "licence": [ + "MIT" + ], + "identifier": "biotools:vcflib" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test_sample_1' ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "VCF file", + "pattern": "*.{vcf,vcf.gz}" + } + }, + { + "tbi": { + "type": "file", + "description": "Index file", + "pattern": "*.{tbi}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Filtered VCF file", + "pattern": "*.{vcf.gz}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@zachary-foster" + ], + "maintainers": [ + "@zachary-foster" + ] + }, + "pipelines": [ + { + "name": "pathogensurveillance", + "version": "dev" + } + ] + }, + { + "name": "vcflib_vcffixup", + "path": "modules/nf-core/vcflib/vcffixup/meta.yml", + "type": "module", + "meta": { + "name": "vcflib_vcffixup", + "description": "Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.", + "keywords": [ + "vcf", + "vcflib", + "vcflib/vcffixup", + "AC/NS/AF" + ], + "tools": [ { - "diff_indv": { - "type": "file", - "description": "Discordance on a individual by individual basis, specified in optional inputs (optional)", - "pattern": "*.diff.indv" - } - }, + "vcflib": { + "description": "Command-line tools for manipulating VCF files", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib#USAGE", + "doi": "10.1101/2021.05.21.445151", + "licence": [ + "MIT" + ], + "identifier": "biotools:vcflib" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.{.vcf.gz,vcf}" + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@atrigila" + ], + "maintainers": [ + "@atrigila" + ] + }, + "pipelines": [ + { + "name": "phaseimpute", + "version": "dev" + } + ] + }, + { + "name": "vcflib_vcfuniq", + "path": "modules/nf-core/vcflib/vcfuniq/meta.yml", + "type": "module", + "meta": { + "name": "vcflib_vcfuniq", + "description": "List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record.", + "keywords": [ + "vcf", + "uniq", + "deduplicate" + ], + "tools": [ { - "diff_discd_matrix": { - "type": "file", - "description": "Discordance matrix between files specified in optional inputs (optional)", - "pattern": "*.diff.discordance.matrix" - } - }, + "vcflib": { + "description": "Command-line tools for manipulating VCF files", + "homepage": "https://github.com/vcflib/vcflib", + "documentation": "https://github.com/vcflib/vcflib#USAGE", + "doi": "10.1101/2021.05.21.445151", + "licence": [ + "MIT" + ], + "identifier": "biotools:vcflib" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vcf": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + }, + { + "tbi": { + "type": "file", + "description": "Index of VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@drpatelh" + ], + "maintainers": [ + "@drpatelh" + ] + }, + "pipelines": [ + { + "name": "viralrecon", + "version": "2.6.0" + } + ] + }, + { + "name": "vcftools", + "path": "modules/nf-core/vcftools/meta.yml", + "type": "module", + "meta": { + "name": "vcftools", + "description": "A set of tools written in Perl and C++ for working with VCF files", + "keywords": [ + "VCFtools", + "VCF", + "sort" + ], + "tools": [ { - "diff_switch_error": { - "type": "file", - "description": "Switch errors found between sites (optional)", - "pattern": "*.diff.switch" - } + "vcftools": { + "description": "A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries", + "homepage": "http://vcftools.sourceforge.net/", + "documentation": "http://vcftools.sourceforge.net/man_latest.html", + "licence": [ + "LGPL" + ], + "identifier": "biotools:vcftools" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "variant_file": { + "type": "file", + "description": "variant input file which can be vcf, vcf.gz, or bcf format." + } + } + ], + [ + { + "bed": { + "type": "file", + "description": "bed file which can be used with different arguments in vcftools (optional)" + } + } + ], + [ + { + "diff_variant_file": { + "type": "file", + "description": "secondary variant file which can be used with the 'diff' suite of tools (optional)" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "vcf file (optional)", + "pattern": "*.vcf" + } + } + ] + }, + { + "bcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bcf": { + "type": "file", + "description": "bcf file (optional)", + "pattern": "*.bcf" + } + } + ] + }, + { + "frq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.frq": { + "type": "file", + "description": "Allele frequency for each site (optional)", + "pattern": "*.frq" + } + } + ] + }, + { + "frq_count": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.frq.count": { + "type": "file", + "description": "Allele counts for each site (optional)", + "pattern": "*.frq.count" + } + } + ] + }, + { + "idepth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.idepth": { + "type": "file", + "description": "mean depth per individual (optional)", + "pattern": "*.idepth" + } + } + ] + }, + { + "ldepth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldepth": { + "type": "file", + "description": "depth per site summed across individuals (optional)", + "pattern": "*.ildepth" + } + } + ] + }, + { + "ldepth_mean": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldepth.mean": { + "type": "file", + "description": "mean depth per site calculated across individuals (optional)", + "pattern": "*.ldepth.mean" + } + } + ] + }, + { + "gdepth": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.gdepth": { + "type": "file", + "description": "depth for each genotype in vcf file (optional)", + "pattern": "*.gdepth" + } + } + ] + }, + { + "hap_ld": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hap.ld": { + "type": "file", + "description": "r2, D, and D’ statistics using phased haplotypes (optional)", + "pattern": "*.hap.ld" + } + } + ] + }, + { + "geno_ld": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.geno.ld": { + "type": "file", + "description": "squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional)", + "pattern": "*.geno.ld" + } + } + ] + }, + { + "geno_chisq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.geno.chisq": { + "type": "file", + "description": "test for genotype independence via the chi-squared statistic (optional)", + "pattern": "*.geno.chisq" + } + } + ] + }, + { + "list_hap_ld": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list.hap.ld": { + "type": "file", + "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", + "pattern": "*.list.hap.ld" + } + } + ] + }, + { + "list_geno_ld": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.list.geno.ld": { + "type": "file", + "description": "r2 statistics of the sites contained in the provided input file verses all other sites (optional)", + "pattern": "*.list.geno.ld" + } + } + ] + }, + { + "interchrom_hap_ld": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interchrom.hap.ld": { + "type": "file", + "description": "r2 statistics for sites (haplotypes) on different chromosomes (optional)", + "pattern": "*.interchrom.hap.ld" + } + } + ] + }, + { + "interchrom_geno_ld": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.interchrom.geno.ld": { + "type": "file", + "description": "r2 statistics for sites (genotypes) on different chromosomes (optional)", + "pattern": "*.interchrom.geno.ld" + } + } + ] + }, + { + "tstv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv": { + "type": "file", + "description": "Transition / Transversion ratio in bins of size defined in options (optional)", + "pattern": "*.TsTv" + } + } + ] + }, + { + "tstv_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv.summary": { + "type": "file", + "description": "Summary of all Transitions and Transversions (optional)", + "pattern": "*.TsTv.summary" + } + } + ] + }, + { + "tstv_count": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv.count": { + "type": "file", + "description": "Transition / Transversion ratio as a function of alternative allele count (optional)", + "pattern": "*.TsTv.count" + } + } + ] + }, + { + "tstv_qual": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.TsTv.qual": { + "type": "file", + "description": "Transition / Transversion ratio as a function of SNP quality threshold (optional)", + "pattern": "*.TsTv.qual" + } + } + ] + }, + { + "filter_summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.FILTER.summary": { + "type": "file", + "description": "Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)", + "pattern": "*.FILTER.summary" + } + } + ] + }, + { + "sites_pi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.sites.pi": { + "type": "file", + "description": "Nucleotide divergency on a per-site basis (optional)", + "pattern": "*.sites.pi" + } + } + ] + }, + { + "windowed_pi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.windowed.pi": { + "type": "file", + "description": "Nucleotide diversity in windows, with window size determined by options (optional)", + "pattern": "*windowed.pi" + } + } + ] + }, + { + "weir_fst": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.weir.fst": { + "type": "file", + "description": "Fst estimate from Weir and Cockerham’s 1984 paper (optional)", + "pattern": "*.weir.fst" + } + } + ] + }, + { + "heterozygosity": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.het": { + "type": "file", + "description": "Heterozygosity on a per-individual basis (optional)", + "pattern": "*.het" + } + } + ] + }, + { + "hwe": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hwe": { + "type": "file", + "description": "Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)", + "pattern": "*.hwe" + } + } + ] + }, + { + "tajima_d": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Tajima.D": { + "type": "file", + "description": "Tajima’s D statistic in bins with size of the specified number in options (optional)", + "pattern": "*.Tajima.D" + } + } + ] + }, + { + "freq_burden": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ifreqburden": { + "type": "file", + "description": "Number of variants within each individual of a specific frequency in options (optional)", + "pattern": "*.ifreqburden" + } + } + ] + }, + { + "lroh": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.LROH": { + "type": "file", + "description": "Long Runs of Homozygosity (optional)", + "pattern": "*.LROH" + } + } + ] + }, + { + "relatedness": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.relatedness": { + "type": "file", + "description": "Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)", + "pattern": "*.relatedness" + } + } + ] + }, + { + "relatedness2": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.relatedness2": { + "type": "file", + "description": "Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)", + "pattern": "*.relatedness2" + } + } + ] + }, + { + "lqual": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lqual": { + "type": "file", + "description": "per-site SNP quality (optional)", + "pattern": "*.lqual" + } + } + ] + }, + { + "missing_individual": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.imiss": { + "type": "file", + "description": "Missingness on a per-individual basis (optional)", + "pattern": "*.imiss" + } + } + ] + }, + { + "missing_site": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.lmiss": { + "type": "file", + "description": "Missingness on a per-site basis (optional)", + "pattern": "*.lmiss" + } + } + ] + }, + { + "snp_density": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.snpden": { + "type": "file", + "description": "Number and density of SNPs in bins of size defined by option (optional)", + "pattern": "*.snpden" + } + } + ] + }, + { + "kept_sites": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.kept.sites": { + "type": "file", + "description": "All sites that have been kept after filtering (optional)", + "pattern": "*.kept.sites" + } + } + ] + }, + { + "removed_sites": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.removed.sites": { + "type": "file", + "description": "All sites that have been removed after filtering (optional)", + "pattern": "*.removed.sites" + } + } + ] + }, + { + "singeltons": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.singletons": { + "type": "file", + "description": "Location of singletons, and the individual they occur in (optional)", + "pattern": "*.singeltons" + } + } + ] + }, + { + "indel_hist": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.indel.hist": { + "type": "file", + "description": "Histogram file of the length of all indels (including SNPs) (optional)", + "pattern": "*.indel_hist" + } + } + ] + }, + { + "hapcount": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.hapcount": { + "type": "file", + "description": "Unique haplotypes within user specified bins (optional)", + "pattern": "*.hapcount" + } + } + ] + }, + { + "mendel": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mendel": { + "type": "file", + "description": "Mendel errors identified in trios (optional)", + "pattern": "*.mendel" + } + } + ] + }, + { + "format": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.FORMAT": { + "type": "file", + "description": "Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional)", + "pattern": "*.FORMAT" + } + } + ] + }, + { + "info": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.INFO": { + "type": "file", + "description": "Extracted information from the INFO field in the VCF file (optional)", + "pattern": "*.INFO" + } + } + ] + }, + { + "genotypes_matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.012": { + "type": "file", + "description": "Genotypes output as large matrix.\nGenotypes of each individual on a separate line.\nGenotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.\nMissing genotypes are represented by -1 (optional)\n", + "pattern": "*.012" + } + } + ] + }, + { + "genotypes_matrix_individual": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.012.indv": { + "type": "file", + "description": "Details the individuals included in the main genotypes_matrix file (optional)", + "pattern": "*.012.indv" + } + } + ] + }, + { + "genotypes_matrix_position": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.012.pos": { + "type": "file", + "description": "Details the site locations included in the main genotypes_matrix file (optional)", + "pattern": "*.012.pos" + } + } + ] + }, + { + "impute_hap": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.impute.hap": { + "type": "file", + "description": "Phased haplotypes in IMPUTE reference-panel format (optional)", + "pattern": "*.impute.hap" + } + } + ] + }, + { + "impute_hap_legend": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.impute.hap.legend": { + "type": "file", + "description": "Impute haplotype legend file (optional)", + "pattern": "*.impute.hap.legend" + } + } + ] + }, + { + "impute_hap_indv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.impute.hap.indv": { + "type": "file", + "description": "Impute haplotype individuals file (optional)", + "pattern": "*.impute.hap.indv" + } + } + ] + }, + { + "ldhat_sites": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldhat.sites": { + "type": "file", + "description": "Output data in LDhat format, sites (optional)", + "pattern": "*.ldhat.sites" + } + } + ] + }, + { + "ldhat_locs": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ldhat.locs": { + "type": "file", + "description": "output data in LDhat format, locations (optional)", + "pattern": "*.ldhat.locs" + } + } + ] + }, + { + "beagle_gl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.BEAGLE.GL": { + "type": "file", + "description": "Genotype likelihoods for biallelic sites (optional)", + "pattern": "*.BEAGLE.GL" + } + } + ] + }, + { + "beagle_pl": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.BEAGLE.PL": { + "type": "file", + "description": "Genotype likelihoods for biallelic sites (optional)", + "pattern": "*.BEAGLE.PL" + } + } + ] + }, + { + "ped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ped": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.ped" + } + } + ] + }, + { + "map_": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.map": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.map" + } + } + ] + }, + { + "tped": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tped": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.tped" + } + } + ] + }, + { + "tfam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.tfam": { + "type": "file", + "description": "output the genotype data in PLINK PED format (optional)", + "pattern": "*.tfam" + } + } + ] + }, + { + "diff_sites_in_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.sites_in_files": { + "type": "file", + "description": "Sites that are common / unique to each file specified in optional inputs (optional)", + "pattern": "*.diff.sites.in.files" + } + } + ] + }, + { + "diff_indv_in_files": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.indv_in_files": { + "type": "file", + "description": "Individuals that are common / unique to each file specified in optional inputs (optional)", + "pattern": "*.diff.indv.in.files" + } + } + ] + }, + { + "diff_sites": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.sites": { + "type": "file", + "description": "Discordance on a site by site basis, specified in optional inputs (optional)", + "pattern": "*.diff.sites" + } + } + ] + }, + { + "diff_indv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.indv": { + "type": "file", + "description": "Discordance on a individual by individual basis, specified in optional inputs (optional)", + "pattern": "*.diff.indv" + } + } + ] + }, + { + "diff_discd_matrix": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.discordance.matrix": { + "type": "file", + "description": "Discordance matrix between files specified in optional inputs (optional)", + "pattern": "*.diff.discordance.matrix" + } + } + ] + }, + { + "diff_switch_error": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.diff.switch": { + "type": "file", + "description": "Switch errors found between sites (optional)", + "pattern": "*.diff.switch" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -140731,66 +180568,86 @@ "doi": "10.1038/s41586-018-0414-6", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "barcodes": { - "type": "file", - "description": "Valid barcodes file, to filter the bam", - "pattern": "*.tsv.gz" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "sorted_bam": { - "type": "file", - "description": "Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam`", - "pattern": "*.bam" - } - }, - { - "gtf": { - "type": "file", - "description": "genome annotation file", - "pattern": "*.gtf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "loom": { - "type": "file", - "description": "Loom file with counts divided in spliced/unspliced/ambiguous.", - "pattern": "*.loom" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "barcodes": { + "type": "file", + "description": "Valid barcodes file, to filter the bam", + "pattern": "*.tsv.gz" + } + }, + { + "bam": { + "type": "file", + "description": "Sorted BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "sorted_bam": { + "type": "file", + "description": "Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam`", + "pattern": "*.bam" + } + } + ], + [ + { + "gtf": { + "type": "file", + "description": "genome annotation file", + "pattern": "*.gtf" + } + } + ] + ], + "output": [ + { + "loom": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*.loom": { + "type": "file", + "description": "Loom file with counts divided in spliced/unspliced/ambiguous.", + "pattern": "*.loom" + } + }, + { + "*.velocyto.log": { + "type": "file", + "description": "Loom file with counts divided in spliced/unspliced/ambiguous.", + "pattern": "*.loom" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -140823,101 +180680,174 @@ "doi": "10.1016/j.ajhg.2012.09.004", "licence": [ "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file.\nIt also requires to contain \"@RG\" header lines to annotation different readGroups (sequencing runs and lanes).\nThe SM tag in the \"@RG\" header should match with one of the genotyped sample.\n", - "pattern": "*.bam" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file BAI", - "pattern": "*.bai" - } - }, - { - "refvcf": { - "type": "file", - "description": "The input VCF file contains\n(1) external genotype information and/or\n(2) allele frequency information as AF entry or AC/AN entries in the INFO field.\n", - "pattern": "*.{vcf,vcf.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "Detailed summary of the verifyBamID result.", - "pattern": "*.log" - } - }, - { - "selfsm": { - "type": "file", - "description": "Per-sample statistics describing how well the sample matches to the annotated sample.", - "pattern": "*.selfSM" - } - }, - { - "depthsm": { - "type": "file", - "description": "The depth distribution of the sequence reads per sample", - "pattern": "*.depthSM" - } - }, - { - "selfrg": { - "type": "file", - "description": "Per-readGroup statistics describing how well each lane matches to the annotated sample. (available only without --ignoreRG option)", - "pattern": "*.selfRG" - } - }, - { - "depthrg": { - "type": "file", - "description": "The depth distribution of the sequence reads per readGroup. (available only without --ignoreRG option)", - "pattern": "*.depthRG" - } - }, - { - "bestsm": { - "type": "file", - "description": "Per-sample best-match statistics with best-matching sample among the genotyped sample (available only with --best option)", - "pattern": "*.bestSM" - } - }, - { - "bestrg": { - "type": "file", - "description": "Per-readgroup best-match statistics with best-matching sample among the genotyped sample (available only with --best and without --ignoreRG option)", - "pattern": "*.bestRG" - } + ], + "identifier": "biotools:verifybamid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file.\nIt also requires to contain \"@RG\" header lines to annotation different readGroups (sequencing runs and lanes).\nThe SM tag in the \"@RG\" header should match with one of the genotyped sample.\n", + "pattern": "*.bam" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file BAI", + "pattern": "*.bai" + } + } + ], + [ + { + "refvcf": { + "type": "file", + "description": "The input VCF file contains\n(1) external genotype information and/or\n(2) allele frequency information as AF entry or AC/AN entries in the INFO field.\n", + "pattern": "*.{vcf,vcf.gz}" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Detailed summary of the verifyBamID result.", + "pattern": "*.log" + } + } + ] + }, + { + "selfsm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.selfSM": { + "type": "file", + "description": "Per-sample statistics describing how well the sample matches to the annotated sample.", + "pattern": "*.selfSM" + } + } + ] + }, + { + "depthsm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthSM": { + "type": "file", + "description": "The depth distribution of the sequence reads per sample", + "pattern": "*.depthSM" + } + } + ] + }, + { + "selfrg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.selfRG": { + "type": "file", + "description": "Per-readGroup statistics describing how well each lane matches to the annotated sample. (available only without --ignoreRG option)", + "pattern": "*.selfRG" + } + } + ] + }, + { + "depthrg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.depthRG": { + "type": "file", + "description": "The depth distribution of the sequence reads per readGroup. (available only without --ignoreRG option)", + "pattern": "*.depthRG" + } + } + ] + }, + { + "bestsm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bestSM": { + "type": "file", + "description": "Per-sample best-match statistics with best-matching sample among the genotyped sample (available only with --best option)", + "pattern": "*.bestSM" + } + } + ] + }, + { + "bestrg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bestRG": { + "type": "file", + "description": "Per-readgroup best-match statistics with best-matching sample among the genotyped sample (available only with --best and without --ignoreRG option)", + "pattern": "*.bestRG" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -140951,122 +180881,189 @@ "doi": "10.1101/gr.246934.118", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/CRAM/SAM file", - "pattern": "*.{bam,cram,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAI/CRAI/CSI index file", - "pattern": "*.{bai,crai,csi}" - } - }, - { - "svd_ud": { - "type": "file", - "description": ".UD matrix file from SVD result of genotype matrix", - "pattern": "*.UD" - } - }, - { - "svd_mu": { - "type": "file", - "description": ".mu matrix file of genotype matrix", - "pattern": "*.mu" - } - }, - { - "svd_bed": { - "type": "file", - "description": ".Bed file for markers used in this analysis,format(chr\\tpos-1\\tpos\\trefAllele\\taltAllele)[Required]", - "pattern": "*.bed" - } - }, - { - "references": { - "type": "file", - "description": "reference file [Required]", - "pattern": "*.fasta" - } - }, - { - "refvcf": { - "type": "file", - "description": "Reference panel VCF with genotype information, for generation of .UD .mu .bed files [Optional]", - "pattern": "*.vcf" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "mu": { - "type": "file", - "description": ".mu matrix file of genotype matrix from customized reference vcf input", - "pattern": "*.mu" - } - }, - { - "ud": { - "type": "file", - "description": ".UD matrix file from customized reference vcf input", - "pattern": "*.UD" - } - }, - { - "bed": { - "type": "file", - "description": ".Bed file from customized reference marker vcf input", - "pattern": "*.bed" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "log": { - "type": "file", - "description": "Detailed summary of the VerifyBamId2 results", - "pattern": "*.log" - } - }, - { - "self_sm": { - "type": "file", - "description": "Shares the same format as legacy VB1 and the key information FREEMIX indicates the estimated contamination level.", - "pattern": "*.selfSM" - } - }, - { - "ancenstry": { - "type": "file", - "description": "PC coordinates for both intended sample and contaminating sample, with each row being one PC.", - "pattern": "*.Ancestry" - } + ], + "identifier": "biotools:verifybamid" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/CRAM/SAM file", + "pattern": "*.{bam,cram,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAI/CRAI/CSI index file", + "pattern": "*.{bai,crai,csi}" + } + } + ], + [ + { + "svd_ud": { + "type": "file", + "description": ".UD matrix file from SVD result of genotype matrix", + "pattern": "*.UD" + } + }, + { + "svd_mu": { + "type": "file", + "description": ".mu matrix file of genotype matrix", + "pattern": "*.mu" + } + }, + { + "svd_bed": { + "type": "file", + "description": ".Bed file for markers used in this analysis,format(chr\\tpos-1\\tpos\\trefAllele\\taltAllele)[Required]", + "pattern": "*.bed" + } + } + ], + [ + { + "refvcf": { + "type": "file", + "description": "Reference panel VCF with genotype information, for generation of .UD .mu .bed files [Optional]", + "pattern": "*.vcf" + } + } + ], + [ + { + "references": { + "type": "file", + "description": "reference file [Required]", + "pattern": "*.fasta" + } + } + ] + ], + "output": [ + { + "log": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.log": { + "type": "file", + "description": "Detailed summary of the VerifyBamId2 results", + "pattern": "*.log" + } + } + ] + }, + { + "ud": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.UD": { + "type": "file", + "description": ".UD matrix file from customized reference vcf input", + "pattern": "*.UD" + } + } + ] + }, + { + "bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bed": { + "type": "file", + "description": ".Bed file from customized reference marker vcf input", + "pattern": "*.bed" + } + } + ] + }, + { + "mu": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mu": { + "type": "file", + "description": ".mu matrix file of genotype matrix from customized reference vcf input", + "pattern": "*.mu" + } + } + ] + }, + { + "self_sm": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.selfSM": { + "type": "file", + "description": "Shares the same format as legacy VB1 and the key information FREEMIX indicates the estimated contamination level.", + "pattern": "*.selfSM" + } + } + ] + }, + { + "ancestry": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.Ancestry": { + "type": "file", + "description": "Ancestry information", + "pattern": "*.Ancestry" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141100,73 +181097,100 @@ "documentation": "https://github.com/vgteam/vg/wiki", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "list", - "description": "Either one or more VCF files containing different contigs or a multiple sequence alignment file\n", - "pattern": "*.{vcf.gz,fa,fasta,fna,clustal}" - } - }, - { - "tbis": { - "type": "list", - "description": "The index files for the VCF files", - "pattern": "*.tbi" - } - }, - { - "insertions_fasta": { - "type": "file", - "description": "A FASTA file containing insertion sequences (referred to in the VCF file(s))", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file (cannot be used in combination with `msa`, but is required when using `vcfs`)", - "pattern": "*.{fa,fasta,fna}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "graph": { - "type": "file", - "description": "The constructed graph", - "pattern": "*.vg" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "list", + "description": "Either one or more VCF files containing different contigs or a multiple sequence alignment file\n", + "pattern": "*.{vcf.gz,fa,fasta,fna,clustal}" + } + }, + { + "tbis": { + "type": "list", + "description": "The index files for the VCF files", + "pattern": "*.tbi" + } + }, + { + "insertions_fasta": { + "type": "file", + "description": "A FASTA file containing insertion sequences (referred to in the VCF file(s))", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file (cannot be used in combination with `msa`, but is required when using `vcfs`)", + "pattern": "*.{fa,fasta,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "graph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vg": { + "type": "file", + "description": "The constructed graph", + "pattern": "*.vg" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141200,59 +181224,74 @@ "documentation": "https://github.com/vgteam/vg/wiki", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "gfa": { - "type": "file", - "description": "Variation graph in GFA format", - "pattern": "*.{gfa}" - } - }, - { - "pb": { - "type": "file", - "description": "Optional snarls file (from vg snarls) to avoid recomputing. Usually ends with \"pb\". See \"vg snarls\".", - "pattern": "*.{pb}" - } - }, - { - "gbwt": { - "type": "file", - "description": "Optional GBWT file (from vg gbwt) so to only consider alt traversals that correspond to GBWT threads FILE.", - "pattern": "*.{gbwt}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "vcf": { - "type": "file", - "description": "Variants in VCF format", - "pattern": "*.{vcf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "gfa": { + "type": "file", + "description": "Variation graph in GFA format", + "pattern": "*.{gfa}" + } + } + ], + [ + { + "pb": { + "type": "file", + "description": "Optional snarls file (from vg snarls) to avoid recomputing. Usually ends with \"pb\". See \"vg snarls\".", + "pattern": "*.{pb}" + } + } + ], + [ + { + "gbwt": { + "type": "file", + "description": "Optional GBWT file (from vg gbwt) so to only consider alt traversals that correspond to GBWT threads FILE.", + "pattern": "*.{gbwt}" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf": { + "type": "file", + "description": "Variants in VCF format", + "pattern": "*.{vcf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141270,66 +181309,87 @@ "meta": { "name": "vg_index", "description": "write your description here", - "keywords": [ - "vg", - "index", - "graph", - "structural_variants" - ], - "tools": [ - { - "vg": { - "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", - "homepage": "https://github.com/vgteam/vg", - "documentation": "https://github.com/vgteam/vg/wiki", - "licence": [ - "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "input": { - "type": "list", - "description": "One or more input graph files created with `vg/construct`", - "pattern": "*.vg" - } - } + "keywords": [ + "vg", + "index", + "graph", + "structural_variants" ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "xg": { - "type": "file", - "description": "File containing a succint, queryable version of the input graph(s) or read for GCSA or distance indexing", - "pattern": "*.xg" - } - }, + "tools": [ { - "vg_index": { - "type": "file", - "description": "An index of the graph(s) created when `--index-sorted-vg` is supplied.", - "pattern": "*.vgi" - } + "vg": { + "description": "Variation graph data structures, interchange formats, alignment, genotyping,\nand variant calling methods.\n", + "homepage": "https://github.com/vgteam/vg", + "documentation": "https://github.com/vgteam/vg/wiki", + "licence": [ + "MIT" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "input": { + "type": "list", + "description": "One or more input graph files created with `vg/construct`", + "pattern": "*.vg" + } + } + ] + ], + "output": [ + { + "xg": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.xg": { + "type": "file", + "description": "File containing a succint, queryable version of the input graph(s) or read for GCSA or distance indexing", + "pattern": "*.xg" + } + } + ] + }, + { + "vg_index": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vgi": { + "type": "file", + "description": "An index of the graph(s) created when `--index-sorted-vg` is supplied.", + "pattern": "*.vgi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141361,52 +181421,73 @@ "doi": "10.1186/1748-7188-6-26", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "rnacofold_fasta": { - "type": "file", - "description": "A fasta file containing RNA or transcript sequences\n", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "rnacofold_csv": { - "type": "file", - "description": "The CSV Output of RNAcofold that has the predicted structure and energies", - "pattern": "*.{csv}" - } - }, - { - "rnacofold_ps": { - "type": "file", - "description": "The text Output of RNAfold that contains the predicted secondary structure in postscript format", - "pattern": "*.{ps}" - } + ], + "identifier": "biotools:viennarna" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "rnacofold_fasta": { + "type": "file", + "description": "A fasta file containing RNA or transcript sequences\n", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "rnacofold_csv": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.csv": { + "type": "file", + "description": "The CSV Output of RNAcofold that has the predicted structure and energies", + "pattern": "*.{csv}" + } + } + ] + }, + { + "rnacofold_ps": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.ps": { + "type": "file", + "description": "The text Output of RNAfold that contains the predicted secondary structure in postscript format", + "pattern": "*.{ps}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141438,40 +181519,82 @@ "doi": "10.1186/1748-7188-6-26", "licence": [ "custom" - ] - } - } - ], - "input": [ - { - "fasta": { - "type": "file", - "description": "A fasta file containing RNA or transcript sequences\n", - "pattern": "*.{fasta,fa}" - } - } - ], - "output": [ - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "rnafold_txt": { - "type": "file", - "description": "The text Output of RNAfold that", - "pattern": "*.{fold}" - } - }, - { - "rnafold_ps": { - "type": "file", - "description": "The text Output of RNAfold that", - "pattern": "*.ss" - } + ], + "identifier": "biotools:viennarna" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "A fasta file containing RNA or transcript sequences\n", + "pattern": "*.{fasta,fa}" + } + } + ] + ], + "output": [ + { + "rnafold_txt": [ + { + "meta": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.{fold}" + } + }, + { + "*.fold": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.{fold}" + } + } + ] + }, + { + "rnafold_ps": [ + { + "meta": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.ss" + } + }, + { + "*.ps": { + "type": "file", + "description": "The text Output of RNAfold that", + "pattern": "*.ss" + } + } + ] + }, + { + "versions": [ + { + "meta": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + }, + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141503,33 +181626,44 @@ "doi": "10.1186/1748-7188-6-26", "licence": [ "custom" - ] + ], + "identifier": "biotools:viennarna" } } ], "input": [ - { - "fasta": { - "type": "file", - "description": "A fasta file containing RNA or transcript sequences\n", - "pattern": "*.{fasta,fa}" + [ + { + "fasta": { + "type": "file", + "description": "A fasta file containing RNA or transcript sequences\n", + "pattern": "*.{fasta,fa}" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "rnalfold_txt": [ + { + "*.lfold": { + "type": "file", + "description": "The text Output of RNALfold", + "pattern": "*.{lfold}" + } + } + ] }, { - "rnalfold_txt": { - "type": "file", - "description": "The text Output of RNALfold", - "pattern": "*.{lfold}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141562,85 +181696,126 @@ "doi": "10.1186/s13059-019-1865-2", "licence": [ "Apache-2.0" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" - } - }, - { - "cell_data": { - "type": "file", - "description": "The cell genotype file in VCF format or cellSNP folder with sparse matrices.", - "pattern": "*.vcf|*/" - } - }, - { - "n_donor": { - "type": "integer", - "description": "Number of donors to demultiplex." - } - }, - { - "donor_file": { - "type": "file", - "description": "The optional donor genotype file in VCF format.", - "pattern": "*.vcf" - } - }, - { - "vartrix_data": { - "type": "file", - "description": "The optional cell genotype files in vartrix outputs." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "summary": { - "type": "file", - "description": "Summary tsv file of deconvolution result.", - "pattern": "*_summary.tsv" - } - }, - { - "donor_ids": { - "type": "file", - "description": "Donor assignment with detailed statistics.", - "pattern": "*_donor_ids.tsv" - } - }, - { - "prob_singlets": { - "type": "file", - "description": "contains probability of classifing singlets", - "pattern": "*_prob_singlet.tsv.gz" - } - }, - { - "prob_doublets": { - "type": "file", - "description": "contains probability of classifing doublets", - "pattern": "*_prob_doublet.tsv.gz" - } + ], + "identifier": "biotools:Vireo" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1']`\n" + } + }, + { + "cell_data": { + "type": "file", + "description": "The cell genotype file in VCF format or cellSNP folder with sparse matrices.", + "pattern": "*.vcf|*/" + } + }, + { + "n_donor": { + "type": "integer", + "description": "Number of donors to demultiplex." + } + }, + { + "donor_file": { + "type": "file", + "description": "The optional donor genotype file in VCF format.", + "pattern": "*.vcf" + } + }, + { + "vartrix_data": { + "type": "file", + "description": "The optional cell genotype files in vartrix outputs." + } + } + ] + ], + "output": [ + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_summary.tsv": { + "type": "file", + "description": "Summary tsv file of deconvolution result.", + "pattern": "*_summary.tsv" + } + } + ] + }, + { + "donor_ids": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_donor_ids.tsv": { + "type": "file", + "description": "Donor assignment with detailed statistics.", + "pattern": "*_donor_ids.tsv" + } + } + ] + }, + { + "prob_singlets": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_prob_singlet.tsv.gz": { + "type": "file", + "description": "contains probability of classifing singlets", + "pattern": "*_prob_singlet.tsv.gz" + } + } + ] + }, + { + "prob_doublets": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1' ]`\n" + } + }, + { + "*_prob_doublet.tsv.gz": { + "type": "file", + "description": "contains probability of classifing doublets", + "pattern": "*_prob_doublet.tsv.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141682,52 +181857,71 @@ "licence": [ "GPL v3 license", "GPL v3" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA file containing contigs/scaffolds input into vRhyme", - "pattern": "*.{fasta,fna,fa}" - } - }, - { - "membership": { - "type": "file", - "description": "TSV file containing information regarding which bins input sequences were placed information", - "pattern": "*.{tsv}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "unbinnned_sequences": { - "type": "file", - "description": "FASTA file containing sequences unbinned by vRhyme", - "pattern": "*_unbinned_sequences.fasta" - } + ], + "identifier": "biotools:vrhyme" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "membership": { + "type": "file", + "description": "TSV file containing information regarding which bins input sequences were placed information", + "pattern": "*.{tsv}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "FASTA file containing contigs/scaffolds input into vRhyme", + "pattern": "*.{fasta,fna,fa}" + } + } + ] + ], + "output": [ + { + "unbinned_sequences": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_unbinned_sequences.fasta": { + "type": "file", + "description": "FASTA file containing unbinned sequences", + "pattern": "*_unbinned_sequences.fasta" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141763,44 +181957,55 @@ "licence": [ "GPL v3 license", "GPL v3" - ] + ], + "identifier": "biotools:vrhyme" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bins": { - "type": "directory", - "description": "Directory file containing bin FASTA files output by vRhyme (each bin having multiple sequences)" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bins": { + "type": "directory", + "description": "Directory file containing bin FASTA files output by vRhyme (each bin having multiple sequences)" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "linked_bins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_linked_bins.fasta": { + "type": "file", + "description": "FASTA file containing all bins that have been linked by N's", + "pattern": "*_linked_bins.fasta" + } + } + ] }, { - "linked_bins": { - "type": "file", - "description": "FASTA file containing all bins that have been linked by N's", - "pattern": "*_linked_bins.fasta" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141836,66 +182041,105 @@ "licence": [ "GPL v3", "GPL v3 license" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "Preprocessed FASTQ file containing sample reads", - "pattern": "*.{fastq}" - } - }, - { - "fasta": { - "type": "file", - "description": "Contigs/scaffolds identified as viral", - "pattern": "*.{fna,fasta,fa}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bins": { - "type": "directory", - "description": "Directory containing bin FASTA files", - "pattern": "**/vRhyme_best_bins_fasta/" - } - }, - { - "membership": { - "type": "file", - "description": "TSV file describing the contig/scaffold membership of each bin", - "pattern": "vRhyme_best_bins.*.membership.tsv" - } - }, - { - "summary": { - "type": "file", - "description": "TSV file summarizing the attributes of each bin", - "pattern": "vRhyme_best_bins.*.summary.tsv" - } + ], + "identifier": "biotools:vrhyme" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "Preprocessed FASTQ file containing sample reads", + "pattern": "*.{fastq}" + } + } + ], + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Contigs/scaffolds identified as viral", + "pattern": "*.{fna,fasta,fa}" + } + } + ] + ], + "output": [ + { + "bins": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "vRhyme_best_bins_fasta/": { + "type": "directory", + "description": "Directory containing bin FASTA files", + "pattern": "**/vRhyme_best_bins_fasta/" + } + } + ] + }, + { + "membership": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "**/vRhyme_best_bins.*.membership.tsv": { + "type": "file", + "description": "TSV file describing the contig/scaffold membership of each bin", + "pattern": "vRhyme_best_bins.*.membership.tsv" + } + } + ] + }, + { + "summary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "**/vRhyme_best_bins.*.summary.tsv": { + "type": "file", + "description": "TSV file summarizing the attributes of each bin", + "pattern": "vRhyme_best_bins.*.summary.tsv" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -141928,94 +182172,243 @@ "doi": "10.7717/peerj.2584", "licence": [ "GPL v3-or-later OR BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequences to cluster in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "aln": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.aln.gz" - } - }, - { - "biom": { - "type": "file", - "description": "Results in an OTU table in the biom version 1.0 file format", - "pattern": "*.biom.gz" - } - }, - { - "mothur": { - "type": "file", - "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", - "pattern": "*.mothur.tsv.gz" - } - }, - { - "otu": { - "type": "file", - "description": "Results in an OTU table in the classic tab-separated plain text format", - "pattern": "*.otu.tsv.gz" - } - }, - { - "bam": { - "type": "file", - "description": "Results written in bam format", - "pattern": "*.bam" - } - }, - { - "out": { - "type": "file", - "description": "Results in tab-separated output, columns defined by user", - "pattern": "*.out.tsv.gz" - } - }, - { - "blast": { - "type": "file", - "description": "Tab delimited results in blast-like tabular format", - "pattern": "*.blast.tsv.gz" - } - }, - { - "uc": { - "type": "file", - "description": "Tab delimited results in a uclust-like format with 10 columns", - "pattern": "*.uc.gz" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "fasta": { + "type": "file", + "description": "Sequences to cluster in FASTA format", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ] + ], + "output": [ + { + "aln": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.aln.gz": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.aln.gz" + } + } + ] + }, + { + "biom": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.biom.gz": { + "type": "file", + "description": "Results in an OTU table in the biom version 1.0 file format", + "pattern": "*.biom.gz" + } + } + ] + }, + { + "mothur": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.mothur.tsv.gz": { + "type": "file", + "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", + "pattern": "*.mothur.tsv.gz" + } + } + ] + }, + { + "otu": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.otu.tsv.gz": { + "type": "file", + "description": "Results in an OTU table in the classic tab-separated plain text format", + "pattern": "*.otu.tsv.gz" + } + } + ] + }, + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Results written in bam format", + "pattern": "*.bam" + } + } + ] + }, + { + "out": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.out.tsv.gz": { + "type": "file", + "description": "Results in tab-separated output, columns defined by user", + "pattern": "*.out.tsv.gz" + } + } + ] + }, + { + "blast": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.blast.tsv.gz": { + "type": "file", + "description": "Tab delimited results in blast-like tabular format", + "pattern": "*.blast.tsv.gz" + } + } + ] + }, + { + "uc": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.uc.tsv.gz": { + "type": "file", + "description": "Tab delimited results in a uclust-like format with 10 columns", + "pattern": "*.uc.gz" + } + } + ] + }, + { + "centroids": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.centroids.fasta.gz": { + "type": "file", + "description": "Centroid sequences in FASTA format", + "pattern": "*.centroids.fasta.gz" + } + } + ] + }, + { + "clusters": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.clusters.fasta*.gz": { + "type": "file", + "description": "Clustered sequences in FASTA format", + "pattern": "*.clusters.fasta*.gz" + } + } + ] + }, + { + "profile": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.profile.txt.gz": { + "type": "file", + "description": "Profile of the clustering results", + "pattern": "*.profile.txt.gz" + } + } + ] + }, + { + "msa": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*.msa.fasta.gz": { + "type": "file", + "description": "Multiple sequence alignment of the centroids", + "pattern": "*.msa.fasta.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142062,59 +182455,84 @@ "doi": "10.7717/peerj.2584", "licence": [ "GPL v3-or-later OR BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequences to be sorted in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]`" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "fasta": { - "type": "file", - "description": "dereplicated fasta", - "pattern": "*.fasta" - } - }, - { - "clustering": { - "type": "file", - "description": "dereplicated derep.uc file", - "pattern": "*.uc" - } - }, - { - "log": { - "type": "file", - "description": "a log file of the run", - "pattern": "*.derep.log" - } + ], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "fasta": { + "type": "file", + "description": "Sequences to be sorted in FASTA format", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}" + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]`" + } + }, + { + "*.derep.fasta": { + "type": "file", + "description": "dereplicated fasta", + "pattern": "*.fasta" + } + } + ] + }, + { + "clustering": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]`" + } + }, + { + "*.derep.uc": { + "type": "file", + "description": "dereplicated derep.uc file", + "pattern": "*.uc" + } + } + ] + }, + { + "log": [ + { + "*.derep.log": { + "type": "file", + "description": "a log file of the run", + "pattern": "*.derep.log" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142150,52 +182568,67 @@ "doi": "10.7717/peerj.2584", "licence": [ "GPL v3-or-later OR BSD-2-clause" - ] + ], + "identifier": "biotools:vsearch" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'sample1']" - } - }, - { - "fastq": { - "type": "file", - "description": "FASTQ file to filter", - "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'sample1']" + } + }, + { + "fastq": { + "type": "file", + "description": "FASTQ file to filter", + "pattern": "*.{fastq,fq,fastq.gz,fq.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'sample1']" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'sample1']" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Filtered FASTA file", + "pattern": "*.fasta" + } + } + ] }, { - "fasta": { - "type": "file", - "description": "Filtered FASTA file", - "pattern": "*.fasta" - } + "log": [ + { + "*.log": { + "type": "file", + "description": "Log file of the run", + "pattern": "*.log" + } + } + ] }, { - "log": { - "type": "file", - "description": "Log file of the run", - "pattern": "*.log" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142227,46 +182660,66 @@ "doi": "10.7717/peerj.2584", "licence": [ "GPL v3-or-later OR BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing query file information e.g. [ id:'test' ]" - } - }, - { - "queryfasta": { - "type": "file", - "description": "Query sequences in FASTA or FASTQ format", - "pattern": "*.{fasta,fa,fna,faa,fastq,fq}" - } - }, - { - "db": { - "type": "file", - "description": "Reference database file in FASTA or UDB format", - "pattern": "*" - } - } - ], - "output": [ - { - "tsv": { - "type": "file", - "description": "Results written to tab-delimited file", - "pattern": "*.{tsv}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing query file information e.g. [ id:'test' ]" + } + }, + { + "queryfasta": { + "type": "file", + "description": "Query sequences in FASTA or FASTQ format", + "pattern": "*.{fasta,fa,fna,faa,fastq,fq}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Reference database file in FASTA or UDB format", + "pattern": "*" + } + } + ] + ], + "output": [ + { + "tsv": [ + { + "meta": { + "type": "file", + "description": "Results written to tab-delimited file", + "pattern": "*.{tsv}" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results written to tab-delimited file", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142291,73 +182744,86 @@ "name": "vsearch_sort", "description": "Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength).", "keywords": [ - "vsearch/sort", - "vsearch", - "sort", - "amplicon sequences", - "metagenomics", - "genomics", - "population genetics" - ], - "tools": [ - { - "vsearch": { - "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", - "homepage": "https://github.com/torognes/vsearch", - "documentation": "https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf", - "tool_dev_url": "https://github.com/torognes/vsearch", - "doi": "10.7717/peerj.2584", - "licence": [ - "GPL v3-or-later OR BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "fasta": { - "type": "file", - "description": "Sequences to be sorted in FASTA format", - "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" - } - }, - { - "sort_arg": { - "type": "string", - "description": "Argument to provide to sort algorithm. Sort by abundance with --sortbysize or by sequence length with --sortbylength.", - "enum": [ - "--sortbysize", - "--sortbylength" - ] - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Sorted FASTA file", - "pattern": "*.{fasta}" - } - }, + "vsearch/sort", + "vsearch", + "sort", + "amplicon sequences", + "metagenomics", + "genomics", + "population genetics" + ], + "tools": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "vsearch": { + "description": "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)", + "homepage": "https://github.com/torognes/vsearch", + "documentation": "https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf", + "tool_dev_url": "https://github.com/torognes/vsearch", + "doi": "10.7717/peerj.2584", + "licence": [ + "GPL v3-or-later OR BSD-2-clause" + ], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "fasta": { + "type": "file", + "description": "Sequences to be sorted in FASTA format", + "pattern": "*.{fasta,fa,fasta.gz,fa.gz}" + } + } + ], + [ + { + "sort_arg": { + "type": "string", + "description": "Argument to provide to sort algorithm. Sort by abundance with --sortbysize or by sequence length with --sortbylength.", + "enum": [ + "--sortbysize", + "--sortbylength" + ] + } + } + ] + ], + "output": [ + { + "fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fasta": { + "type": "file", + "description": "Sorted FASTA file", + "pattern": "*.{fasta}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142396,121 +182862,235 @@ "doi": "10.7717/peerj.2584", "licence": [ "GPL v3-or-later OR BSD-2-clause" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information e.g. [ id:'test' ]" - } - }, - { - "queryfasta": { - "type": "file", - "description": "Query sequences in FASTA format", - "pattern": "*.{fasta,fa,fna,faa}" - } - }, - { - "db": { - "type": "file", - "description": "Reference database file in FASTA or UDB format", - "pattern": "*" - } - }, - { - "idcutoff": { - "type": "float", - "description": "Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)" - } - }, - { - "outoption": { - "type": "string", - "description": "Specify the type of output file to be generated by selecting one of the vsearch output file options", - "pattern": "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" - } - }, - { - "user_columns": { - "type": "string", - "description": "If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string." - } - } - ], - "output": [ - { - "aln": { - "type": "file", - "description": "Results in pairwise alignment format", - "pattern": "*.{aln}" - } - }, - { - "biom": { - "type": "file", - "description": "Results in an OTU table in the biom version 1.0 file format", - "pattern": "*.{biom}" - } - }, - { - "lca": { - "type": "file", - "description": "Last common ancestor (LCA) information about the hits of each query in tab-separated format", - "pattern": "*.{lca}" - } - }, - { - "mothur": { - "type": "file", - "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", - "pattern": "*.{mothur}" - } - }, - { - "otu": { - "type": "file", - "description": "Results in an OTU table in the classic tab-separated plain text format", - "pattern": "*.{otu}" - } - }, - { - "sam": { - "type": "file", - "description": "Results written in sam format", - "pattern": "*.{sam}" - } - }, - { - "tsv": { - "type": "file", - "description": "Results in tab-separated output, columns defined by user", - "pattern": "*.{tsv}" - } - }, - { - "txt": { - "type": "file", - "description": "Tab delimited results in blast-like tabular format", - "pattern": "*.{txt}" - } - }, - { - "uc": { - "type": "file", - "description": "Tab delimited results in a uclust-like format with 10 columns", - "pattern": "*.{uc}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:vsearch" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information e.g. [ id:'test' ]" + } + }, + { + "queryfasta": { + "type": "file", + "description": "Query sequences in FASTA format", + "pattern": "*.{fasta,fa,fna,faa}" + } + } + ], + [ + { + "db": { + "type": "file", + "description": "Reference database file in FASTA or UDB format", + "pattern": "*" + } + } + ], + [ + { + "idcutoff": { + "type": "float", + "description": "Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)" + } + } + ], + [ + { + "outoption": { + "type": "string", + "description": "Specify the type of output file to be generated by selecting one of the vsearch output file options", + "pattern": "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" + } + } + ], + [ + { + "user_columns": { + "type": "string", + "description": "If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string." + } + } + ] + ], + "output": [ + { + "aln": [ + { + "meta": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}" + } + }, + { + "*.aln": { + "type": "file", + "description": "Results in pairwise alignment format", + "pattern": "*.{aln}" + } + } + ] + }, + { + "biom": [ + { + "meta": { + "type": "file", + "description": "Results in an OTU table in the biom version 1.0 file format", + "pattern": "*.{biom}" + } + }, + { + "*.biom": { + "type": "file", + "description": "Results in an OTU table in the biom version 1.0 file format", + "pattern": "*.{biom}" + } + } + ] + }, + { + "lca": [ + { + "meta": { + "type": "file", + "description": "Last common ancestor (LCA) information about the hits of each query in tab-separated format", + "pattern": "*.{lca}" + } + }, + { + "*.lca": { + "type": "file", + "description": "Last common ancestor (LCA) information about the hits of each query in tab-separated format", + "pattern": "*.{lca}" + } + } + ] + }, + { + "mothur": [ + { + "meta": { + "type": "file", + "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", + "pattern": "*.{mothur}" + } + }, + { + "*.mothur": { + "type": "file", + "description": "Results in an OTU table in the mothur ’shared’ tab-separated plain text file format", + "pattern": "*.{mothur}" + } + } + ] + }, + { + "otu": [ + { + "meta": { + "type": "file", + "description": "Results in an OTU table in the classic tab-separated plain text format", + "pattern": "*.{otu}" + } + }, + { + "*.otu": { + "type": "file", + "description": "Results in an OTU table in the classic tab-separated plain text format", + "pattern": "*.{otu}" + } + } + ] + }, + { + "sam": [ + { + "meta": { + "type": "file", + "description": "Results written in sam format", + "pattern": "*.{sam}" + } + }, + { + "*.sam": { + "type": "file", + "description": "Results written in sam format", + "pattern": "*.{sam}" + } + } + ] + }, + { + "tsv": [ + { + "meta": { + "type": "file", + "description": "Results in tab-separated output, columns defined by user", + "pattern": "*.{tsv}" + } + }, + { + "*.tsv": { + "type": "file", + "description": "Results in tab-separated output, columns defined by user", + "pattern": "*.{tsv}" + } + } + ] + }, + { + "txt": [ + { + "meta": { + "type": "file", + "description": "Tab delimited results in blast-like tabular format", + "pattern": "*.{txt}" + } + }, + { + "*.txt": { + "type": "file", + "description": "Tab delimited results in blast-like tabular format", + "pattern": "*.{txt}" + } + } + ] + }, + { + "uc": [ + { + "meta": { + "type": "file", + "description": "Tab delimited results in a uclust-like format with 10 columns", + "pattern": "*.{uc}" + } + }, + { + "*.uc": { + "type": "file", + "description": "Tab delimited results in a uclust-like format with 10 columns", + "pattern": "*.{uc}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142550,52 +183130,63 @@ "tool_dev_url": "https://github.com/atks/vt", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file to decompose", - "pattern": "*.vcf(.gz)?" - } - }, - { - "intervals": { - "type": "file", - "description": "The intervals of the variants of decompose", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The decomposed VCF file", - "pattern": "*.vcf.gz" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file to decompose", + "pattern": "*.vcf(.gz)?" + } + }, + { + "intervals": { + "type": "file", + "description": "The intervals of the variants of decompose", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The decomposed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142628,92 +183219,117 @@ "tool_dev_url": "https://github.com/atks/vt", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "vcf": { - "type": "file", - "description": "The VCF file to normalize", - "pattern": "*.vcf(.gz)?" - } - }, - { - "tbi": { - "type": "file", - "description": "The tabix index of the VCF file when bgzipped", - "pattern": "*.tbi" - } - }, - { - "intervals": { - "type": "file", - "description": "The intervals of the variants of normalize", - "pattern": "*.bed" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference fasta file", - "pattern": "*.{fasta,fn,fna,fa}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference index information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "fai": { - "type": "file", - "description": "The index of the reference fasta file (OPTIONAL)", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "The normalized VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "fai": { - "type": "file", - "description": "The created index of the reference fasta file (only when the fai wasn't supplied)", - "pattern": "*.fai" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "vcf": { + "type": "file", + "description": "The VCF file to normalize", + "pattern": "*.vcf(.gz)?" + } + }, + { + "tbi": { + "type": "file", + "description": "The tabix index of the VCF file when bgzipped", + "pattern": "*.tbi" + } + }, + { + "intervals": { + "type": "file", + "description": "The intervals of the variants of normalize", + "pattern": "*.bed" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference fasta file", + "pattern": "*.{fasta,fn,fna,fa}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference index information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "fai": { + "type": "file", + "description": "The index of the reference fasta file (OPTIONAL)", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "The normalized VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "fai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n" + } + }, + { + "${fasta}.fai": { + "type": "file", + "description": "The created index of the reference fasta file (only when the fai wasn't supplied)", + "pattern": "*.fai" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142748,79 +183364,94 @@ "doi": "10.5281/zenodo.6949373", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta_gz": { - "type": "file", - "description": "BGZIPPED FASTA target file to create the mappings from.", - "pattern": "{fa.gz,fna.gz,fasta.gz}" - } - }, - { - "paf": { - "type": "file", - "description": "Optional inpute file in PAF format to derive the precise alignments for.", - "pattern": "*.{paf}" - } - }, - { - "query_self": { - "type": "boolean", - "description": "If set to true, the input FASTA will also be used as the query FASTA." - } - }, - { - "gzi": { - "type": "file", - "description": "The GZI index of the input FASTA file.", - "pattern": "*.{gzi}" - } - }, - { - "fai": { - "type": "file", - "description": "The FASTA index of the input FASTA file.", - "pattern": "*.{fai}" - } - }, - { - "fasta_query_list": { - "type": "file", - "description": "Optional inpute file in FASTA format specifying the query sequences as a list.", - "pattern": "*.{fa,fna,fasta}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "paf": { - "type": "file", - "description": "Alignments in PAF format", - "pattern": "*.{paf}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta_gz": { + "type": "file", + "description": "BGZIPPED FASTA target file to create the mappings from.", + "pattern": "{fa.gz,fna.gz,fasta.gz}" + } + }, + { + "paf": { + "type": "file", + "description": "Optional inpute file in PAF format to derive the precise alignments for.", + "pattern": "*.{paf}" + } + }, + { + "gzi": { + "type": "file", + "description": "The GZI index of the input FASTA file.", + "pattern": "*.{gzi}" + } + }, + { + "fai": { + "type": "file", + "description": "The FASTA index of the input FASTA file.", + "pattern": "*.{fai}" + } + } + ], + [ + { + "query_self": { + "type": "boolean", + "description": "If set to true, the input FASTA will also be used as the query FASTA." + } + } + ], + [ + { + "fasta_query_list": { + "type": "file", + "description": "Optional inpute file in FASTA format specifying the query sequences as a list.", + "pattern": "*.{fa,fna,fasta}" + } + } + ] + ], + "output": [ + { + "paf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.paf": { + "type": "file", + "description": "Alignments in PAF format", + "pattern": "*.{paf}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142858,45 +183489,56 @@ "tool_dev_url": "https://github.com/lh3/wgsim", "licence": [ "MIT" - ] + ], + "identifier": "biotools:wgsim" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Genome fasta file", - "pattern": "*.{fa,fasta}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Genome fasta file", + "pattern": "*.{fa,fasta}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "fastq": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.fastq": { + "type": "file", + "description": "Simulated FASTQ read files", + "pattern": "*.{fastq}" + } + } + ] }, { - "fastq": { - "type": "file", - "description": "Simulated FASTQ read files", - "pattern": "*.{fastq}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -142931,73 +183573,115 @@ "doi": "10.1371/journal.pcbi.1004572", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "BAM/SAM file", - "pattern": "*.{bam,sam}" - } - }, - { - "bai": { - "type": "file", - "description": "BAM index file", - "pattern": "*.bai" - } - }, - { - "fasta": { - "type": "file", - "description": "Reference Fasta file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "Index of the reference Fasta", - "pattern": "*.fai" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "vcf": { - "type": "file", - "description": "Compressed VCF file", - "pattern": "*.vcf.gz" - } - }, - { - "tbi": { - "type": "file", - "description": "Index of the VCF file", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "BAM/SAM file", + "pattern": "*.{bam,sam}" + } + }, + { + "bai": { + "type": "file", + "description": "BAM index file", + "pattern": "*.bai" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "Reference Fasta file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fasta_fai": { + "type": "file", + "description": "Index of the reference Fasta", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Compressed VCF file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of the VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "graph": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "Graph file", + "pattern": "*.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143029,45 +183713,55 @@ "doi": "10.1016/S0022-2836(05)80360-2", "licence": [ "US-Government-Work" - ] + ], + "identifier": "biotools:windowmasker" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "counts": { - "type": "file", - "description": "valid unit counts file", - "pattern": "*.{ascii,binary,oascii,obinary,txt}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "counts": { + "type": "file", + "description": "valid unit counts file", + "pattern": "*.{ascii,binary,oascii,obinary,txt}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "counts": { - "type": "file", - "description": "valid unit counts file", - "pattern": "*.{ascii,binary,oascii,obinary}" - } + "converted": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output}": { + "type": "file", + "description": "converted file" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143098,44 +183792,55 @@ "documentation": "https://ncbi.github.io/cxx-toolkit/", "licence": [ "MIT" - ] + ], + "identifier": "biotools:windowmasker" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "An input nucleotide fasta file." + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "An input nucleotide fasta file." + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "intervals": { - "type": "file", - "description": "An output file containing genomic locations of low\ncomplexity and highly repetitive regions\n", - "pattern": "${prefix}.txt" - } + "counts": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.txt": { + "type": "file", + "description": "A file containing frequency counts of repetitive units.", + "pattern": "*.txt" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143166,56 +183871,68 @@ "documentation": "https://ncbi.github.io/cxx-toolkit/", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "counts": { - "type": "file", - "description": "Contains count data of repetitive regions." - } - }, - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "ref": { - "type": "file", - "description": "An input nucleotide fasta file." - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "wm_intervals": { - "type": "file", - "description": "An output file containing genomic locations of low\ncomplexity and highly repetitive regions\n", - "pattern": "${output}" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "biotools:windowmasker" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "counts": { + "type": "file", + "description": "Contains count data of repetitive regions." + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "ref": { + "type": "file", + "description": "An input nucleotide fasta file." + } + } + ] + ], + "output": [ + { + "intervals": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${output}": { + "type": "file", + "description": "intervals" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143236,90 +183953,105 @@ "keywords": [ "bam", "cram", - "copy-number" - ], - "tools": [ - { - "wisecondorx": { - "description": "WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes", - "homepage": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", - "documentation": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", - "tool_dev_url": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", - "doi": "10.1093/nar/gky1263", - "licence": [ - "Attribution-NonCommercial-ShareAlike CC BY-NC-SA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "bam": { - "type": "file", - "description": "Reads in BAM/CRAM format", - "pattern": "*.{bam,cram}" - } - }, - { - "bai": { - "type": "file", - "description": "index of the BAM/CRAM file", - "pattern": "*.{bai,crai}" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference fasta meta information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "The reference FASTA file (mandatory when using CRAM files)", - "pattern": "*.{fasta,fa,fna}" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing reference fasta index meta information\ne.g. [ id:'test' ]\n" - } - }, - { - "fasta_fai": { - "type": "file", - "description": "The index of the reference FASTA file (mandatory when using CRAM files)", - "pattern": "*.fai" - } - } + "copy-number" ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, + "tools": [ { - "npz": { - "type": "file", - "description": "The output NPZ file", - "pattern": "*.npz" - } + "wisecondorx": { + "description": "WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes", + "homepage": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "documentation": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "tool_dev_url": "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX", + "doi": "10.1093/nar/gky1263", + "licence": [ + "Attribution-NonCommercial-ShareAlike CC BY-NC-SA" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "bam": { + "type": "file", + "description": "Reads in BAM/CRAM format", + "pattern": "*.{bam,cram}" + } + }, + { + "bai": { + "type": "file", + "description": "index of the BAM/CRAM file", + "pattern": "*.{bai,crai}" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference fasta meta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "The reference FASTA file (mandatory when using CRAM files)", + "pattern": "*.{fasta,fa,fna}" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing reference fasta index meta information\ne.g. [ id:'test' ]\n" + } + }, + { + "fasta_fai": { + "type": "file", + "description": "The index of the reference FASTA file (mandatory when using CRAM files)", + "pattern": "*.fai" + } + } + ] + ], + "output": [ + { + "npz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.npz": { + "type": "file", + "description": "The output NPZ file", + "pattern": "*.npz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143352,52 +184084,64 @@ "doi": "10.1093/nar/gky1263", "licence": [ "Attribution-NonCommercial-ShareAlike CC BY-NC-SA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "npz": { - "type": "file", - "description": "Single sample NPZ file (from which to determine the gender)", - "pattern": "*.npz" - } - }, - { - "reference": { - "type": "file", - "description": "Reference NPZ file", - "pattern": "*.npz" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "gender": { - "type": "string", - "description": "The gender of the input NPZ file", - "pattern": "(fe)?male" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "npz": { + "type": "file", + "description": "Single sample NPZ file (from which to determine the gender)", + "pattern": "*.npz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "Reference NPZ file", + "pattern": "*.npz" + } + } + ] + ], + "output": [ + { + "gender": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143430,45 +184174,56 @@ "doi": "10.1093/nar/gky1263", "licence": [ "Attribution-NonCommercial-ShareAlike CC BY-NC-SA" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "inputs": { + "type": "file", + "description": "Multiple NPZ files from healthy patients", + "pattern": "*.{npz}" + } } - }, - { - "inputs": { - "type": "file", - "description": "Multiple NPZ files from healthy patients", - "pattern": "*.{npz}" - } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "npz": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.npz": { + "type": "file", + "description": "The reference NPZ file", + "pattern": "*.{npz}" + } + } + ] }, { - "npz": { - "type": "file", - "description": "The reference NPZ file", - "pattern": "*.{npz}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143502,106 +184257,171 @@ "doi": "10.1093/nar/gky1263", "licence": [ "Attribution-NonCommercial-ShareAlike CC BY-NC-SA" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "npz": { - "type": "file", - "description": "An NPZ file created with WisecondorX convert", - "pattern": "*.npz" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reference": { - "type": "file", - "description": "A reference NPZ file created with WisecondorX newref", - "pattern": "*.npz" - } - }, - { - "meta3": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "blacklist": { - "type": "file", - "description": "OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small)", - "pattern": "*.bed" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "aberrations_bed": { - "type": "file", - "description": "OPTIONAL - Output abberations in BED format. This gets created with the `--bed` option", - "pattern": "*_aberrations.bed" - } - }, - { - "bins_bed": { - "type": "file", - "description": "OPTIONAL - Output bins in BED format. This gets created with the `--bed` option", - "pattern": "*_bins.bed" - } - }, - { - "segments_bed": { - "type": "file", - "description": "OPTIONAL - Output segments in BED format. This gets created with the `--bed` option", - "pattern": "*_segments.bed" - } - }, - { - "chr_statistics": { - "type": "file", - "description": "OPTIONAL - Statistics per chromosome in TXT format. This gets created with the `--bed` option", - "pattern": "*_chr_statistics.txt" - } - }, - { - "chr_plots": { - "type": "list", - "description": "OPTIONAL - A list containing the CNV plots of each chromosome. This gets created with the `--plot` option", - "pattern": "[!genome_wide]*.png" - } - }, - { - "genome_plot": { - "type": "file", - "description": "OPTIONAL - A plot containing the CNV information of the whole genome", - "pattern": "genome_wide.png" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "npz": { + "type": "file", + "description": "An NPZ file created with WisecondorX convert", + "pattern": "*.npz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing reference information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reference": { + "type": "file", + "description": "A reference NPZ file created with WisecondorX newref", + "pattern": "*.npz" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "blacklist": { + "type": "file", + "description": "OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small)", + "pattern": "*.bed" + } + } + ] + ], + "output": [ + { + "aberrations_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_aberrations.bed": { + "type": "file", + "description": "OPTIONAL - Output abberations in BED format. This gets created with the `--bed` option", + "pattern": "*_aberrations.bed" + } + } + ] + }, + { + "bins_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_bins.bed": { + "type": "file", + "description": "OPTIONAL - Output bins in BED format. This gets created with the `--bed` option", + "pattern": "*_bins.bed" + } + } + ] + }, + { + "segments_bed": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_segments.bed": { + "type": "file", + "description": "OPTIONAL - Output segments in BED format. This gets created with the `--bed` option", + "pattern": "*_segments.bed" + } + } + ] + }, + { + "chr_statistics": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*_chr_statistics.txt": { + "type": "file", + "description": "OPTIONAL - Statistics per chromosome in TXT format. This gets created with the `--bed` option", + "pattern": "*_chr_statistics.txt" + } + } + ] + }, + { + "chr_plots": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "[!genome_wide]*.png": { + "type": "list", + "description": "OPTIONAL - A list containing the CNV plots of each chromosome. This gets created with the `--plot` option", + "pattern": "[!genome_wide]*.png" + } + } + ] + }, + { + "genome_plot": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "genome_wide.png": { + "type": "file", + "description": "OPTIONAL - A plot containing the CNV information of the whole genome", + "pattern": "genome_wide.png" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143633,80 +184453,111 @@ "tool_dev_url": "https://github.com/Illumina/witty.er", "licence": [ "BSD-2" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "query_vcf": { - "type": "file", - "description": "A VCF with called variants to benchmark against the standard", - "pattern": "*.{vcf}" - } - }, - { - "truth_vcf": { - "type": "file", - "description": "A standard VCF to compare against", - "pattern": "*.{vcf}" - } - }, - { - "bed": { - "type": "file", - "description": "A BED file specifying regions to be included in the analysis (optional)", - "pattern": "*.bed" - } - }, - { - "wittyer_config": { - "type": "file", - "description": "Config file in json format used to specify per variant type settings.\nUsed in place of include bed arguments. (optional)\n", - "pattern": "*.json" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "report": { - "type": "file", - "description": "Detailed per-sample-pair, per-svtype, per-bin stats", - "pattern": "*.json" - } - }, - { - "bench_vcf": { - "type": "file", - "description": "Updated query and truth entries merged into one file", - "pattern": "*.vcf.gz" - } - }, - { - "bench_vcf_tbi": { - "type": "file", - "description": "Index of merged query and truth entries VCF file", - "pattern": "*.vcf.gz.tbi" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "query_vcf": { + "type": "file", + "description": "A VCF with called variants to benchmark against the standard", + "pattern": "*.{vcf}" + } + }, + { + "truth_vcf": { + "type": "file", + "description": "A standard VCF to compare against", + "pattern": "*.{vcf}" + } + }, + { + "bed": { + "type": "file", + "description": "A BED file specifying regions to be included in the analysis (optional)", + "pattern": "*.bed" + } + }, + { + "wittyer_config": { + "type": "file", + "description": "Config file in json format used to specify per variant type settings.\nUsed in place of include bed arguments. (optional)\n", + "pattern": "*.json" + } + } + ] + ], + "output": [ + { + "report": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.json": { + "type": "file", + "description": "Detailed per-sample-pair, per-svtype, per-bin stats", + "pattern": "*.json" + } + } + ] + }, + { + "bench_vcf": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz": { + "type": "file", + "description": "Updated query and truth entries merged into one file", + "pattern": "*.vcf.gz" + } + } + ] + }, + { + "bench_vcf_tbi": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.vcf.gz.tbi": { + "type": "file", + "description": "Index of merged query and truth entries VCF file", + "pattern": "*.vcf.gz.tbi" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143749,63 +184600,86 @@ "doi": "10.4230/LIPIcs.WABI.2020.4", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "host_fasta": { - "type": "file", - "description": "Reference genome fasta file from host, compressed or uncompressed.\n" - } - }, - { - "graft_fasta": { - "type": "file", - "description": "Reference genome fasta file from graft, compressed or uncompressed.\n" - } - }, - { - "index": { - "type": "string", - "description": "File name prefix to store index files.\n" - } - }, - { - "nobjects": { - "type": "string", - "description": "Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000.\n" - } - }, - { - "mask": { - "type": "string", - "description": "Gapped k-mer mask (quoted string like '#__##_##__#').\n" - } - } - ], - "output": [ - { - "hash": { - "type": "file", - "description": "File with index hash file.", - "pattern": "*hash" - } - }, - { - "info": { - "type": "file", - "description": "File with index info file.", - "pattern": "*info" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "host_fasta": { + "type": "file", + "description": "Reference genome fasta file from host, compressed or uncompressed.\n" + } + } + ], + [ + { + "graft_fasta": { + "type": "file", + "description": "Reference genome fasta file from graft, compressed or uncompressed.\n" + } + } + ], + [ + { + "index": { + "type": "string", + "description": "File name prefix to store index files.\n" + } + } + ], + [ + { + "nobjects": { + "type": "string", + "description": "Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000.\n" + } + } + ], + [ + { + "mask": { + "type": "string", + "description": "Gapped k-mer mask (quoted string like '#__##_##__#').\n" + } + } + ] + ], + "output": [ + { + "hash": [ + { + "${index}.hash": { + "type": "file", + "description": "File with index hash file.", + "pattern": "*hash" + } + } + ] + }, + { + "info": [ + { + "${index}.info": { + "type": "file", + "description": "File with index info file.", + "pattern": "*info" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143839,45 +184713,56 @@ "GNU LGPLv2.1", "GNU GPLv2", "GNU GPLv3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "raw_file": { - "type": "file", - "description": "File to be compressed", - "pattern": "*.*" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "raw_file": { + "type": "file", + "description": "File to be compressed", + "pattern": "*.*" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "archive": { - "type": "file", - "description": "The compressed file", - "pattern": "*.xz" - } + "archive": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$archive": { + "type": "file", + "description": "The compressed file", + "pattern": "*.xz" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143911,45 +184796,56 @@ "GNU LGPLv2.1", "GNU GPLv2", "GNU GPLv3" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "archive": { - "type": "file", - "description": "File to be decompressed", - "pattern": "*.{xz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "archive": { + "type": "file", + "description": "File to be decompressed", + "pattern": "*.{xz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "file": { - "type": "file", - "description": "The decompressed file", - "pattern": "*.*" - } + "file": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "$decompressed_file": { + "type": "file", + "description": "The decompressed file", + "pattern": "*.*" + } + } + ] }, { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -143983,73 +184879,108 @@ "doi": "10.1093/bioinformatics/btac808", "licence": [ "MIT" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "hic_map": { - "type": "file", - "description": "BED file containing coordinates of read alignments", - "pattern": "*.{bed,bam,bin}" - } - }, - { - "fasta": { - "type": "file", - "description": "FASTA reference file", - "pattern": "*.{fasta,fa}" - } - }, - { - "fai": { - "type": "file", - "description": "index of the reference file", - "pattern": "*.{fai}" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "scaffolds_fasta": { - "type": "file", - "description": "FASTA file with resulting contigs", - "pattern": "*scaffolds_final.fa" - } - }, - { - "scaffolds_agp": { - "type": "file", - "description": "AGP file containing contigs placing coordinates", - "pattern": "*scaffolds_final.agp" - } - }, - { - "binary": { - "type": "file", - "description": "BIN file with alignment results of Hi-C reads to the contigs in internal YaHS binary format", - "pattern": "*bin" - } + ], + "identifier": "biotools:yahs" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "hic_map": { + "type": "file", + "description": "BED file containing coordinates of read alignments", + "pattern": "*.{bed,bam,bin}" + } + } + ], + [ + { + "fasta": { + "type": "file", + "description": "FASTA reference file", + "pattern": "*.{fasta,fa}" + } + } + ], + [ + { + "fai": { + "type": "file", + "description": "index of the reference file", + "pattern": "*.{fai}" + } + } + ] + ], + "output": [ + { + "scaffolds_fasta": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*scaffolds_final.fa": { + "type": "file", + "description": "FASTA file with resulting contigs", + "pattern": "*scaffolds_final.fa" + } + } + ] + }, + { + "scaffolds_agp": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*scaffolds_final.agp": { + "type": "file", + "description": "AGP file containing contigs placing coordinates", + "pattern": "*scaffolds_final.agp" + } + } + ] + }, + { + "binary": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n" + } + }, + { + "*bin": { + "type": "file", + "description": "BIN file with alignment results of Hi-C reads to the contigs in internal YaHS binary format", + "pattern": "*bin" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -144083,45 +185014,56 @@ "tool_dev_url": "https://github.com/lh3/yak", "licence": [ "MIT" - ] + ], + "identifier": "" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "fastq": { - "type": "file", - "description": "reads fastq/fasta file", - "pattern": "*.{fastq.gz,fq.gz,fasta.gz,fa.gz}" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastq": { + "type": "file", + "description": "reads fastq/fasta file", + "pattern": "*.{fastq.gz,fq.gz,fasta.gz,fa.gz}" + } } - } + ] ], "output": [ { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "yak": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*.yak": { + "type": "file", + "description": "k-mer hash table of input", + "pattern": "*.{yak}" + } + } + ] }, { - "yak": { - "type": "file", - "description": "k-mer hash table of input", - "pattern": "*.{yak}" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -144155,38 +185097,56 @@ "tool_dev_url": "https://github.com/seqan/seqan", "licence": [ "https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE" - ] + ], + "identifier": "biotools:yara" } } ], "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "fasta": { - "type": "file", - "description": "Input genome fasta file" + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "fasta": { + "type": "file", + "description": "Input genome fasta file" + } } - } + ] ], "output": [ { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + "index": [ + { + "meta": { + "type": "file", + "description": "YARA genome index files", + "pattern": "yara.*" + } + }, + { + "${fasta}*": { + "type": "file", + "description": "YARA genome index files", + "pattern": "yara.*" + } + } + ] }, { - "index": { - "type": "file", - "description": "YARA genome index files", - "pattern": "yara.*" - } + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -144224,63 +185184,86 @@ "tool_dev_url": "https://github.com/seqan/seqan", "licence": [ "https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "reads": { - "type": "file", - "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" - } - }, - { - "meta2": { - "type": "map", - "description": "Groovy Map containing index information\ne.g. [ id:'test' ]\n" - } - }, - { - "index": { - "type": "file", - "description": "YARA genome index files" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } - }, - { - "bam": { - "type": "file", - "description": "Sorted BAM file", - "pattern": "*.{bam}" - } - }, - { - "bai": { - "type": "file", - "description": "Sorted BAM file index", - "pattern": "*.{bai}" - } + ], + "identifier": "biotools:yara" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data,\nrespectively.\n" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing index information\ne.g. [ id:'test' ]\n" + } + }, + { + "index": { + "type": "file", + "description": "YARA genome index files" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapped.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.{bam}" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.mapped.bam.bai": { + "type": "file", + "description": "Sorted BAM file index", + "pattern": "*.{bai}" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ @@ -144319,44 +185302,55 @@ "tool_dev_url": "https://sourceforge.net/projects/p7zip\"", "licence": [ "LGPL-2.1-or-later" - ] - } - } - ], - "input": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "files": { - "type": "file", - "description": "File or list of files to be zipped" - } - } - ], - "output": [ - { - "meta": { - "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" - } - }, - { - "zipped_archive": { - "type": "file", - "description": "ZIP file", - "pattern": "*.zip" - } - }, - { - "versions": { - "type": "file", - "description": "File containing software versions", - "pattern": "versions.yml" - } + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "files": { + "type": "file", + "description": "File or list of files to be zipped" + } + } + ] + ], + "output": [ + { + "zipped_archive": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "${prefix}.zip": { + "type": "file", + "description": "ZIP file", + "pattern": "*.zip" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] } ], "authors": [ diff --git a/public/pipelines.json b/public/pipelines.json index 35dfd55a5d..217c0f5a9f 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -5492,7 +5492,7 @@ } }, "network_count": 3, - "subscribers_count": 163, + "subscribers_count": 162, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -5657,7 +5657,7 @@ "forks_count": 25, "archived": false, "disabled": false, - "open_issues_count": 22, + "open_issues_count": 23, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -5669,7 +5669,7 @@ ], "visibility": "public", "forks": 25, - "open_issues": 22, + "open_issues": 23, "watchers": 25, "default_branch": "master", "temp_clone_token": "", @@ -6936,7 +6936,7 @@ } }, "network_count": 3, - "subscribers_count": 199, + "subscribers_count": 198, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -7980,7 +7980,7 @@ } }, "network_count": 6, - "subscribers_count": 190, + "subscribers_count": 189, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9147,7 +9147,7 @@ } }, "network_count": 2, - "subscribers_count": 189, + "subscribers_count": 188, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9392,7 +9392,7 @@ } }, "network_count": 4, - "subscribers_count": 164, + "subscribers_count": 163, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9882,7 +9882,7 @@ "forks_count": 31, "archived": false, "disabled": false, - "open_issues_count": 41, + "open_issues_count": 42, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -9900,7 +9900,7 @@ ], "visibility": "public", "forks": 31, - "open_issues": 41, + "open_issues": 42, "watchers": 56, "default_branch": "master", "temp_clone_token": "", @@ -9998,7 +9998,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 3, + "open_pr_count": 4, "repository_url": "https://github.com/nf-core/differentialabundance", "contributors": [ { @@ -10630,9 +10630,9 @@ "url": "https://api.github.com/repos/nf-core/eager", "created_at": "2018-06-03T15:52:24Z", "updated_at": "2024-09-18T04:06:49Z", - 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