diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 625143e93f..7aa34767d1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -199,6 +199,15 @@ jobs: NXF_VER: - "23.04.0" - "latest-everything" + exclude: + - tags: "bwa/index" + - tags: "bwa/mem" + - tags: "cat/cat" + - tags: "cat/fastq" + - tags: "custom/dumpsoftwareversions" + - tags: "fastp" + - tags: "fastqc" + - tags: "samtools/stats" env: NXF_ANSI_LOG: false TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" diff --git a/CHANGELOG.md b/CHANGELOG.md index 6007bc48c9..2b11cbe4e8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1278](https://github.com/nf-core/sarek/pull/1278) - Hide sentieon parameters similar to other variant callers - [#1280](https://github.com/nf-core/sarek/pull/1280) - Replacing link to `SentieonDNAscopeModel1.1.model` in Sentieon's S3 with link to same file in igenomes' S3 - [#1303](https://github.com/nf-core/sarek/pull/1303) - Ressurect vep_version params and changed its scope to pipeline to enable usage for vep loftee plugin +- [#1304](https://github.com/nf-core/sarek/pull/1304) - Update modules ### Fixed @@ -35,6 +36,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ---------- | ----------- | ----------- | +| fastqc | 0.11.9 | 0.12.1 | +| multiqc | 1.15 | 1.17 | + +### Modules / Subworkflows + +| script | Old name | New name | +| ----------------------------- | ----------------------------- | ----------------------------- | +| `gatk4spark/applybqsr` | `GATK4_APPLYBQSRSPARK` | `GATK4SPARK_APPLYBQSR` | +| `gatk4spark/baserecalibrator` | `GATK4_BASERECALIBRATORSPARK` | `GATK4SPARK_BASERECALIBRATOR` | +| `gatk4spark/markduplicates` | `GATK4_MARKDUPLICATESSPARK` | `GATK4SPARK_MARKDUPLICATES` | ## [3.3.2](https://github.com/nf-core/sarek/releases/tag/3.3.2) - Ráhpajávvre diff --git a/conf/base.config b/conf/base.config index 446e88b99b..a132f3cb6b 100644 --- a/conf/base.config +++ b/conf/base.config @@ -74,11 +74,11 @@ process { label = "process_high" memory = { check_max( 36.GB * task.attempt, 'memory' ) } } - withName: 'GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK' { + withName: 'GATK4_MARKDUPLICATES|GATK4SPARK_MARKDUPLICATES' { cpus = { check_max( 6 * task.attempt, 'cpus' ) } memory = { check_max( 30.GB * task.attempt, 'memory' ) } } - withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS'{ + withName:'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR|GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS'{ cpus = { check_max( 2 * task.attempt, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index 7356645add..87ca891277 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -64,7 +64,7 @@ process { if (params.tools && params.tools.split(',').contains('bcfann')) { withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' { ext.args = '--output-type z' - ext.prefix = { "${vcf.baseName.minus(".vcf")}_BCF.ann" } + ext.prefix = { input.baseName - ".vcf" + "_BCF.ann" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, diff --git a/conf/modules/markduplicates.config b/conf/modules/markduplicates.config index 702b9b721b..ef106423ef 100644 --- a/conf/modules/markduplicates.config +++ b/conf/modules/markduplicates.config @@ -90,7 +90,7 @@ process { ] } - withName: 'GATK4_MARKDUPLICATES_SPARK' { + withName: 'GATK4SPARK_MARKDUPLICATES' { ext.args = '--remove-sequencing-duplicates false -VS LENIENT' ext.prefix = { "${meta.id}.md.cram" } publishDir = [ diff --git a/conf/modules/prepare_recalibration.config b/conf/modules/prepare_recalibration.config index cb394f0a2f..915075d5b4 100644 --- a/conf/modules/prepare_recalibration.config +++ b/conf/modules/prepare_recalibration.config @@ -15,7 +15,7 @@ process { - withName: 'GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK' { + withName: 'GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR' { ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" } publishDir = [ mode: params.publish_dir_mode, diff --git a/conf/modules/recalibrate.config b/conf/modules/recalibrate.config index 9602e33caf..c46a1bb82b 100644 --- a/conf/modules/recalibrate.config +++ b/conf/modules/recalibrate.config @@ -15,7 +15,7 @@ process { - withName: 'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK' { + withName: 'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR' { ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" } publishDir = [ enabled: !params.save_output_as_bam, diff --git a/modules.json b/modules.json index 4cd099c32d..1b5a25a36b 100644 --- a/modules.json +++ b/modules.json @@ -7,476 +7,476 @@ "nf-core": { "ascat": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bcftools/annotate": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bcftools/mpileup": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "d6d112a1af2ee8c97fc1932df008183341e7d8fe", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", - "git_sha": "e2693a7e2d773b92e0649b25880ee22fe82bb79d", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bwa/index": { "branch": "master", - "git_sha": "bfed129da5134b4439b1821c917972570d44d39c", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", - "git_sha": "3dc300ddcaa563c1e3503477557c0e0def6df2ce", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bwamem2/index": { "branch": "master", - "git_sha": "bfed129da5134b4439b1821c917972570d44d39c", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", - "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "cat/cat": { "branch": "master", - 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"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/bam2fq": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/collatefastq": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013", + "git_sha": "e7ce60acc8a33fa17429e966364657a63016e870", "installed_by": ["modules"] }, "samtools/mpileup": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "samtools/view": { "branch": "master", - "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "sentieon/applyvarcal": { "branch": "master", - "git_sha": "6c9c11ee96796e53a01b4719286acce6af14bc3a", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", - "git_sha": "149b4746c6e16ef84f64db5bb245d5b9495fdc3f", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", - "git_sha": "915a0b16ba3e40ef59e7b44843b3118e17a9c906", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "sentieon/dnamodelapply": { "branch": "master", - "git_sha": "43ef68091a1188fd8dc4c03f9341b556803c7514", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "sentieon/dnascope": { "branch": "master", - "git_sha": "4fb6fdc8046ec09cd30f92a2a252e9a0ba4a6309", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "sentieon/gvcftyper": { "branch": "master", - "git_sha": "6c9c11ee96796e53a01b4719286acce6af14bc3a", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "sentieon/haplotyper": { "branch": "master", - "git_sha": "b9172e8c26a3db5009f7872654c44587e254f094", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "sentieon/varcal": { "branch": "master", - "git_sha": "6c9c11ee96796e53a01b4719286acce6af14bc3a", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "snpeff/download": { "branch": "master", - "git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["vcf_annotate_snpeff", "modules"] }, "strelka/germline": { "branch": "master", - "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "strelka/somatic": { "branch": "master", - "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["vcf_annotate_snpeff", "modules"] }, "tabix/tabix": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["vcf_annotate_ensemblvep", "modules"] }, "tiddit/sv": { "branch": "master", - "git_sha": "1c90a501d102b800c27697f5ef39a6e217ab1915", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "unzip": { "branch": "master", - "git_sha": "cf67a6d7d043e2bd6a3099be84c72046fc71508f", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "vcftools": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] } } @@ -485,12 +485,12 @@ "nf-core": { "vcf_annotate_ensemblvep": { "branch": "master", - "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", "installed_by": ["subworkflows"] }, "vcf_annotate_snpeff": { "branch": "master", - "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/ascat/environment.yml b/modules/nf-core/ascat/environment.yml new file mode 100644 index 0000000000..6708ce86a8 --- /dev/null +++ b/modules/nf-core/ascat/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::ascat=3.1.1 + - bioconda::cancerit-allelecount=4.3.0 diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index 922f8b3cac..8aeb9847b5 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -2,7 +2,7 @@ process ASCAT { tag "$meta.id" label 'process_medium' - conda "bioconda::ascat=3.1.1 bioconda::cancerit-allelecount=4.3.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:ba3e6d2157eac2d38d22e62ec87675e12adb1010-0': 'biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:ba3e6d2157eac2d38d22e62ec87675e12adb1010-0' }" diff --git a/modules/nf-core/ascat/meta.yml b/modules/nf-core/ascat/meta.yml index 104ef0fb33..34ea2e51d9 100644 --- a/modules/nf-core/ascat/meta.yml +++ b/modules/nf-core/ascat/meta.yml @@ -7,12 +7,10 @@ keywords: tools: - ascat: description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome). - documentation: https://github.com/VanLoo-lab/ascat/tree/master/man tool_dev_url: https://github.com/VanLoo-lab/ascat doi: "10.1093/bioinformatics/btaa538" licence: ["GPL v3"] - input: - args: type: map @@ -38,7 +36,6 @@ input: ] } ``` - - meta: type: map description: | @@ -46,8 +43,7 @@ input: e.g. [ id:'test', single_end:false ] - 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/. + 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 @@ -66,10 +62,7 @@ input: 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` + 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) @@ -118,3 +111,9 @@ authors: - "@FriederikeHanssen" - "@maxulysse" - "@SusiJo" +maintainers: + - "@aasNGC" + - "@lassefolkersen" + - "@FriederikeHanssen" + - "@maxulysse" + - "@SusiJo" diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff index 7025cfaa26..4376af5172 100644 --- a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff +++ b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff @@ -1,89 +1,28 @@ Changes in module 'nf-core/bcftools/annotate' --- modules/nf-core/bcftools/annotate/main.nf +++ modules/nf-core/bcftools/annotate/main.nf -@@ -5,14 +5,17 @@ - conda "bioconda::bcftools=1.17" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': -- 'biocontainers/bcftools:1.17--haef29d1_0' }" -+ 'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }" +@@ -8,7 +8,10 @@ + 'biocontainers/bcftools:1.17--haef29d1_0' }" input: - tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(header_lines) -+ tuple val(meta), path(vcf) -+ path bcftools_annotations -+ path bcftools_annotations_index -+ path bcftools_header_lines ++ tuple val(meta), path(input) ++ path annotations ++ path annotations_index ++ path header_lines output: -- tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf -- path "versions.yml" , emit: versions -+ tuple val(meta), path("*.vcf.gz"), emit: vcf -+ path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when -@@ -20,15 +23,19 @@ - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" -- def header_file = header_lines ? "--header-lines ${header_lines}" : '' -- def annotations_file = annotations ? "--annotations ${annotations}" : '' -+ def header_file = bcftools_header_lines ? "--header-lines ${bcftools_header_lines}" : '' -+ def annotations_file = bcftools_annotations ? "--annotations ${bcftools_annotations}" : '' - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf +@@ -29,6 +32,10 @@ "vcf" -- if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" -+ if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ + bcftools \\ + index \\ -+ $vcf -+ ++ $input ++ bcftools \\ annotate \\ $args \\ -@@ -36,7 +43,7 @@ - $header_file \\ - --output ${prefix}.${extension} \\ - --threads $task.cpus \\ -- $input -+ $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": -@@ -60,4 +67,4 @@ - bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' ) - END_VERSIONS - """ --} -+} ---- modules/nf-core/bcftools/annotate/meta.yml -+++ modules/nf-core/bcftools/annotate/meta.yml -@@ -26,13 +26,13 @@ - - index: - type: file - description: Index of the query VCF or BCF file -- - annotations: -+ - bcftools_annotations: - type: file - description: Bgzip-compressed file with annotations -- - annotations_index: -+ - bcftools_annotations_index: - type: file - description: Index of the annotations file -- - header_lines: -+ - bcftools_header_lines: - type: file - description: Contains lines to append to the output VCF header - -@@ -53,4 +53,4 @@ - - authors: - - "@projectoriented" -- - "@ramprasadn" -+ - "@ramprasadn" + ************************************************************ diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml new file mode 100644 index 0000000000..57631f42ea --- /dev/null +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bcftools=1.17 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 58c189a60f..f00c5fe2d7 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -2,20 +2,20 @@ process BCFTOOLS_ANNOTATE { tag "$meta.id" label 'process_low' - conda "bioconda::bcftools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': - 'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }" + 'biocontainers/bcftools:1.17--haef29d1_0' }" input: - tuple val(meta), path(vcf) - path bcftools_annotations - path bcftools_annotations_index - path bcftools_header_lines + tuple val(meta), path(input) + path annotations + path annotations_index + path header_lines output: - tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -23,19 +23,19 @@ process BCFTOOLS_ANNOTATE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def header_file = bcftools_header_lines ? "--header-lines ${bcftools_header_lines}" : '' - def annotations_file = bcftools_annotations ? "--annotations ${bcftools_annotations}" : '' + def header_file = header_lines ? "--header-lines ${header_lines}" : '' + def annotations_file = annotations ? "--annotations ${annotations}" : '' def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" - if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ bcftools \\ index \\ - $vcf - + $input + bcftools \\ annotate \\ $args \\ @@ -43,7 +43,7 @@ process BCFTOOLS_ANNOTATE { $header_file \\ --output ${prefix}.${extension} \\ --threads $task.cpus \\ - $vcf + $input cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -67,4 +67,4 @@ process BCFTOOLS_ANNOTATE { bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' ) END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index c8a389697e..f3aa463bf5 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -13,7 +13,6 @@ tools: documentation: https://samtools.github.io/bcftools/bcftools.html#annotate doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] - input: - meta: type: map @@ -26,16 +25,15 @@ input: - index: type: file description: Index of the query VCF or BCF file - - bcftools_annotations: + - annotations: type: file description: Bgzip-compressed file with annotations - - bcftools_annotations_index: + - annotations_index: type: file description: Index of the annotations file - - bcftools_header_lines: + - header_lines: type: file description: Contains lines to append to the output VCF header - output: - meta: type: map @@ -50,7 +48,9 @@ output: type: file description: Compressed annotated VCF file pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - authors: - "@projectoriented" - "@ramprasadn" +maintainers: + - "@projectoriented" + - "@ramprasadn" diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml new file mode 100644 index 0000000000..57631f42ea --- /dev/null +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bcftools=1.17 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 244a42ccf0..2ff690b1be 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -2,7 +2,7 @@ process BCFTOOLS_CONCAT { tag "$meta.id" label 'process_medium' - conda "bioconda::bcftools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': 'biocontainers/bcftools:1.17--haef29d1_0' }" diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index e8c83cd685..8731b17bc8 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -5,7 +5,6 @@ keywords: - concat - bcftools - VCF - tools: - concat: description: | @@ -47,3 +46,6 @@ output: authors: - "@abhi18av" - "@nvnieuwk" +maintainers: + - "@abhi18av" + - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml new file mode 100644 index 0000000000..57631f42ea --- /dev/null +++ b/modules/nf-core/bcftools/mpileup/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bcftools=1.17 diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index aa9e811fa1..83bec8ef5f 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -2,14 +2,14 @@ process BCFTOOLS_MPILEUP { tag "$meta.id" label 'process_medium' - conda "bioconda::bcftools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': 'biocontainers/bcftools:1.17--haef29d1_0' }" input: tuple val(meta), path(bam), path(intervals) - path fasta + tuple val(meta2), path(fasta) val save_mpileup output: diff --git a/modules/nf-core/bcftools/mpileup/meta.yml b/modules/nf-core/bcftools/mpileup/meta.yml index 5619a6f511..65410ddd66 100644 --- a/modules/nf-core/bcftools/mpileup/meta.yml +++ b/modules/nf-core/bcftools/mpileup/meta.yml @@ -25,6 +25,10 @@ input: - 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' ] - fasta: type: file description: FASTA reference file @@ -61,3 +65,6 @@ output: authors: - "@joseespinosa" - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml new file mode 100644 index 0000000000..57631f42ea --- /dev/null +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bcftools=1.17 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 702d510f37..c842daf232 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -2,7 +2,7 @@ process BCFTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda "bioconda::bcftools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': 'biocontainers/bcftools:1.17--haef29d1_0' }" diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index 0c244a486e..84747c6d89 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -12,7 +12,6 @@ tools: tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] - input: - meta: type: map @@ -23,7 +22,6 @@ input: type: file description: The VCF/BCF file to be sorted pattern: "*.{vcf.gz,vcf,bcf}" - output: - meta: type: map @@ -38,6 +36,7 @@ output: type: file description: Sorted VCF file pattern: "*.{vcf.gz}" - authors: - "@Gwennid" +maintainers: + - "@Gwennid" diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml new file mode 100644 index 0000000000..57631f42ea --- /dev/null +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bcftools=1.17 diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 7ccb9bf6cb..b3a5f23ba6 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -2,7 +2,7 @@ process BCFTOOLS_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::bcftools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': 'biocontainers/bcftools:1.17--haef29d1_0' }" diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml index 5850d25f71..7ea2103e3b 100644 --- a/modules/nf-core/bcftools/stats/meta.yml +++ b/modules/nf-core/bcftools/stats/meta.yml @@ -70,3 +70,8 @@ authors: - "@drpatelh" - "@SusiJo" - "@TCLamnidis" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@SusiJo" + - "@TCLamnidis" diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml new file mode 100644 index 0000000000..c5b0826008 --- /dev/null +++ b/modules/nf-core/bwa/index/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa=0.7.17 diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index c30d194d05..24b5a2ea99 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -2,7 +2,7 @@ process BWA_INDEX { tag "$fasta" label 'process_single' - conda "bioconda::bwa=0.7.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : 'biocontainers/bwa:0.7.17--hed695b0_7' }" diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 2c6cfcd795..730628d005 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -40,3 +40,6 @@ output: authors: - "@drpatelh" - "@maxulysse" +maintainers: + - "@drpatelh" + - "@maxulysse" diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test new file mode 100644 index 0000000000..5fc8d49662 --- /dev/null +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -0,0 +1,33 @@ +nextflow_process { + + name "Test Process BWA_INDEX" + tag "modules_nfcore" + tag "modules" + tag "bwa" + tag "bwa/index" + script "../main.nf" + process "BWA_INDEX" + + test("BWA index") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bwa/index/tests/main.nf.test.snap b/modules/nf-core/bwa/index/tests/main.nf.test.snap new file mode 100644 index 0000000000..e51ad5bf2b --- /dev/null +++ b/modules/nf-core/bwa/index/tests/main.nf.test.snap @@ -0,0 +1,43 @@ +{ + "BWA index": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "1": [ + "versions.yml:md5,0f20525da90e7489a7ebb02adca3265f" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "versions": [ + "versions.yml:md5,0f20525da90e7489a7ebb02adca3265f" + ] + } + ], + "timestamp": "2023-10-17T17:20:20.180927714" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwa/index/tests/tags.yml b/modules/nf-core/bwa/index/tests/tags.yml new file mode 100644 index 0000000000..28bb483c4e --- /dev/null +++ b/modules/nf-core/bwa/index/tests/tags.yml @@ -0,0 +1,2 @@ +bwa/index: + - modules/nf-core/bwa/index/** diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml new file mode 100644 index 0000000000..34f50c48b4 --- /dev/null +++ b/modules/nf-core/bwa/mem/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa=0.7.17 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 8ba99dfdb7..17e6fbd06c 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -2,7 +2,7 @@ process BWA_MEM { tag "$meta.id" label 'process_high' - conda "bioconda::bwa=0.7.17 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' : 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' }" diff --git a/modules/nf-core/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml index 62357bf8d5..440fb1f9cf 100644 --- a/modules/nf-core/bwa/mem/meta.yml +++ b/modules/nf-core/bwa/mem/meta.yml @@ -53,3 +53,6 @@ output: authors: - "@drpatelh" - "@jeremy1805" +maintainers: + - "@drpatelh" + - "@jeremy1805" diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test new file mode 100644 index 0000000000..b199bb70f6 --- /dev/null +++ b/modules/nf-core/bwa/mem/tests/main.nf.test @@ -0,0 +1,172 @@ +nextflow_process { + + name "Test Process BWA_MEM" + tag "modules_nfcore" + tag "modules" + tag "bwa" + tag "bwa/mem" + script "../main.nf" + process "BWA_MEM" + + test("Single-End") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BWA_INDEX.out.index + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Single-End Sort") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BWA_INDEX.out.index + input[2] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Paired-End") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BWA_INDEX.out.index + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Paired-End Sort") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BWA_INDEX.out.index + input[2] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test.snap b/modules/nf-core/bwa/mem/tests/main.nf.test.snap new file mode 100644 index 0000000000..ea3bfed4fd --- /dev/null +++ b/modules/nf-core/bwa/mem/tests/main.nf.test.snap @@ -0,0 +1,126 @@ +{ + "Single-End": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,3d43027d4163ada97911b814001511e5" + ] + ], + "1": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,3d43027d4163ada97911b814001511e5" + ] + ], + "versions": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ] + } + ], + "timestamp": "2023-10-18T11:02:55.420631681" + }, + "Single-End Sort": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,61eac1213d2bf5e88e225e545010e9b8" + ] + ], + "1": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,61eac1213d2bf5e88e225e545010e9b8" + ] + ], + "versions": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ] + } + ], + "timestamp": "2023-10-18T11:03:02.646869498" + }, + "Paired-End": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,809ccfe4300fa5005a9d0d4dc09b1a36" + ] + ], + "1": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,809ccfe4300fa5005a9d0d4dc09b1a36" + ] + ], + "versions": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ] + } + ], + "timestamp": "2023-10-18T11:03:09.793041294" + }, + "Paired-End Sort": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,2622f4380f992c505af7dab8c256313f" + ] + ], + "1": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,2622f4380f992c505af7dab8c256313f" + ] + ], + "versions": [ + "versions.yml:md5,809f4a8c7f0c8497a9099dab9d6cc71e" + ] + } + ], + "timestamp": "2023-10-18T11:04:43.662093286" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwa/mem/tests/tags.yml b/modules/nf-core/bwa/mem/tests/tags.yml new file mode 100644 index 0000000000..82992d1f0b --- /dev/null +++ b/modules/nf-core/bwa/mem/tests/tags.yml @@ -0,0 +1,3 @@ +bwa/mem: + - modules/nf-core/bwa/index/** + - modules/nf-core/bwa/mem/** diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml new file mode 100644 index 0000000000..cef9ec4e78 --- /dev/null +++ b/modules/nf-core/bwamem2/index/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa-mem2=2.2.1 diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 244e1005a1..b7688285d7 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -2,7 +2,7 @@ process BWAMEM2_INDEX { tag "$fasta" label 'process_single' - conda "bioconda::bwa-mem2=2.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : 'biocontainers/bwa-mem2:2.2.1--he513fc3_0' }" diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml index 40c26c3873..c14a109252 100644 --- a/modules/nf-core/bwamem2/index/meta.yml +++ b/modules/nf-core/bwamem2/index/meta.yml @@ -38,3 +38,5 @@ output: pattern: "versions.yml" authors: - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml new file mode 100644 index 0000000000..2d75270b2b --- /dev/null +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa-mem2=2.2.1 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index d427dea3c4..cbec7eef50 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -2,7 +2,7 @@ process BWAMEM2_MEM { tag "$meta.id" label 'process_high' - conda "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' : 'biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' }" diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index bc3dfcdd0e..04891b26a9 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -57,3 +57,5 @@ output: pattern: "versions.yml" authors: - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml new file mode 100644 index 0000000000..cdad6baafc --- /dev/null +++ b/modules/nf-core/cat/cat/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 9f062219bb..4264a92ccc 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -2,7 +2,7 @@ process CAT_CAT { tag "$meta.id" label 'process_low' - conda "conda-forge::pigz=2.3.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : 'biocontainers/pigz:2.3.4' }" diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml index 8acc0bfac5..00a8db0bca 100644 --- a/modules/nf-core/cat/cat/meta.yml +++ b/modules/nf-core/cat/cat/meta.yml @@ -7,9 +7,7 @@ keywords: tools: - cat: description: Just concatenation - documentation: https://man7.org/linux/man-pages/man1/cat.1.html - licence: ["GPL-3.0-or-later"] input: - meta: @@ -21,7 +19,6 @@ input: type: file description: List of compressed / uncompressed files pattern: "*" - output: - versions: type: file @@ -31,7 +28,9 @@ output: type: file description: Concatenated file. Will be gzipped if file_out ends with ".gz" pattern: "${file_out}" - authors: - "@erikrikarddaniel" - "@FriederikeHanssen" +maintainers: + - "@erikrikarddaniel" + - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test new file mode 100644 index 0000000000..5766daafbe --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -0,0 +1,153 @@ +nextflow_process { + + name "Test Process CAT_CAT" + script "../main.nf" + process "CAT_CAT" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/cat" + + test("test_cat_unzipped_unzipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + + test("test_cat_zipped_zipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} + ) + } + } + + test("test_cat_zipped_unzipped") { + config './nextflow_zipped_unzipped.config' + + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_cat_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} + ) + } + } + + test("test_cat_one_file_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")} + ) + } + } +} + diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap new file mode 100644 index 0000000000..423571ba27 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -0,0 +1,121 @@ +{ + "test_cat_unzipped_zipped_size": { + "content": [ + 375 + ], + "timestamp": "2023-10-16T14:33:08.049445686" + }, + "test_cat_unzipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:18.500464399" + }, + "test_cat_zipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:49.642741302" + }, + "test_cat_zipped_zipped_lines": { + "content": [ + [ + "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", + "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1", + "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", + "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" + ] + ], + "timestamp": "2023-10-16T14:32:33.629048645" + }, + "test_cat_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:08.038830506" + }, + "test_cat_one_file_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:21.39642399" + }, + "test_cat_zipped_zipped_size": { + "content": [ + 78 + ], + "timestamp": "2023-10-16T14:32:33.641869244" + }, + "test_cat_one_file_unzipped_zipped_size": { + "content": [ + 374 + ], + "timestamp": "2023-10-16T14:33:21.4094373" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config new file mode 100644 index 0000000000..ec26b0fdc6 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config @@ -0,0 +1,6 @@ + +process { + withName: CAT_CAT { + ext.prefix = 'cat.txt.gz' + } +} diff --git a/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config new file mode 100644 index 0000000000..fbc79783d5 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config @@ -0,0 +1,8 @@ + +process { + + withName: CAT_CAT { + ext.prefix = 'cat.txt' + } + +} diff --git a/modules/nf-core/cat/cat/tests/tags.yml b/modules/nf-core/cat/cat/tests/tags.yml new file mode 100644 index 0000000000..37b578f523 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/tags.yml @@ -0,0 +1,2 @@ +cat/cat: + - modules/nf-core/cat/cat/** diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml new file mode 100644 index 0000000000..222b301f38 --- /dev/null +++ b/modules/nf-core/cat/fastq/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 5021e6fcbb..3d963784cb 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ process CAT_FASTQ { tag "$meta.id" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index 8a39e309fb..db4ac3c79a 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -34,7 +34,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@joseespinosa" - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test new file mode 100644 index 0000000000..f5f941825c --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -0,0 +1,143 @@ +nextflow_process { + + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_paired_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_single_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_paired_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_single_end_single_file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } +} diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap new file mode 100644 index 0000000000..ec2342e549 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -0,0 +1,78 @@ +{ + "test_cat_fastq_single_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d" + ] + ] + ], + "timestamp": "2023-10-17T23:19:12.990284837" + }, + "test_cat_fastq_single_end_same_name": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66" + ] + ] + ], + "timestamp": "2023-10-17T23:19:31.554568147" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,e325ef7deb4023447a1f074e285761af" + ] + ] + ], + "timestamp": "2023-10-17T23:19:49.629360033" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66", + "test_2.merged.fastq.gz:md5,fe9f266f43a6fc3dcab690a18419a56e" + ] + ] + ] + ], + "timestamp": "2023-10-17T23:19:40.711617539" + }, + "test_cat_fastq_paired_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d", + "test_2.merged.fastq.gz:md5,77c8e966e130d8c6b6ec9be52fcb2bda" + ] + ] + ] + ], + "timestamp": "2023-10-18T07:53:20.923560211" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml new file mode 100644 index 0000000000..6ac4361405 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/tags.yml @@ -0,0 +1,2 @@ +cat/fastq: + - modules/nf-core/cat/fastq/** diff --git a/modules/nf-core/cnvkit/antitarget/environment.yml b/modules/nf-core/cnvkit/antitarget/environment.yml new file mode 100644 index 0000000000..ef6bec487e --- /dev/null +++ b/modules/nf-core/cnvkit/antitarget/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::cnvkit=0.9.10 + - bioconda::samtools=1.17 diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index cda05c635b..795145451b 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -2,7 +2,7 @@ process CNVKIT_ANTITARGET { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" diff --git a/modules/nf-core/cnvkit/antitarget/meta.yml b/modules/nf-core/cnvkit/antitarget/meta.yml index f22c07b13e..d879092d33 100644 --- a/modules/nf-core/cnvkit/antitarget/meta.yml +++ b/modules/nf-core/cnvkit/antitarget/meta.yml @@ -15,7 +15,6 @@ tools: tool_dev_url: "https://github.com/etal/cnvkit" doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] - input: - meta: type: map @@ -26,7 +25,6 @@ input: type: file description: File containing genomic regions pattern: "*.{bed}" - output: - meta: type: map @@ -41,8 +39,11 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@adamrtalbot" - "@priesgo" - "@SusiJo" +maintainers: + - "@adamrtalbot" + - "@priesgo" + - "@SusiJo" diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml new file mode 100644 index 0000000000..ef6bec487e --- /dev/null +++ b/modules/nf-core/cnvkit/batch/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::cnvkit=0.9.10 + - bioconda::samtools=1.17 diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index b253d6ab11..3ccc9faa44 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -2,17 +2,17 @@ process CNVKIT_BATCH { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' : 'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' }" input: tuple val(meta), path(tumor), path(normal) - path fasta - path fasta_fai - path targets - path reference + tuple val(meta2), path(fasta) + tuple val(meta3), path(fasta_fai) + tuple val(meta4), path(targets) + tuple val(meta5), path(reference) val panel_of_normals output: diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml index 950b0c9589..4f88ba3f9b 100644 --- a/modules/nf-core/cnvkit/batch/meta.yml +++ b/modules/nf-core/cnvkit/batch/meta.yml @@ -26,18 +26,38 @@ input: type: file description: | Input normal sample bam file (or cram) + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: type: file description: | Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided) + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta_fai: type: file description: | Input reference genome fasta index (optional, but recommended for cram_input) + - meta4: + type: map + description: | + Groovy Map containing information about target file + e.g. [ id:'test' ] - targetfile: type: file description: | Input target bed file + - meta5: + type: map + description: | + Groovy Map containing information about reference file + e.g. [ id:'test' ] - reference: type: file description: | @@ -86,3 +106,13 @@ authors: - "@MaxUlysse" - "@priesgo" - "@SusiJo" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@fbdtemme" + - "@kaurravneet4123" + - "@KevinMenden" + - "@lassefolkersen" + - "@MaxUlysse" + - "@priesgo" + - "@SusiJo" diff --git a/modules/nf-core/cnvkit/genemetrics/environment.yml b/modules/nf-core/cnvkit/genemetrics/environment.yml new file mode 100644 index 0000000000..ef6bec487e --- /dev/null +++ b/modules/nf-core/cnvkit/genemetrics/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::cnvkit=0.9.10 + - bioconda::samtools=1.17 diff --git a/modules/nf-core/cnvkit/genemetrics/main.nf b/modules/nf-core/cnvkit/genemetrics/main.nf index 6058994866..825b12bdac 100755 --- a/modules/nf-core/cnvkit/genemetrics/main.nf +++ b/modules/nf-core/cnvkit/genemetrics/main.nf @@ -2,7 +2,7 @@ process CNVKIT_GENEMETRICS { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml index 115a4a87bb..4bef28c7d5 100755 --- a/modules/nf-core/cnvkit/genemetrics/meta.yml +++ b/modules/nf-core/cnvkit/genemetrics/meta.yml @@ -40,8 +40,11 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@adamrtalbot" - "@marrip" - "@priesgo" +maintainers: + - "@adamrtalbot" + - "@marrip" + - "@priesgo" diff --git a/modules/nf-core/cnvkit/reference/environment.yml b/modules/nf-core/cnvkit/reference/environment.yml new file mode 100644 index 0000000000..ef6bec487e --- /dev/null +++ b/modules/nf-core/cnvkit/reference/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::cnvkit=0.9.10 + - bioconda::samtools=1.17 diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 57e1aed4f0..0e0b20a01e 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -2,7 +2,7 @@ process CNVKIT_REFERENCE { tag "$fasta" label 'process_low' - conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" diff --git a/modules/nf-core/cnvkit/reference/meta.yml b/modules/nf-core/cnvkit/reference/meta.yml index eae82c75e7..8c561c9953 100644 --- a/modules/nf-core/cnvkit/reference/meta.yml +++ b/modules/nf-core/cnvkit/reference/meta.yml @@ -15,7 +15,6 @@ tools: tool_dev_url: https://github.com/etal/cnvkit doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] - input: - fasta: type: file @@ -29,7 +28,6 @@ input: type: file description: File containing off-target genomic regions pattern: "*.{bed}" - output: - meta: type: map @@ -44,8 +42,11 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@adamrtalbot" - "@priesgo" - "@SusiJo" +maintainers: + - "@adamrtalbot" + - "@priesgo" + - "@SusiJo" diff --git a/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff b/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff index a80891d309..c8ace426e4 100644 --- a/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff +++ b/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff @@ -1,12 +1,9 @@ Changes in module 'nf-core/controlfreec/assesssignificance' --- modules/nf-core/controlfreec/assesssignificance/main.nf +++ modules/nf-core/controlfreec/assesssignificance/main.nf -@@ -2,10 +2,10 @@ - tag "$meta.id" - label 'process_low' +@@ -4,8 +4,8 @@ -- conda "bioconda::control-freec=11.6b" -+ conda "bioconda::control-freec=11.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' : - 'biocontainers/control-freec:11.6b--hdbdd923_0' }" @@ -16,4 +13,13 @@ Changes in module 'nf-core/controlfreec/assesssignificance' input: tuple val(meta), path(cnvs), path(ratio) +--- modules/nf-core/controlfreec/assesssignificance/environment.yml ++++ modules/nf-core/controlfreec/assesssignificance/environment.yml +@@ -3,4 +3,4 @@ + - bioconda + - defaults + dependencies: +- - bioconda::control-freec=11.6b ++ - bioconda::control-freec=11.6 + ************************************************************ diff --git a/modules/nf-core/controlfreec/assesssignificance/environment.yml b/modules/nf-core/controlfreec/assesssignificance/environment.yml new file mode 100644 index 0000000000..f1047dbbbb --- /dev/null +++ b/modules/nf-core/controlfreec/assesssignificance/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::control-freec=11.6 diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index 8c5cd42b41..4be70b176d 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { tag "$meta.id" label 'process_low' - conda "bioconda::control-freec=11.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1' : 'biocontainers/control-freec:11.6--h1b792b2_1' }" diff --git a/modules/nf-core/controlfreec/assesssignificance/meta.yml b/modules/nf-core/controlfreec/assesssignificance/meta.yml index 0451cca349..b8cda6dd50 100644 --- a/modules/nf-core/controlfreec/assesssignificance/meta.yml +++ b/modules/nf-core/controlfreec/assesssignificance/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] - input: # Only when we have meta - meta: @@ -30,7 +29,6 @@ input: type: file description: ratio file generated by FREEC pattern: "*.ratio.txt" - output: - meta: type: map @@ -45,6 +43,7 @@ output: type: file description: CNV file containing p_values for each call pattern: "*.p.value.txt" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/controlfreec/freec/environment.yml b/modules/nf-core/controlfreec/freec/environment.yml new file mode 100644 index 0000000000..83094f46ca --- /dev/null +++ b/modules/nf-core/controlfreec/freec/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 213ef92927..65cae5cba8 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_FREEC { tag "$meta.id" label 'process_low' - conda "bioconda::control-freec=11.6b" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' : 'biocontainers/control-freec:11.6b--hdbdd923_0' }" diff --git a/modules/nf-core/controlfreec/freec/meta.yml b/modules/nf-core/controlfreec/freec/meta.yml index bbb152d432..1442bbe44a 100644 --- a/modules/nf-core/controlfreec/freec/meta.yml +++ b/modules/nf-core/controlfreec/freec/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] - input: - args: type: map @@ -68,7 +67,6 @@ input: ] } ``` - - meta: type: map description: | @@ -130,7 +128,6 @@ input: type: file description: Sorted bed file containing capture regions (optional) pattern: "*.bed" - output: - meta: type: map @@ -177,6 +174,7 @@ output: type: file description: Config file used to run Control-FREEC pattern: "config.txt" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/controlfreec/freec2bed/environment.yml b/modules/nf-core/controlfreec/freec2bed/environment.yml new file mode 100644 index 0000000000..83094f46ca --- /dev/null +++ b/modules/nf-core/controlfreec/freec2bed/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index 0d5332a2d7..d2649cf95b 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_FREEC2BED { tag "$meta.id" label 'process_low' - conda "bioconda::control-freec=11.6b" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' : 'biocontainers/control-freec:11.6b--hdbdd923_0' }" diff --git a/modules/nf-core/controlfreec/freec2bed/meta.yml b/modules/nf-core/controlfreec/freec2bed/meta.yml index 47fff8ab80..b10c8ab377 100644 --- a/modules/nf-core/controlfreec/freec2bed/meta.yml +++ b/modules/nf-core/controlfreec/freec2bed/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] - input: - meta: type: map @@ -25,7 +24,6 @@ input: type: file description: ratio file generated by FREEC pattern: "*.ratio.txt" - output: - meta: type: map @@ -40,6 +38,7 @@ output: type: file description: Bed file pattern: "*.bed" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/controlfreec/freec2circos/environment.yml b/modules/nf-core/controlfreec/freec2circos/environment.yml new file mode 100644 index 0000000000..83094f46ca --- /dev/null +++ b/modules/nf-core/controlfreec/freec2circos/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index c748af8be7..f80116799c 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_FREEC2CIRCOS { tag "$meta.id" label 'process_low' - conda "bioconda::control-freec=11.6b" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' : 'biocontainers/control-freec:11.6b--hdbdd923_0' }" diff --git a/modules/nf-core/controlfreec/freec2circos/meta.yml b/modules/nf-core/controlfreec/freec2circos/meta.yml index ff845a826c..2c6b77d611 100644 --- a/modules/nf-core/controlfreec/freec2circos/meta.yml +++ b/modules/nf-core/controlfreec/freec2circos/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] - input: - meta: type: map @@ -25,7 +24,6 @@ input: type: file description: ratio file generated by FREEC pattern: "*.ratio.txt" - output: - meta: type: map @@ -40,6 +38,7 @@ output: type: file description: Txt file pattern: "*.circos.txt" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph/environment.yml new file mode 100644 index 0000000000..83094f46ca --- /dev/null +++ b/modules/nf-core/controlfreec/makegraph/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index 533065c6e4..8d489f71f7 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_MAKEGRAPH { tag "$meta.id" label 'process_low' - conda "bioconda::control-freec=11.6b" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' : 'biocontainers/control-freec:11.6b--hdbdd923_0' }" diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml index 7b97dcf9bc..6f91db38aa 100644 --- a/modules/nf-core/controlfreec/makegraph/meta.yml +++ b/modules/nf-core/controlfreec/makegraph/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] - input: # Only when we have meta - meta: @@ -33,7 +32,6 @@ input: - ploidy: type: integer description: Ploidy value for which graph should be created - output: - meta: type: map @@ -56,6 +54,7 @@ output: type: file description: Image of ratio plot pattern: "*_ratio.png" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 0000000000..7ca221616b --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.15 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b113..e562259e7d 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de7a..9414c32d71 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 0000000000..eec1db10a2 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 0000000000..8713b92164 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + ], + "1": [ + "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + ], + "2": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + ], + "versions": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "yml": [ + "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + ] + } + ], + "timestamp": "2023-10-11T17:10:02.930699" + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 0000000000..405aa24ae3 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/deepvariant/environment.yml b/modules/nf-core/deepvariant/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/deepvariant/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml index c7d11ae3b1..a50dc57d9a 100644 --- a/modules/nf-core/deepvariant/meta.yml +++ b/modules/nf-core/deepvariant/meta.yml @@ -12,7 +12,6 @@ tools: tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] - input: - meta: type: map @@ -58,7 +57,6 @@ input: type: file description: GZI index of reference fasta file pattern: "*.gzi" - output: - meta: type: map @@ -77,7 +75,9 @@ output: type: file description: File containing software version pattern: "*.{version.txt}" - authors: - "@abhi18av" - "@ramprasadn" +maintainers: + - "@abhi18av" + - "@ramprasadn" diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml new file mode 100644 index 0000000000..66482a4f9f --- /dev/null +++ b/modules/nf-core/dragmap/align/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::dragmap=1.2.1 + - bioconda::samtools=1.15.1 + - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index 6221fde67f..6eddb2d6c0 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -2,7 +2,7 @@ process DRAGMAP_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': 'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }" diff --git a/modules/nf-core/dragmap/align/meta.yml b/modules/nf-core/dragmap/align/meta.yml index 763e00525c..f0def75567 100644 --- a/modules/nf-core/dragmap/align/meta.yml +++ b/modules/nf-core/dragmap/align/meta.yml @@ -12,7 +12,6 @@ tools: homepage: https://github.com/Illumina/dragmap documentation: https://github.com/Illumina/dragmap tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage - licence: ["GPL v3"] input: - meta: @@ -45,3 +44,5 @@ output: pattern: "versions.yml" authors: - "@Emiller88" +maintainers: + - "@Emiller88" diff --git a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff index 069f133e61..aeb9694244 100644 --- a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff +++ b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff @@ -1,12 +1,9 @@ Changes in module 'nf-core/dragmap/hashtable' --- modules/nf-core/dragmap/hashtable/main.nf +++ modules/nf-core/dragmap/hashtable/main.nf -@@ -2,10 +2,10 @@ - tag "$fasta" - label 'process_high' +@@ -4,8 +4,8 @@ -- conda "bioconda::dragmap=1.3.0" -+ conda "bioconda::dragmap=1.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/dragmap:1.3.0--h72d16da_1': - 'biocontainers/dragmap:1.3.0--h72d16da_1' }" @@ -16,4 +13,13 @@ Changes in module 'nf-core/dragmap/hashtable' input: tuple val(meta), path(fasta) +--- modules/nf-core/dragmap/hashtable/environment.yml ++++ modules/nf-core/dragmap/hashtable/environment.yml +@@ -3,4 +3,4 @@ + - bioconda + - defaults + dependencies: +- - bioconda::dragmap=1.3.0 ++ - bioconda::dragmap=1.2.1 + ************************************************************ diff --git a/modules/nf-core/dragmap/hashtable/environment.yml b/modules/nf-core/dragmap/hashtable/environment.yml new file mode 100644 index 0000000000..c8e351255f --- /dev/null +++ b/modules/nf-core/dragmap/hashtable/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::dragmap=1.2.1 diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 73f6c2785a..604052f33f 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -2,7 +2,7 @@ process DRAGMAP_HASHTABLE { tag "$fasta" label 'process_high' - conda "bioconda::dragmap=1.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--h72d16da_1': 'biocontainers/dragmap:1.2.1--h72d16da_1' }" diff --git a/modules/nf-core/dragmap/hashtable/meta.yml b/modules/nf-core/dragmap/hashtable/meta.yml index 133cc9fc67..8daca83273 100644 --- a/modules/nf-core/dragmap/hashtable/meta.yml +++ b/modules/nf-core/dragmap/hashtable/meta.yml @@ -11,7 +11,6 @@ tools: homepage: https://github.com/Illumina/dragmap documentation: https://github.com/Illumina/dragmap tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage - licence: ["GPL v3"] input: - meta: @@ -38,3 +37,5 @@ output: pattern: "versions.yml" authors: - "@Emiller88" +maintainers: + - "@Emiller88" diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml new file mode 100644 index 0000000000..d3805c0c05 --- /dev/null +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::ensembl-vep=110.0 diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index 4873b91d57..a770cbfc6f 100644 --- a/modules/nf-core/ensemblvep/download/main.nf +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -2,7 +2,7 @@ process ENSEMBLVEP_DOWNLOAD { tag "$meta.id" label 'process_medium' - conda "bioconda::ensembl-vep=110.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index acb337c399..0183a435b8 100644 --- a/modules/nf-core/ensemblvep/download/meta.yml +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -41,3 +41,5 @@ output: pattern: "versions.yml" authors: - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml new file mode 100644 index 0000000000..d3805c0c05 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::ensembl-vep=110.0 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index da0e36460a..3a2b742348 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -2,7 +2,7 @@ process ENSEMBLVEP_VEP { tag "$meta.id" label 'process_medium' - conda "bioconda::ensembl-vep=110.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 7783847dc4..61d29d3fb1 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -86,3 +86,7 @@ authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml new file mode 100644 index 0000000000..19ccec2564 --- /dev/null +++ b/modules/nf-core/fastp/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 831b7f128e..c8e815aead 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -2,7 +2,7 @@ process FASTP { tag "$meta.id" label 'process_medium' - conda "bioconda::fastp=0.23.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' : 'biocontainers/fastp:0.23.4--h5f740d0_0' }" diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 197ea7ca65..c22a16abd9 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -33,7 +33,6 @@ input: - save_merged: type: boolean description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz` - output: - meta: type: map @@ -71,3 +70,6 @@ output: authors: - "@drpatelh" - "@kevinmenden" +maintainers: + - "@drpatelh" + - "@kevinmenden" diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test new file mode 100644 index 0000000000..f610b735e2 --- /dev/null +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -0,0 +1,485 @@ +nextflow_process { + + name "Test Process FASTP" + script "../main.nf" + process "FASTP" + tag "modules" + tag "modules_nfcore" + tag "fastp" + + test("test_fastp_single_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ + [ id:'test', single_end:true ], + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)" ] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 198'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("fastp test_fastp_interleaved") { + config './nextflow.config' + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "paired end (151 cycles + 151 cycles)"] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 198"] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("fastp test_fastp_interleaved_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_single_end_trim_fail") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)"] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { failed_read_lines.each { failed_read_line -> + { assert path(process.out.reads_fail.get(0).get(1)).linesGzip.contains(failed_read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_trim_fail_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_trim_fail") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 198'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { failed_read2_lines.each { failed_read2_line -> + { assert path(process.out.reads_fail.get(0).get(1).get(1)).linesGzip.contains(failed_read2_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_merged") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = true + + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "
"] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683'] + def read1_lines = [ "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_merged_adapterlist") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta", checkIfExists: true) + save_trimmed_fail = false + save_merged = true + + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "
"] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683',"--adapter_fasta"] + def read1_lines = ["@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap new file mode 100644 index 0000000000..0fa68c7d71 --- /dev/null +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "fastp test_fastp_interleaved_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,168f516f7bd4b7b6c32da7cba87299a4" + ] + ] + ], + "timestamp": "2023-10-17T11:04:45.794175881" + }, + "test_fastp_single_end_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" + ] + ] + ], + "timestamp": "2023-10-17T11:04:10.566343705" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "timestamp": "2023-10-17T11:04:10.582076024" + }, + "test_fastp_single_end_trim_fail_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5" + ] + ] + ], + "timestamp": "2023-10-17T11:05:00.379878948" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastp/tests/nextflow.config b/modules/nf-core/fastp/tests/nextflow.config new file mode 100644 index 0000000000..0f7849ad96 --- /dev/null +++ b/modules/nf-core/fastp/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + + withName: FASTP { + ext.args = "--interleaved_in" + } +} diff --git a/modules/nf-core/fastp/tests/tags.yml b/modules/nf-core/fastp/tests/tags.yml new file mode 100644 index 0000000000..c1afcce75f --- /dev/null +++ b/modules/nf-core/fastp/tests/tags.yml @@ -0,0 +1,2 @@ +fastp: + - modules/nf-core/fastp/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 0000000000..f52a53a0fa --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f90644d..50e59f2b8c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a06..ee5507e06b 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 0000000000..6437a144d9 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,41 @@ +nextflow_process { + + name "Test Process FASTQC" + script "../main.nf" + process "FASTQC" + tag "modules" + tag "modules_nfcore" + tag "fastqc" + + test("Single-Read") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) + } + } +} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 0000000000..636a32cead --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-10-09T23:40:54+0000" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 0000000000..7834294ba0 --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml new file mode 100644 index 0000000000..d64c6844b3 --- /dev/null +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fgbio=2.0.2 diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 4515040cc9..e9f209ef16 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -2,7 +2,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { tag "$meta.id" label 'process_medium' - conda "bioconda::fgbio=2.0.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : 'biocontainers/fgbio:2.0.2--hdfd78af_0' }" diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml index 371825123a..f4a6ab1bb8 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml @@ -1,6 +1,5 @@ name: fgbio_callmolecularconsensusreads description: Calls consensus sequences from reads with the same unique molecular tag. - keywords: - UMIs - consensus sequence @@ -12,7 +11,6 @@ tools: homepage: https://github.com/fulcrumgenomics/fgbio documentation: http://fulcrumgenomics.github.io/fgbio/ licence: ["MIT"] - input: - meta: type: map @@ -24,7 +22,6 @@ input: description: | The input SAM or BAM file. pattern: "*.{bam,sam}" - output: - meta: type: map @@ -40,6 +37,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@sruthipsuresh" +maintainers: + - "@sruthipsuresh" diff --git a/modules/nf-core/fgbio/fastqtobam/environment.yml b/modules/nf-core/fgbio/fastqtobam/environment.yml new file mode 100644 index 0000000000..d64c6844b3 --- /dev/null +++ b/modules/nf-core/fgbio/fastqtobam/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fgbio=2.0.2 diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index 74016d3c45..f7302171b8 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -2,7 +2,7 @@ process FGBIO_FASTQTOBAM { tag "$meta.id" label 'process_low' - conda "bioconda::fgbio=2.0.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : 'biocontainers/fgbio:2.0.2--hdfd78af_0' }" diff --git a/modules/nf-core/fgbio/fastqtobam/meta.yml b/modules/nf-core/fgbio/fastqtobam/meta.yml index f85485cab8..4b37cd530f 100644 --- a/modules/nf-core/fgbio/fastqtobam/meta.yml +++ b/modules/nf-core/fgbio/fastqtobam/meta.yml @@ -10,15 +10,12 @@ tools: homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ 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 @@ -37,7 +34,9 @@ output: type: file description: Unaligned, unsorted CRAM file pattern: "*.{cram}" - authors: - "@lescai" - "@matthdsm" +maintainers: + - "@lescai" + - "@matthdsm" diff --git a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml new file mode 100644 index 0000000000..d64c6844b3 --- /dev/null +++ b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fgbio=2.0.2 diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 879e453452..7179290c91 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -2,7 +2,7 @@ process FGBIO_GROUPREADSBYUMI { tag "$meta.id" label 'process_low' - conda "bioconda::fgbio=2.0.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : 'biocontainers/fgbio:2.0.2--hdfd78af_0' }" diff --git a/modules/nf-core/fgbio/groupreadsbyumi/meta.yml b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml index f40a5ac7fc..02ca91f19f 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/meta.yml +++ b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml @@ -16,9 +16,7 @@ tools: homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio - licence: ["MIT"] - input: - meta: type: map @@ -35,7 +33,6 @@ input: description: | Reguired argument: defines the UMI assignment strategy. Must be chosen among: Identity, Edit, Adjacency, Paired. - output: - meta: type: map @@ -54,6 +51,7 @@ output: type: file description: A text file containing the tag family size counts pattern: "*.txt" - authors: - "@lescai" +maintainers: + - "@lescai" diff --git a/modules/nf-core/freebayes/environment.yml b/modules/nf-core/freebayes/environment.yml new file mode 100644 index 0000000000..b074f213f4 --- /dev/null +++ b/modules/nf-core/freebayes/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::freebayes=1.3.6 diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 1466f085e8..8a1c641ded 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -2,7 +2,7 @@ process FREEBAYES { tag "$meta.id" label 'process_single' - conda "bioconda::freebayes=1.3.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hbfe0e7f_2' : 'biocontainers/freebayes:1.3.6--hbfe0e7f_2' }" diff --git a/modules/nf-core/freebayes/meta.yml b/modules/nf-core/freebayes/meta.yml index 17d83cba2b..e2cf1a175c 100644 --- a/modules/nf-core/freebayes/meta.yml +++ b/modules/nf-core/freebayes/meta.yml @@ -8,7 +8,6 @@ keywords: - germline variant calling - bacterial variant calling - bayesian - tools: - freebayes: description: Bayesian haplotype-based polymorphism discovery and genotyping @@ -17,7 +16,6 @@ tools: tool_dev_url: https://github.com/freebayes/freebayes doi: "10.48550/arXiv.1207.3907" licence: ["MIT"] - input: - meta: type: map @@ -60,7 +58,6 @@ input: or a region-specific format: seq_name start end sample_name copy_number pattern: "*.bed" - output: - meta: type: map @@ -75,8 +72,11 @@ output: type: file description: Compressed VCF file pattern: "*.vcf.gz" - authors: - "@maxibor" - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@maxibor" + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index e5e6bf99c7..7e49563739 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -2,7 +2,7 @@ process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/applybqsr/meta.yml b/modules/nf-core/gatk4/applybqsr/meta.yml index 2085fa97b2..ab9efea3f4 100644 --- a/modules/nf-core/gatk4/applybqsr/meta.yml +++ b/modules/nf-core/gatk4/applybqsr/meta.yml @@ -16,7 +16,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -49,7 +48,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - output: - meta: type: map @@ -68,7 +66,9 @@ output: type: file description: Recalibrated CRAM file pattern: "*.{cram}" - authors: - "@yocra3" - "@FriederikeHanssen" +maintainers: + - "@yocra3" + - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 8413f2bb3b..21afe9a528 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -2,7 +2,7 @@ process GATK4_APPLYVQSR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/applyvqsr/meta.yml b/modules/nf-core/gatk4/applyvqsr/meta.yml index e1e121a661..de5d6d067a 100644 --- a/modules/nf-core/gatk4/applyvqsr/meta.yml +++ b/modules/nf-core/gatk4/applyvqsr/meta.yml @@ -19,7 +19,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -58,7 +57,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - output: - vcf: type: file @@ -72,6 +70,7 @@ output: type: file description: File containing software versions. pattern: "versions.yml" - authors: - "@GCJMackenzie" +maintainers: + - "@GCJMackenzie" diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 5375289a16..e893b65036 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -2,7 +2,7 @@ process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/baserecalibrator/meta.yml b/modules/nf-core/gatk4/baserecalibrator/meta.yml index db4fecfc92..8252b8c290 100644 --- a/modules/nf-core/gatk4/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4/baserecalibrator/meta.yml @@ -16,7 +16,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -54,7 +53,6 @@ input: type: file description: Tabix index of the known_sites (optional) pattern: "*.vcf.gz.tbi" - output: - meta: type: map @@ -69,8 +67,11 @@ output: type: file description: Recalibration table from BaseRecalibrator pattern: "*.{table}" - authors: - "@yocra3" - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@yocra3" + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 9dd961bec0..8d43c4ee6b 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -2,7 +2,7 @@ process GATK4_CALCULATECONTAMINATION { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/calculatecontamination/meta.yml b/modules/nf-core/gatk4/calculatecontamination/meta.yml index 7767bd0807..b0ffe814c5 100644 --- a/modules/nf-core/gatk4/calculatecontamination/meta.yml +++ b/modules/nf-core/gatk4/calculatecontamination/meta.yml @@ -17,7 +17,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -32,7 +31,6 @@ input: 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 @@ -46,7 +44,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@GCJMackenzie" - "@maxulysse" +maintainers: + - "@GCJMackenzie" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/gatk4/cnnscorevariants/meta.yml b/modules/nf-core/gatk4/cnnscorevariants/meta.yml index a2fe3d47c6..8a9d0f51c2 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/meta.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/meta.yml @@ -14,7 +14,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -56,7 +55,6 @@ input: type: file description: Keras model HD5 file with neural net weights. (optional) pattern: "*.hd5" - output: - meta: type: map @@ -75,6 +73,7 @@ output: type: file description: VCF index file pattern: "*.vcf.gz.tbi" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 3e4efdd983..b47ad16221 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -2,7 +2,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index 9b8b8c8917..f9d70be098 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -15,7 +15,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -38,3 +37,6 @@ output: authors: - "@maxulysse" - "@ramprasadn" +maintainers: + - "@maxulysse" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 81fc83513d..c0eef7b327 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -2,7 +2,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml index 2783152a59..2d5bddf6c9 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] - input: - meta: type: map @@ -36,7 +35,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - output: - meta: type: map @@ -51,7 +49,9 @@ output: type: file description: File containing metrics on the input files pattern: "*.{metrics}" - authors: - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 623b91aece..fa6b46ab3c 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -2,7 +2,7 @@ process GATK4_FILTERMUTECTCALLS { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/filtermutectcalls/meta.yml b/modules/nf-core/gatk4/filtermutectcalls/meta.yml index 095a28e321..736c838625 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/meta.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/meta.yml @@ -16,7 +16,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - input: - meta: type: map @@ -77,7 +76,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - output: - vcf: type: file @@ -95,8 +93,11 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@GCJMackenzie" - "@maxulysse" - "@ramprasadn" +maintainers: + - "@GCJMackenzie" + - "@maxulysse" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 90cbf5f0a6..9da47ab739 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -2,7 +2,7 @@ process GATK4_FILTERVARIANTTRANCHES { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/filtervarianttranches/meta.yml b/modules/nf-core/gatk4/filtervarianttranches/meta.yml index c5325b4891..9346d2b4a4 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/meta.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/meta.yml @@ -14,7 +14,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -49,7 +48,6 @@ input: type: file description: GATK sequence dictionary pattern: ".dict" - output: - meta: type: map @@ -68,6 +66,7 @@ output: type: file description: VCF index file pattern: "*.vcf.gz.tbi" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 3eeca5ad90..e783701017 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -2,7 +2,7 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/gatherbqsrreports/meta.yml b/modules/nf-core/gatk4/gatherbqsrreports/meta.yml index d9faf09d45..b9f5bf5f8b 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/meta.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] - input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: File(s) containing BQSR table(s) pattern: "*.table" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index f315e1af3b..1863133d2c 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -2,7 +2,7 @@ process GATK4_GATHERPILEUPSUMMARIES { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml b/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml index 6b8569dd5b..35381a3b51 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml @@ -12,7 +12,6 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] - input: - meta: type: map @@ -23,7 +22,6 @@ input: type: file description: Pileup files from gatk4/getpileupsummaries pattern: "*.pileups.table" - output: - meta: type: map @@ -38,7 +36,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index a8725d3f9a..916037ebef 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -2,7 +2,7 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/genomicsdbimport/meta.yml b/modules/nf-core/gatk4/genomicsdbimport/meta.yml index ff114d7d20..ca8fe3d076 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/meta.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/meta.yml @@ -15,7 +15,6 @@ tools: 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 @@ -26,42 +25,34 @@ input: 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" - - intervalfile: type: file description: file containing the intervals to be used when creating the genomicsdb pattern: "*.interval_list" - - intervalval: 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 @@ -79,6 +70,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@GCJMackenzie" +maintainers: + - "@GCJMackenzie" diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index a3e3129fcf..c6c0ba501d 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -2,7 +2,7 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" label 'process_high' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml index d759270d6a..8f1e377eb9 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/meta.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] - input: - meta: type: map @@ -57,7 +56,6 @@ input: type: file description: dbSNP VCF index file pattern: "*.tbi" - output: - meta: type: map @@ -76,7 +74,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@santiagorevale" - "@maxulysse" +maintainers: + - "@santiagorevale" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index f7d0f2942c..d509cdf3bb 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -2,7 +2,7 @@ process GATK4_GETPILEUPSUMMARIES { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/getpileupsummaries/meta.yml b/modules/nf-core/gatk4/getpileupsummaries/meta.yml index 6aaa4b9e7c..fab3c1435e 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/meta.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/meta.yml @@ -16,7 +16,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -70,7 +69,6 @@ input: type: file description: Index file for the germline resource. pattern: "*.vcf.gz.tbi" - output: - pileup: type: file @@ -80,6 +78,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@GCJMackenzie" +maintainers: + - "@GCJMackenzie" diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 9ac87518e9..fdecf5f830 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -2,7 +2,7 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index 03afe29427..f38dc37dd0 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -14,7 +14,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -54,7 +53,6 @@ input: - dbsnp_tbi: type: file description: VCF index of dbsnp (optional) - output: - meta: type: map @@ -77,7 +75,9 @@ output: type: file description: Assembled haplotypes and locally realigned reads pattern: "*.realigned.bam" - authors: - "@suzannejin" - "@FriederikeHanssen" +maintainers: + - "@suzannejin" + - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 2537f0aa68..89772081e0 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -2,7 +2,7 @@ process GATK4_INTERVALLISTTOBED { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/intervallisttobed/meta.yml b/modules/nf-core/gatk4/intervallisttobed/meta.yml index df3705aa15..28d264dfef 100644 --- a/modules/nf-core/gatk4/intervallisttobed/meta.yml +++ b/modules/nf-core/gatk4/intervallisttobed/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] - input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Interval list pattern: "*.{interval,interval_list}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 89a6ae77b6..c4e39db74a 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -2,7 +2,7 @@ process GATK4_LEARNREADORIENTATIONMODEL { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml b/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml index e29fee2251..4b73a51adb 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml @@ -16,7 +16,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -27,7 +26,6 @@ input: type: list description: list of f1r2 files to be used as input. pattern: "*.f1r2.tar.gz" - output: - artifactprior: type: file @@ -37,6 +35,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@GCJMackenzie" +maintainers: + - "@GCJMackenzie" diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml new file mode 100644 index 0000000000..8c0c6bb279 --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 + - bioconda::samtools=1.17 diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index e4c01f9a2e..564b86d3dd 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0 bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0': 'biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0' }" @@ -65,4 +65,21 @@ process GATK4_MARKDUPLICATES { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}.bam" + prefix_no_suffix = task.ext.prefix ? prefix.tokenize('.')[0] : "${meta.id}" + """ + touch ${prefix_no_suffix}.bam + touch ${prefix_no_suffix}.cram + touch ${prefix_no_suffix}.cram.crai + touch ${prefix_no_suffix}.bai + touch ${prefix}.metrics + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml index d3e755054a..b0f09d4b84 100644 --- a/modules/nf-core/gatk4/markduplicates/meta.yml +++ b/modules/nf-core/gatk4/markduplicates/meta.yml @@ -7,16 +7,12 @@ keywords: - sort tools: - gatk4: - description: - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["MIT"] - input: - meta: type: map @@ -35,7 +31,6 @@ input: type: file description: Fasta index file pattern: "*.{fai}" - output: - meta: type: map @@ -66,8 +61,11 @@ output: type: file description: Duplicate metrics file generated by GATK pattern: "*.{metrics.txt}" - authors: - "@ajodeh-juma" - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@ajodeh-juma" + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 269721cbf9..3a4913220c 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -2,7 +2,7 @@ process GATK4_MERGEMUTECTSTATS { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/mergemutectstats/meta.yml b/modules/nf-core/gatk4/mergemutectstats/meta.yml index f75833c9bc..1269525657 100644 --- a/modules/nf-core/gatk4/mergemutectstats/meta.yml +++ b/modules/nf-core/gatk4/mergemutectstats/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] - input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Stats file pattern: "*.{stats}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: Stats file pattern: "*.vcf.gz.stats" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 29c08e169c..3362c2bdad 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -2,7 +2,7 @@ process GATK4_MERGEVCFS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml index 4e11311c17..30290a854f 100644 --- a/modules/nf-core/gatk4/mergevcfs/meta.yml +++ b/modules/nf-core/gatk4/mergevcfs/meta.yml @@ -33,7 +33,6 @@ input: type: file description: Optional Sequence Dictionary as input pattern: "*.dict" - output: - vcf: type: file @@ -43,10 +42,11 @@ output: type: file description: index files for the merged vcf files pattern: "*.tbi" - - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@kevinmenden" +maintainers: + - "@kevinmenden" diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 4e353979db..721e94f3e4 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -2,7 +2,7 @@ process GATK4_MUTECT2 { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/mutect2/meta.yml b/modules/nf-core/gatk4/mutect2/meta.yml index 693aeb296a..21c928ed96 100644 --- a/modules/nf-core/gatk4/mutect2/meta.yml +++ b/modules/nf-core/gatk4/mutect2/meta.yml @@ -17,7 +17,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -79,7 +78,6 @@ input: type: file description: Index for the panel of normals. pattern: "*.vcf.gz.tbi" - output: - vcf: type: file @@ -101,7 +99,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@GCJMackenzie" - "@ramprasadn" +maintainers: + - "@GCJMackenzie" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml new file mode 100644 index 0000000000..16241b6d94 --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index fa262e4a95..f9cd45ac94 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -2,7 +2,7 @@ process GATK4_VARIANTRECALIBRATOR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/variantrecalibrator/meta.yml b/modules/nf-core/gatk4/variantrecalibrator/meta.yml index 5ade4d89b1..39a415b61c 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/meta.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/meta.yml @@ -18,7 +18,6 @@ tools: 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 @@ -80,3 +79,6 @@ output: authors: - "@GCJMackenzie" - "@nickhsmith" +maintainers: + - "@GCJMackenzie" + - "@nickhsmith" diff --git a/modules/nf-core/gatk4spark/applybqsr/environment.yml b/modules/nf-core/gatk4spark/applybqsr/environment.yml new file mode 100644 index 0000000000..821728a662 --- /dev/null +++ b/modules/nf-core/gatk4spark/applybqsr/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4-spark=4.4.0.0 diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4spark/applybqsr/main.nf similarity index 81% rename from modules/nf-core/gatk4/applybqsrspark/main.nf rename to modules/nf-core/gatk4spark/applybqsr/main.nf index 7a4c29bbca..170dbeeafd 100644 --- a/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/modules/nf-core/gatk4spark/applybqsr/main.nf @@ -1,9 +1,11 @@ -process GATK4_APPLYBQSR_SPARK { +process GATK4SPARK_APPLYBQSR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" - container "nf-core/gatk:4.4.0.0" + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applybqsrspark/meta.yml b/modules/nf-core/gatk4spark/applybqsr/meta.yml similarity index 94% rename from modules/nf-core/gatk4/applybqsrspark/meta.yml rename to modules/nf-core/gatk4spark/applybqsr/meta.yml index b253fc78ce..4904568d2e 100644 --- a/modules/nf-core/gatk4/applybqsrspark/meta.yml +++ b/modules/nf-core/gatk4spark/applybqsr/meta.yml @@ -1,12 +1,11 @@ -name: gatk4_applybqsr_spark +name: gatk4spark_applybqsr description: Apply base quality score recalibration (BQSR) to a bam file keywords: - bam - base quality score recalibration - bqsr - cram - - gatk4 - - spark + - gatk4spark tools: - gatk4: description: | @@ -17,7 +16,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -50,7 +48,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - output: - meta: type: map @@ -69,8 +66,11 @@ output: type: file description: Recalibrated CRAM file pattern: "*.{cram}" - authors: - "@yocra3" - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@yocra3" + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml new file mode 100644 index 0000000000..821728a662 --- /dev/null +++ b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4-spark=4.4.0.0 diff --git a/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/gatk4spark/baserecalibrator/main.nf similarity index 80% rename from modules/nf-core/gatk4/baserecalibratorspark/main.nf rename to modules/nf-core/gatk4spark/baserecalibrator/main.nf index 6db088bb75..ee44bf7d66 100644 --- a/modules/nf-core/gatk4/baserecalibratorspark/main.nf +++ b/modules/nf-core/gatk4spark/baserecalibrator/main.nf @@ -1,9 +1,11 @@ -process GATK4_BASERECALIBRATOR_SPARK { +process GATK4SPARK_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.4.0.0 conda-forge::openjdk=8.0.312" - container "nf-core/gatk:4.4.0.0" + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/baserecalibratorspark/meta.yml b/modules/nf-core/gatk4spark/baserecalibrator/meta.yml similarity index 94% rename from modules/nf-core/gatk4/baserecalibratorspark/meta.yml rename to modules/nf-core/gatk4spark/baserecalibrator/meta.yml index d175ca13a1..dd334a225f 100644 --- a/modules/nf-core/gatk4/baserecalibratorspark/meta.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/meta.yml @@ -1,12 +1,11 @@ -name: gatk4_baserecalibrator_spark +name: gatk4spark_baserecalibrator description: Generate recalibration table for Base Quality Score Recalibration (BQSR) keywords: - base quality score recalibration - table - bqsr - - gatk4 + - gatk4spark - sort - - spark tools: - gatk4: description: | @@ -17,7 +16,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -55,7 +53,6 @@ input: type: file description: Tabix index of the known_sites (optional) pattern: "*.vcf.gz.tbi" - output: - meta: type: map @@ -70,8 +67,11 @@ output: type: file description: Recalibration table from BaseRecalibrator pattern: "*.{table}" - authors: - "@yocra3" - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@yocra3" + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/gatk4spark/markduplicates/environment.yml b/modules/nf-core/gatk4spark/markduplicates/environment.yml new file mode 100644 index 0000000000..821728a662 --- /dev/null +++ b/modules/nf-core/gatk4spark/markduplicates/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4-spark=4.4.0.0 diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4spark/markduplicates/main.nf similarity index 81% rename from modules/nf-core/gatk4/markduplicatesspark/main.nf rename to modules/nf-core/gatk4spark/markduplicates/main.nf index f318ed50a6..61e295c839 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/modules/nf-core/gatk4spark/markduplicates/main.nf @@ -1,9 +1,11 @@ -process GATK4_MARKDUPLICATES_SPARK { +process GATK4SPARK_MARKDUPLICATES { tag "$meta.id" label 'process_high' - conda "bioconda::gatk4=4.4.0.0 conda-forge::openjdk=8.0.312" - container "nf-core/gatk:4.4.0.0" + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/markduplicatesspark/meta.yml b/modules/nf-core/gatk4spark/markduplicates/meta.yml similarity index 78% rename from modules/nf-core/gatk4/markduplicatesspark/meta.yml rename to modules/nf-core/gatk4spark/markduplicates/meta.yml index c9bb263a96..016a215b25 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/meta.yml +++ b/modules/nf-core/gatk4spark/markduplicates/meta.yml @@ -1,23 +1,18 @@ -name: gatk4_markduplicates_spark +name: gatk4spark_markduplicates description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. keywords: - bam - - gatk4 + - gatk4spark - markduplicates - sort - - spark tools: - gatk4: - description: - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["MIT"] - input: - meta: type: map @@ -40,7 +35,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - output: - meta: type: map @@ -59,9 +53,13 @@ output: type: file description: Optional BAM index file pattern: "*.bai" - authors: - "@ajodeh-juma" - "@FriederikeHanssen" - "@maxulysse" - "@SusiJo" +maintainers: + - "@ajodeh-juma" + - "@FriederikeHanssen" + - "@maxulysse" + - "@SusiJo" diff --git a/modules/nf-core/manta/germline/environment.yml b/modules/nf-core/manta/germline/environment.yml new file mode 100644 index 0000000000..235b1ba75d --- /dev/null +++ b/modules/nf-core/manta/germline/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::manta=1.6.0 diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index e052b7c9f0..5d5666c6e5 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -3,7 +3,7 @@ process MANTA_GERMLINE { label 'process_medium' label 'error_retry' - conda "bioconda::manta=1.6.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : 'biocontainers/manta:1.6.0--h9ee0642_1' }" @@ -13,6 +13,7 @@ process MANTA_GERMLINE { tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) + path(config) output: tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf @@ -31,27 +32,29 @@ process MANTA_GERMLINE { def prefix = task.ext.prefix ?: "${meta.id}" def input_files = input.collect{"--bam ${it}"}.join(' ') def options_manta = target_bed ? "--callRegions $target_bed" : "" + def config_option = config ? "--config ${config}" : "" """ - configManta.py \ - ${input_files} \ - --reference $fasta \ - --runDir manta \ - $options_manta \ + configManta.py \\ + ${input_files} \\ + ${config_option} \\ + --reference $fasta \\ + --runDir manta \\ + $options_manta \\ $args python manta/runWorkflow.py -m local -j $task.cpus - mv manta/results/variants/candidateSmallIndels.vcf.gz \ + mv manta/results/variants/candidateSmallIndels.vcf.gz \\ ${prefix}.candidate_small_indels.vcf.gz - mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \ + mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \\ ${prefix}.candidate_small_indels.vcf.gz.tbi - mv manta/results/variants/candidateSV.vcf.gz \ + mv manta/results/variants/candidateSV.vcf.gz \\ ${prefix}.candidate_sv.vcf.gz - mv manta/results/variants/candidateSV.vcf.gz.tbi \ + mv manta/results/variants/candidateSV.vcf.gz.tbi \\ ${prefix}.candidate_sv.vcf.gz.tbi - mv manta/results/variants/diploidSV.vcf.gz \ + mv manta/results/variants/diploidSV.vcf.gz \\ ${prefix}.diploid_sv.vcf.gz - mv manta/results/variants/diploidSV.vcf.gz.tbi \ + mv manta/results/variants/diploidSV.vcf.gz.tbi \\ ${prefix}.diploid_sv.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/manta/germline/meta.yml b/modules/nf-core/manta/germline/meta.yml index 2eb16ada53..72ed15f8bc 100644 --- a/modules/nf-core/manta/germline/meta.yml +++ b/modules/nf-core/manta/germline/meta.yml @@ -16,7 +16,6 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] - input: - meta: type: map @@ -57,7 +56,10 @@ input: type: file description: Genome reference FASTA index file pattern: "*.{fa.fai,fasta.fai}" - + - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" output: - meta: type: map @@ -92,7 +94,11 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@maxulysse" - "@ramprasadn" + - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@ramprasadn" + - "@nvnieuwk" diff --git a/modules/nf-core/manta/somatic/environment.yml b/modules/nf-core/manta/somatic/environment.yml new file mode 100644 index 0000000000..235b1ba75d --- /dev/null +++ b/modules/nf-core/manta/somatic/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::manta=1.6.0 diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index 8ff8d90a11..07511b2f0b 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -3,15 +3,16 @@ process MANTA_SOMATIC { label 'process_medium' label 'error_retry' - conda "bioconda::manta=1.6.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : 'biocontainers/manta:1.6.0--h9ee0642_1' }" input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) - path fasta - path fai + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + path(config) output: tuple val(meta), path("*.candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf @@ -31,26 +32,53 @@ process MANTA_SOMATIC { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def options_manta = target_bed ? "--callRegions $target_bed" : "" - + def config_option = config ? "--config ${config}" : "" """ - configManta.py \ - --tumorBam $input_tumor \ - --normalBam $input_normal \ - --reference $fasta \ - --runDir manta \ - $options_manta \ + configManta.py \\ + --tumorBam $input_tumor \\ + --normalBam $input_normal \\ + --reference $fasta \\ + ${config_option} \\ + --runDir manta \\ + $options_manta \\ $args python manta/runWorkflow.py -m local -j $task.cpus - mv manta/results/variants/candidateSmallIndels.vcf.gz ${prefix}.candidate_small_indels.vcf.gz - mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi ${prefix}.candidate_small_indels.vcf.gz.tbi - mv manta/results/variants/candidateSV.vcf.gz ${prefix}.candidate_sv.vcf.gz - mv manta/results/variants/candidateSV.vcf.gz.tbi ${prefix}.candidate_sv.vcf.gz.tbi - mv manta/results/variants/diploidSV.vcf.gz ${prefix}.diploid_sv.vcf.gz - mv manta/results/variants/diploidSV.vcf.gz.tbi ${prefix}.diploid_sv.vcf.gz.tbi - mv manta/results/variants/somaticSV.vcf.gz ${prefix}.somatic_sv.vcf.gz - mv manta/results/variants/somaticSV.vcf.gz.tbi ${prefix}.somatic_sv.vcf.gz.tbi + mv manta/results/variants/candidateSmallIndels.vcf.gz \\ + ${prefix}.candidate_small_indels.vcf.gz + mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \\ + ${prefix}.candidate_small_indels.vcf.gz.tbi + mv manta/results/variants/candidateSV.vcf.gz \\ + ${prefix}.candidate_sv.vcf.gz + mv manta/results/variants/candidateSV.vcf.gz.tbi \\ + ${prefix}.candidate_sv.vcf.gz.tbi + mv manta/results/variants/diploidSV.vcf.gz \\ + ${prefix}.diploid_sv.vcf.gz + mv manta/results/variants/diploidSV.vcf.gz.tbi \\ + ${prefix}.diploid_sv.vcf.gz.tbi + mv manta/results/variants/somaticSV.vcf.gz \\ + ${prefix}.somatic_sv.vcf.gz + mv manta/results/variants/somaticSV.vcf.gz.tbi \\ + ${prefix}.somatic_sv.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + manta: \$( configManta.py --version ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.candidate_small_indels.vcf.gz + touch ${prefix}.candidate_small_indels.vcf.gz.tbi + touch ${prefix}.candidate_sv.vcf.gz + touch ${prefix}.candidate_sv.vcf.gz.tbi + touch ${prefix}.diploid_sv.vcf.gz + touch ${prefix}.diploid_sv.vcf.gz.tbi + touch ${prefix}.somatic_sv.vcf.gz + touch ${prefix}.somatic_sv.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/manta/somatic/meta.yml b/modules/nf-core/manta/somatic/meta.yml index 457d66a5fd..e658edaaa4 100644 --- a/modules/nf-core/manta/somatic/meta.yml +++ b/modules/nf-core/manta/somatic/meta.yml @@ -16,7 +16,6 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] - input: - meta: type: map @@ -47,15 +46,28 @@ input: 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 + e.g. [ id:'genome' ] - fasta: type: file description: Genome reference FASTA file pattern: "*.{fa,fasta}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - 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 @@ -98,6 +110,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@FriederikeHanssen" + - "@nvnieuwk" +maintainers: + - "@FriederikeHanssen" + - "@nvnieuwk" diff --git a/modules/nf-core/manta/tumoronly/environment.yml b/modules/nf-core/manta/tumoronly/environment.yml new file mode 100644 index 0000000000..235b1ba75d --- /dev/null +++ b/modules/nf-core/manta/tumoronly/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::manta=1.6.0 diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index e3d6ca1b14..b047299571 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -3,15 +3,16 @@ process MANTA_TUMORONLY { label 'process_medium' label 'error_retry' - conda "bioconda::manta=1.6.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : 'biocontainers/manta:1.6.0--h9ee0642_1' }" input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) - path fasta - path fai + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + path(config) output: tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf @@ -29,27 +30,29 @@ process MANTA_TUMORONLY { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def options_manta = target_bed ? "--callRegions $target_bed" : "" + def config_option = config ? "--config ${config}" : "" """ - configManta.py \ - --tumorBam $input \ - --reference $fasta \ - --runDir manta \ - $options_manta \ + configManta.py \\ + --tumorBam $input \\ + --reference $fasta \\ + ${config_option} \\ + --runDir manta \\ + $options_manta \\ $args python manta/runWorkflow.py -m local -j $task.cpus - mv manta/results/variants/candidateSmallIndels.vcf.gz \ + mv manta/results/variants/candidateSmallIndels.vcf.gz \\ ${prefix}.candidate_small_indels.vcf.gz - mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \ + mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \\ ${prefix}.candidate_small_indels.vcf.gz.tbi - mv manta/results/variants/candidateSV.vcf.gz \ + mv manta/results/variants/candidateSV.vcf.gz \\ ${prefix}.candidate_sv.vcf.gz - mv manta/results/variants/candidateSV.vcf.gz.tbi \ + mv manta/results/variants/candidateSV.vcf.gz.tbi \\ ${prefix}.candidate_sv.vcf.gz.tbi - mv manta/results/variants/tumorSV.vcf.gz \ + mv manta/results/variants/tumorSV.vcf.gz \\ ${prefix}.tumor_sv.vcf.gz - mv manta/results/variants/tumorSV.vcf.gz.tbi \ + mv manta/results/variants/tumorSV.vcf.gz.tbi \\ ${prefix}.tumor_sv.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml @@ -57,4 +60,20 @@ process MANTA_TUMORONLY { manta: \$( configManta.py --version ) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.candidate_small_indels.vcf.gz + touch ${prefix}.candidate_small_indels.vcf.gz.tbi + touch ${prefix}.candidate_sv.vcf.gz + touch ${prefix}.candidate_sv.vcf.gz.tbi + touch ${prefix}.tumor_sv.vcf.gz + touch ${prefix}.tumor_sv.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + manta: \$( configManta.py --version ) + END_VERSIONS + """ } diff --git a/modules/nf-core/manta/tumoronly/meta.yml b/modules/nf-core/manta/tumoronly/meta.yml index 398d684365..63556c59b4 100644 --- a/modules/nf-core/manta/tumoronly/meta.yml +++ b/modules/nf-core/manta/tumoronly/meta.yml @@ -16,7 +16,6 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] - input: - meta: type: map @@ -39,15 +38,28 @@ input: 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 + e.g. [ id:'genome' ] - fasta: type: file description: Genome reference FASTA file pattern: "*.{fa,fasta}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - 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 @@ -82,6 +94,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@maxulysse" + - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@nvnieuwk" diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml new file mode 100644 index 0000000000..f1521e08a2 --- /dev/null +++ b/modules/nf-core/mosdepth/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::mosdepth=0.3.3 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 74db3a274b..7dd13ffb51 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -2,7 +2,7 @@ process MOSDEPTH { tag "$meta.id" label 'process_medium' - conda "bioconda::mosdepth=0.3.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : 'biocontainers/mosdepth:0.3.3--hdfd78af_1'}" diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index adf3893f3e..76263b5af9 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -107,3 +107,8 @@ authors: - "@drpatelh" - "@ramprasadn" - "@matthdsm" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@ramprasadn" + - "@matthdsm" diff --git a/modules/nf-core/msisensorpro/msisomatic/environment.yml b/modules/nf-core/msisensorpro/msisomatic/environment.yml new file mode 100644 index 0000000000..6d85f22481 --- /dev/null +++ b/modules/nf-core/msisensorpro/msisomatic/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::msisensor-pro=1.2.0 diff --git a/modules/nf-core/msisensorpro/msisomatic/main.nf b/modules/nf-core/msisensorpro/msisomatic/main.nf index 50287cb3cd..9b0084d949 100644 --- a/modules/nf-core/msisensorpro/msisomatic/main.nf +++ b/modules/nf-core/msisensorpro/msisomatic/main.nf @@ -2,7 +2,7 @@ process MSISENSORPRO_MSISOMATIC { tag "$meta.id" label 'process_low' - conda "bioconda::msisensor-pro=1.2.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : 'biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" diff --git a/modules/nf-core/msisensorpro/msisomatic/meta.yml b/modules/nf-core/msisensorpro/msisomatic/meta.yml index bcd95dc72b..a6dda66ff2 100644 --- a/modules/nf-core/msisensorpro/msisomatic/meta.yml +++ b/modules/nf-core/msisensorpro/msisomatic/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: https://github.com/xjtu-omics/msisensor-pro doi: "10.1016/j.gpb.2020.02.001" licence: ["Custom Licence"] - input: - meta: type: map @@ -48,7 +47,6 @@ input: type: file description: Output from msisensor-pro/scan, conaining list of msi regions pattern: "*.list" - output: - meta: type: map @@ -75,6 +73,7 @@ output: type: file description: File containing microsatellite list pattern: "*.{list}" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/msisensorpro/scan/environment.yml b/modules/nf-core/msisensorpro/scan/environment.yml new file mode 100644 index 0000000000..6d85f22481 --- /dev/null +++ b/modules/nf-core/msisensorpro/scan/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::msisensor-pro=1.2.0 diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index 760d51aa22..9c7dce2596 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -2,7 +2,7 @@ process MSISENSORPRO_SCAN { tag "$meta.id" label 'process_low' - conda "bioconda::msisensor-pro=1.2.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : 'biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" diff --git a/modules/nf-core/msisensorpro/scan/meta.yml b/modules/nf-core/msisensorpro/scan/meta.yml index 47f4d3529f..aec743ede5 100644 --- a/modules/nf-core/msisensorpro/scan/meta.yml +++ b/modules/nf-core/msisensorpro/scan/meta.yml @@ -12,7 +12,6 @@ tools: tool_dev_url: https://github.com/xjtu-omics/msisensor-pro doi: "10.1016/j.gpb.2020.02.001" licence: ["Custom Licence"] - input: - meta: type: map @@ -23,7 +22,6 @@ input: type: file description: Reference genome pattern: "*.{fasta}" - output: - meta: type: map @@ -38,6 +36,7 @@ output: type: file description: File containing microsatellite list pattern: "*.{list}" - authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 0000000000..9d0e6b2090 --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 65d7dd0de1..2bbc3983fa 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee519..a61223ed7a 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/samblaster/environment.yml b/modules/nf-core/samblaster/environment.yml new file mode 100644 index 0000000000..3a79aaf8ea --- /dev/null +++ b/modules/nf-core/samblaster/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samblaster=0.1.26 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index af1f71d6e5..4622d3691d 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -2,7 +2,7 @@ process SAMBLASTER { tag "$meta.id" label 'process_low' - conda "bioconda::samblaster=0.1.26 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:cee56b506ceb753d4bbef7e05b81e1bfc25d937f-0' : 'biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:cee56b506ceb753d4bbef7e05b81e1bfc25d937f-0' }" diff --git a/modules/nf-core/samblaster/meta.yml b/modules/nf-core/samblaster/meta.yml index f090c89816..ccb48320c1 100644 --- a/modules/nf-core/samblaster/meta.yml +++ b/modules/nf-core/samblaster/meta.yml @@ -19,12 +19,10 @@ tools: It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. By default, samblaster reads SAM input from stdin and writes SAM to stdout. - documentation: https://github.com/GregoryFaust/samblaster tool_dev_url: https://github.com/GregoryFaust/samblaster doi: "10.1093/bioinformatics/btu314" licence: ["MIT"] - input: - meta: type: map @@ -35,7 +33,6 @@ input: type: file description: BAM file pattern: "*.bam" - output: - meta: type: map @@ -50,6 +47,7 @@ output: type: file description: Tagged or filtered BAM file pattern: "*.bam" - authors: - "@lescai" +maintainers: + - "@lescai" diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index 858f2ae3d7..016d91d992 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_BAM2FQ { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/bam2fq/meta.yml b/modules/nf-core/samtools/bam2fq/meta.yml index c7ad3ba834..7769046b54 100644 --- a/modules/nf-core/samtools/bam2fq/meta.yml +++ b/modules/nf-core/samtools/bam2fq/meta.yml @@ -9,11 +9,8 @@ keywords: tools: - samtools: description: Tools for dealing with SAM, BAM and CRAM files - documentation: http://www.htslib.org/doc/1.1/samtools.html - licence: ["MIT"] - input: - meta: type: map @@ -32,7 +29,6 @@ input: Note: choosing TRUE will generate 4 different files. Choosing FALSE will produce a single file, which will be interleaved in case the input contains paired reads. - output: - meta: type: map @@ -49,6 +45,7 @@ output: FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) or a single interleaved .fq.gz file if the user chooses not to split the reads. pattern: "*.fq.gz" - authors: - "@lescai" +maintainers: + - "@lescai" diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 4469fafcca..537b88cca4 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_COLLATEFASTQ { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/collatefastq/meta.yml b/modules/nf-core/samtools/collatefastq/meta.yml index b647cba454..898cdbdad7 100644 --- a/modules/nf-core/samtools/collatefastq/meta.yml +++ b/modules/nf-core/samtools/collatefastq/meta.yml @@ -9,11 +9,8 @@ keywords: tools: - samtools: description: Tools for dealing with SAM, BAM and CRAM files - documentation: http://www.htslib.org/doc/1.1/samtools.html - licence: ["MIT"] - input: - meta: type: map @@ -69,8 +66,11 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@lescai" - "@maxulysse" - "@matthdsm" +maintainers: + - "@lescai" + - "@maxulysse" + - "@matthdsm" diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/convert/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index 29722ba787..ddf17d2dee 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_CONVERT { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml index 866c228fef..f8a1612fc2 100644 --- a/modules/nf-core/samtools/convert/meta.yml +++ b/modules/nf-core/samtools/convert/meta.yml @@ -50,3 +50,6 @@ output: authors: - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 59ed308876..3aa988224e 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 957b25e52b..e189af28fd 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -55,3 +55,7 @@ authors: - "@drpatelh" - "@ewels" - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/index/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4bb8..256bd7c469 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 8bd2fa6fb4..01a4ee03eb 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -51,3 +51,7 @@ authors: - "@drpatelh" - "@ewels" - "@maxulysse" +maintainers: + - "@drpatelh" + - "@ewels" + - "@maxulysse" diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/merge/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index b73b7cb2a9..21f785cfdc 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_MERGE { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" @@ -16,6 +16,7 @@ process SAMTOOLS_MERGE { tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram tuple val(meta), path("*.csi") , optional:true, emit: csi + tuple val(meta), path("*.crai") , optional:true, emit: crai path "versions.yml" , emit: versions diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 3a815f74b9..2e8f3dbbb5 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -65,9 +65,19 @@ output: type: file description: BAM index file (optional) pattern: "*.csi" + - crai: + type: file + description: CRAM index file (optional) + pattern: "*.crai" authors: - "@drpatelh" - "@yuukiiwa " - "@maxulysse" - "@FriederikeHanssen" - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@yuukiiwa " + - "@maxulysse" + - "@FriederikeHanssen" + - "@ramprasadn" diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index d772498415..ed102582c4 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_MPILEUP { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/mpileup/meta.yml b/modules/nf-core/samtools/mpileup/meta.yml index 7597ef41ab..13038fbc9b 100644 --- a/modules/nf-core/samtools/mpileup/meta.yml +++ b/modules/nf-core/samtools/mpileup/meta.yml @@ -50,3 +50,6 @@ output: authors: - "@drpatelh" - "@joseespinosa" +maintainers: + - "@drpatelh" + - "@joseespinosa" diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/stats/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 4a2607ded0..07286ef410 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 90e6345f53..735ff8122a 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -57,3 +57,7 @@ authors: - "@drpatelh" - "@FriederikeHanssen" - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@FriederikeHanssen" + - "@ramprasadn" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test new file mode 100644 index 0000000000..e037132ca2 --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -0,0 +1,78 @@ +nextflow_process { + + name "Test Process SAMTOOLS_STATS" + script "../main.nf" + process "SAMTOOLS_STATS" + tag "modules" + tag "modules/nf-core" + tag "samtools" + tag "samtools/stats" + + test("SAMTOOLS STATS Should run without failures") { + + when { + params { + + outdir = "$outputDir" + } + process { + """ + // define inputs of the process here. + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + + ] + input[1] = [[],[]] + """ + + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + + } + + test("SAMTOOLS CRAM Should run without failures") { + + when { + params { + + outdir = "$outputDir" + } + process { + """ + // define inputs of the process here + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) + + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + + + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + + } + + +} diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap new file mode 100644 index 0000000000..516b2b0192 --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -0,0 +1,64 @@ +{ + "SAMTOOLS STATS Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + ] + ], + "1": [ + "versions.yml:md5,08035f3409d934d47a416150884bb0df" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + ] + ], + "versions": [ + "versions.yml:md5,08035f3409d934d47a416150884bb0df" + ] + } + ], + "timestamp": "2023-10-18T12:12:42.998746" + }, + "SAMTOOLS CRAM Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + ] + ], + "1": [ + "versions.yml:md5,08035f3409d934d47a416150884bb0df" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + ] + ], + "versions": [ + "versions.yml:md5,08035f3409d934d47a416150884bb0df" + ] + } + ], + "timestamp": "2023-10-18T12:13:30.747222" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/tests/tags.yml b/modules/nf-core/samtools/stats/tests/tags.yml new file mode 100644 index 0000000000..7c28e30f3f --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/stats: + - modules/nf-core/samtools/stats/** diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml new file mode 100644 index 0000000000..04c82f1423 --- /dev/null +++ b/modules/nf-core/samtools/view/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index cb91facf8c..ddf3f88ae5 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 3b05450b2e..3dadafae75 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -82,3 +82,8 @@ authors: - "@joseespinosa" - "@FriederikeHanssen" - "@priyanka-surana" +maintainers: + - "@drpatelh" + - "@joseespinosa" + - "@FriederikeHanssen" + - "@priyanka-surana" diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/applyvarcal/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/applyvarcal/meta.yml b/modules/nf-core/sentieon/applyvarcal/meta.yml index bbe23ea375..da92ce3436 100644 --- a/modules/nf-core/sentieon/applyvarcal/meta.yml +++ b/modules/nf-core/sentieon/applyvarcal/meta.yml @@ -17,7 +17,6 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ - input: - meta: type: map @@ -82,3 +81,5 @@ output: pattern: "versions.yml" authors: - "@assp8200" +maintainers: + - "@assp8200" diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml index 9987e8c900..0859a923ca 100644 --- a/modules/nf-core/sentieon/bwamem/meta.yml +++ b/modules/nf-core/sentieon/bwamem/meta.yml @@ -71,3 +71,5 @@ output: pattern: "versions.yml" authors: - "@asp8200" +maintainers: + - "@asp8200" diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/dedup/meta.yml b/modules/nf-core/sentieon/dedup/meta.yml index ec0565d923..0efbb96c22 100644 --- a/modules/nf-core/sentieon/dedup/meta.yml +++ b/modules/nf-core/sentieon/dedup/meta.yml @@ -86,3 +86,5 @@ output: pattern: "versions.yml" authors: - "@asp8200" +maintainers: + - "@asp8200" diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml index ec429bea21..bc7d323ed5 100644 --- a/modules/nf-core/sentieon/dnamodelapply/meta.yml +++ b/modules/nf-core/sentieon/dnamodelapply/meta.yml @@ -12,7 +12,6 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ - input: - meta: type: map @@ -54,7 +53,6 @@ input: type: file description: machine learning model file pattern: "*.model" - output: - meta: type: map @@ -73,6 +71,7 @@ output: type: file description: Index of the input VCF file pattern: "*.{tbi}" - authors: - "@ramprasadn" +maintainers: + - "@ramprasadn" diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/dnascope/meta.yml b/modules/nf-core/sentieon/dnascope/meta.yml index 34e0b97b4c..6b61cee828 100644 --- a/modules/nf-core/sentieon/dnascope/meta.yml +++ b/modules/nf-core/sentieon/dnascope/meta.yml @@ -114,6 +114,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@ramprasadn" +maintainers: + - "@ramprasadn" diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/gvcftyper/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/gvcftyper/meta.yml b/modules/nf-core/sentieon/gvcftyper/meta.yml index c373b2c5cc..ceef173e3e 100644 --- a/modules/nf-core/sentieon/gvcftyper/meta.yml +++ b/modules/nf-core/sentieon/gvcftyper/meta.yml @@ -47,7 +47,6 @@ input: type: file description: dbSNP VCF index file pattern: "*.tbi" - output: - meta: type: map @@ -68,3 +67,5 @@ output: pattern: "versions.yml" authors: - "@asp8200" +maintainers: + - "@asp8200" diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/haplotyper/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/haplotyper/meta.yml b/modules/nf-core/sentieon/haplotyper/meta.yml index 33217808f8..c248db3fca 100644 --- a/modules/nf-core/sentieon/haplotyper/meta.yml +++ b/modules/nf-core/sentieon/haplotyper/meta.yml @@ -80,3 +80,5 @@ output: pattern: "versions.yml" authors: - "@asp8200" +maintainers: + - "@asp8200" diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml new file mode 100644 index 0000000000..bcd3a8b1c6 --- /dev/null +++ b/modules/nf-core/sentieon/varcal/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/sentieon/varcal/meta.yml b/modules/nf-core/sentieon/varcal/meta.yml index 5de37f6ad1..cad7ee106f 100644 --- a/modules/nf-core/sentieon/varcal/meta.yml +++ b/modules/nf-core/sentieon/varcal/meta.yml @@ -70,3 +70,5 @@ output: pattern: "*.versions.yml" authors: - "@asp8200" +maintainers: + - "@asp8200" diff --git a/modules/nf-core/snpeff/download/environment.yml b/modules/nf-core/snpeff/download/environment.yml new file mode 100644 index 0000000000..7d54aa5bdb --- /dev/null +++ b/modules/nf-core/snpeff/download/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::snpeff=5.1 diff --git a/modules/nf-core/snpeff/download/main.nf b/modules/nf-core/snpeff/download/main.nf index 9a3a0d3167..f1fc4cc395 100644 --- a/modules/nf-core/snpeff/download/main.nf +++ b/modules/nf-core/snpeff/download/main.nf @@ -2,7 +2,7 @@ process SNPEFF_DOWNLOAD { tag "$meta.id" label 'process_medium' - conda "bioconda::snpeff=5.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : 'biocontainers/snpeff:5.1--hdfd78af_2' }" diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index 3c03c2f602..26e728f71a 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -39,3 +39,5 @@ output: pattern: "versions.yml" authors: - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/modules/nf-core/snpeff/snpeff/environment.yml b/modules/nf-core/snpeff/snpeff/environment.yml new file mode 100644 index 0000000000..7d54aa5bdb --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::snpeff=5.1 diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index e92c1597e7..cc4f2ccb36 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -2,7 +2,7 @@ process SNPEFF_SNPEFF { tag "$meta.id" label 'process_medium' - conda "bioconda::snpeff=5.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : 'biocontainers/snpeff:5.1--hdfd78af_2' }" diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 44bada2303..0b771447ff 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -56,3 +56,5 @@ output: pattern: "versions.yml" authors: - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/modules/nf-core/strelka/germline/environment.yml b/modules/nf-core/strelka/germline/environment.yml new file mode 100644 index 0000000000..5c9c1cf81a --- /dev/null +++ b/modules/nf-core/strelka/germline/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::strelka=2.9.10 diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 74712df16b..8f93356160 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -3,7 +3,7 @@ process STRELKA_GERMLINE { label 'process_medium' label 'error_retry' - conda "bioconda::strelka=2.9.10" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : 'biocontainers/strelka:2.9.10--h9ee0642_1' }" diff --git a/modules/nf-core/strelka/germline/meta.yml b/modules/nf-core/strelka/germline/meta.yml index c119532d16..6ee656683e 100644 --- a/modules/nf-core/strelka/germline/meta.yml +++ b/modules/nf-core/strelka/germline/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x licence: ["GPL v3"] - input: - meta: type: map @@ -61,3 +60,5 @@ output: pattern: "versions.yml" authors: - "@arontommi" +maintainers: + - "@arontommi" diff --git a/modules/nf-core/strelka/somatic/environment.yml b/modules/nf-core/strelka/somatic/environment.yml new file mode 100644 index 0000000000..5c9c1cf81a --- /dev/null +++ b/modules/nf-core/strelka/somatic/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::strelka=2.9.10 diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 17d700c136..dd975bd563 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -3,7 +3,7 @@ process STRELKA_SOMATIC { label 'process_medium' label 'error_retry' - conda "bioconda::strelka=2.9.10" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : 'biocontainers/strelka:2.9.10--h9ee0642_1' }" diff --git a/modules/nf-core/strelka/somatic/meta.yml b/modules/nf-core/strelka/somatic/meta.yml index b2a2550462..6032cd6d5f 100644 --- a/modules/nf-core/strelka/somatic/meta.yml +++ b/modules/nf-core/strelka/somatic/meta.yml @@ -14,7 +14,6 @@ tools: tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x licence: ["GPL v3"] - input: - meta: type: map @@ -61,7 +60,6 @@ input: type: file description: Index for BED file containing target regions for variant calling pattern: "*.{bed.tbi}" - output: - meta: type: map @@ -88,6 +86,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml new file mode 100644 index 0000000000..e31e204e3d --- /dev/null +++ b/modules/nf-core/svdb/merge/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::svdb=2.8.1 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 0bd94499ab..0d9967dda9 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -1,7 +1,7 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' - conda "bioconda::svdb=2.8.1 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0': 'biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0' }" diff --git a/modules/nf-core/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml index 92a5a128ea..84265acb84 100644 --- a/modules/nf-core/svdb/merge/meta.yml +++ b/modules/nf-core/svdb/merge/meta.yml @@ -39,3 +39,5 @@ output: pattern: "*_sv_merge.vcf.gz" authors: - "@ramprasadn" +maintainers: + - "@ramprasadn" diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml new file mode 100644 index 0000000000..fdd84057b8 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index d6c5a760f3..f9482690ba 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -2,7 +2,7 @@ process TABIX_BGZIPTABIX { tag "$meta.id" label 'process_single' - conda "bioconda::tabix=1.11" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : 'biocontainers/tabix:1.11--hdfd78af_0' }" diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 2761e27183..438aba4d18 100644 --- a/modules/nf-core/tabix/bgziptabix/meta.yml +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -48,3 +48,6 @@ output: authors: - "@maxulysse" - "@DLBPointon" +maintainers: + - "@maxulysse" + - "@DLBPointon" diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml new file mode 100644 index 0000000000..fdd84057b8 --- /dev/null +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 5bf332ef84..c304a8a34b 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -2,7 +2,7 @@ process TABIX_TABIX { tag "$meta.id" label 'process_single' - conda "bioconda::tabix=1.11" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : 'biocontainers/tabix:1.11--hdfd78af_0' }" diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index fcc6e52463..ae5b4f439f 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -43,3 +43,7 @@ authors: - "@joseespinosa" - "@drpatelh" - "@maxulysse" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/nf-core/tiddit/sv/environment.yml b/modules/nf-core/tiddit/sv/environment.yml new file mode 100644 index 0000000000..69963f7c4b --- /dev/null +++ b/modules/nf-core/tiddit/sv/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::tiddit=3.6.1 diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 67a0670dbc..0f4bc7cb52 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -2,7 +2,7 @@ process TIDDIT_SV { tag "$meta.id" label 'process_medium' - conda "bioconda::tiddit=3.6.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.6.1--py38h24c8ff8_0' : 'biocontainers/tiddit:3.6.1--py38h24c8ff8_0' }" diff --git a/modules/nf-core/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml index 8b41c69cf5..b13ae5cdcb 100644 --- a/modules/nf-core/tiddit/sv/meta.yml +++ b/modules/nf-core/tiddit/sv/meta.yml @@ -53,3 +53,5 @@ output: pattern: "versions.yml" authors: - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml new file mode 100644 index 0000000000..2d52ce64ac --- /dev/null +++ b/modules/nf-core/untar/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 + - conda-forge::grep=3.11 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 61461c3917..8a75bb957d 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index db241a6e5e..a9a2110f55 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -39,3 +39,8 @@ authors: - "@drpatelh" - "@matthdsm" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@matthdsm" + - "@jfy133" diff --git a/modules/nf-core/unzip/environment.yml b/modules/nf-core/unzip/environment.yml new file mode 100644 index 0000000000..157fe95c01 --- /dev/null +++ b/modules/nf-core/unzip/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::p7zip=16.02 diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index cf977f1dcb..08cfc3c406 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -2,7 +2,7 @@ process UNZIP { tag "$archive" label 'process_single' - conda "conda-forge::p7zip=16.02" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/p7zip:16.02' : 'biocontainers/p7zip:16.02' }" diff --git a/modules/nf-core/unzip/meta.yml b/modules/nf-core/unzip/meta.yml index 2910e0fd3f..e8e377e2af 100644 --- a/modules/nf-core/unzip/meta.yml +++ b/modules/nf-core/unzip/meta.yml @@ -12,7 +12,6 @@ tools: documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] - input: - meta: type: map @@ -23,7 +22,6 @@ input: type: file description: ZIP file pattern: "*.zip" - output: - meta: type: map @@ -38,6 +36,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@jfy133" +maintainers: + - "@jfy133" diff --git a/modules/nf-core/vcftools/environment.yml b/modules/nf-core/vcftools/environment.yml new file mode 100644 index 0000000000..875817e21d --- /dev/null +++ b/modules/nf-core/vcftools/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::vcftools=0.1.16 diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index cf6d296281..0153a60891 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -2,7 +2,7 @@ process VCFTOOLS { tag "$meta.id" label 'process_single' - conda "bioconda::vcftools=0.1.16" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' : 'biocontainers/vcftools:0.1.16--he513fc3_4' }" diff --git a/modules/nf-core/vcftools/meta.yml b/modules/nf-core/vcftools/meta.yml index 04b786f0e6..f361db4a8f 100644 --- a/modules/nf-core/vcftools/meta.yml +++ b/modules/nf-core/vcftools/meta.yml @@ -9,7 +9,6 @@ tools: homepage: http://vcftools.sourceforge.net/ documentation: http://vcftools.sourceforge.net/man_latest.html licence: ["LGPL"] - input: - meta: type: map @@ -25,7 +24,6 @@ input: - diff_variant_file: type: file description: secondary variant file which can be used with the 'diff' suite of tools (optional) - output: - meta: type: map @@ -288,6 +286,7 @@ output: type: file description: Switch errors found between sites (optional) pattern: "*.diff.switch" - authors: - "@Mark-S-Hill" +maintainers: + - "@Mark-S-Hill" diff --git a/subworkflows/local/bam_applybqsr_spark/main.nf b/subworkflows/local/bam_applybqsr_spark/main.nf index 99a63e0976..cfb86ef6a4 100644 --- a/subworkflows/local/bam_applybqsr_spark/main.nf +++ b/subworkflows/local/bam_applybqsr_spark/main.nf @@ -4,7 +4,7 @@ // For all modules here: // A when clause condition is defined in the conf/modules.config to determine if the module should be run -include { GATK4_APPLYBQSR_SPARK } from '../../../modules/nf-core/gatk4/applybqsrspark/main' +include { GATK4SPARK_APPLYBQSR } from '../../../modules/nf-core/gatk4spark/applybqsr/main' include { CRAM_MERGE_INDEX_SAMTOOLS } from '../cram_merge_index_samtools/main' workflow BAM_APPLYBQSR_SPARK { @@ -24,10 +24,10 @@ workflow BAM_APPLYBQSR_SPARK { .map{ meta, cram, crai, recal, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, recal, intervals ] } // RUN APPLYBQSR SPARK - GATK4_APPLYBQSR_SPARK(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] }) + GATK4SPARK_APPLYBQSR(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] }) // Gather the recalibrated cram files - cram_to_merge = GATK4_APPLYBQSR_SPARK.out.cram.map{ meta, cram -> [ groupKey(meta, meta.num_intervals), cram ] }.groupTuple() + cram_to_merge = GATK4SPARK_APPLYBQSR.out.cram.map{ meta, cram -> [ groupKey(meta, meta.num_intervals), cram ] }.groupTuple() // Merge and index the recalibrated cram files CRAM_MERGE_INDEX_SAMTOOLS(cram_to_merge, fasta, fasta_fai) @@ -37,7 +37,7 @@ workflow BAM_APPLYBQSR_SPARK { .map{ meta, cram, crai -> [ meta - meta.subMap('num_intervals'), cram, crai ] } // Gather versions of all tools used - versions = versions.mix(GATK4_APPLYBQSR_SPARK.out.versions) + versions = versions.mix(GATK4SPARK_APPLYBQSR.out.versions) versions = versions.mix(CRAM_MERGE_INDEX_SAMTOOLS.out.versions) emit: diff --git a/subworkflows/local/bam_baserecalibrator_spark/main.nf b/subworkflows/local/bam_baserecalibrator_spark/main.nf index 04bb491b4c..d6e12c39e0 100644 --- a/subworkflows/local/bam_baserecalibrator_spark/main.nf +++ b/subworkflows/local/bam_baserecalibrator_spark/main.nf @@ -4,8 +4,8 @@ // For all modules here: // A when clause condition is defined in the conf/modules.config to determine if the module should be run -include { GATK4_BASERECALIBRATOR_SPARK } from '../../../modules/nf-core/gatk4/baserecalibratorspark/main' -include { GATK4_GATHERBQSRREPORTS } from '../../../modules/nf-core/gatk4/gatherbqsrreports/main' +include { GATK4SPARK_BASERECALIBRATOR } from '../../../modules/nf-core/gatk4spark/baserecalibrator/main' +include { GATK4_GATHERBQSRREPORTS } from '../../../modules/nf-core/gatk4/gatherbqsrreports/main' workflow BAM_BASERECALIBRATOR_SPARK { take: @@ -26,10 +26,10 @@ workflow BAM_BASERECALIBRATOR_SPARK { .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] } // RUN BASERECALIBRATOR SPARK - GATK4_BASERECALIBRATOR_SPARK(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi) + GATK4SPARK_BASERECALIBRATOR(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi) // Figuring out if there is one or more table(s) from the same sample - table_to_merge = GATK4_BASERECALIBRATOR_SPARK.out.table.map{ meta, table -> [ groupKey(meta, meta.num_intervals), table ] }.groupTuple().branch{ + table_to_merge = GATK4SPARK_BASERECALIBRATOR.out.table.map{ meta, table -> [ groupKey(meta, meta.num_intervals), table ] }.groupTuple().branch{ // Use meta.num_intervals to asses number of intervals single: it[0].num_intervals <= 1 multiple: it[0].num_intervals > 1 @@ -44,7 +44,7 @@ workflow BAM_BASERECALIBRATOR_SPARK { .map{ meta, table -> [ meta - meta.subMap('num_intervals'), table ] } // Gather versions of all tools used - versions = versions.mix(GATK4_BASERECALIBRATOR_SPARK.out.versions) + versions = versions.mix(GATK4SPARK_BASERECALIBRATOR.out.versions) versions = versions.mix(GATK4_GATHERBQSRREPORTS.out.versions) emit: diff --git a/subworkflows/local/bam_markduplicates_spark/main.nf b/subworkflows/local/bam_markduplicates_spark/main.nf index e978bf5a38..8e7d0ee023 100644 --- a/subworkflows/local/bam_markduplicates_spark/main.nf +++ b/subworkflows/local/bam_markduplicates_spark/main.nf @@ -4,10 +4,10 @@ // For all modules here: // A when clause condition is defined in the conf/modules.config to determine if the module should be run -include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main' -include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main' -include { GATK4_MARKDUPLICATES_SPARK } from '../../../modules/nf-core/gatk4/markduplicatesspark/main' -include { SAMTOOLS_INDEX as INDEX_MARKDUPLICATES } from '../../../modules/nf-core/samtools/index/main' +include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main' +include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main' +include { GATK4SPARK_MARKDUPLICATES } from '../../../modules/nf-core/gatk4spark/markduplicates/main' +include { SAMTOOLS_INDEX as INDEX_MARKDUPLICATES } from '../../../modules/nf-core/samtools/index/main' workflow BAM_MARKDUPLICATES_SPARK { take: @@ -22,13 +22,13 @@ workflow BAM_MARKDUPLICATES_SPARK { reports = Channel.empty() // RUN MARKUPDUPLICATES SPARK - GATK4_MARKDUPLICATES_SPARK(bam, fasta, fasta_fai, dict) + GATK4SPARK_MARKDUPLICATES(bam, fasta, fasta_fai, dict) // Index cram - INDEX_MARKDUPLICATES(GATK4_MARKDUPLICATES_SPARK.out.output) + INDEX_MARKDUPLICATES(GATK4SPARK_MARKDUPLICATES.out.output) // Join with the crai file - cram = GATK4_MARKDUPLICATES_SPARK.out.output.join(INDEX_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true) + cram = GATK4SPARK_MARKDUPLICATES.out.output.join(INDEX_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true) // QC on CRAM CRAM_QC_MOSDEPTH_SAMTOOLS(cram, fasta, intervals_bed_combined) @@ -42,7 +42,7 @@ workflow BAM_MARKDUPLICATES_SPARK { // Gather versions of all tools used versions = versions.mix(GATK4_ESTIMATELIBRARYCOMPLEXITY.out.versions) - versions = versions.mix(GATK4_MARKDUPLICATES_SPARK.out.versions) + versions = versions.mix(GATK4SPARK_MARKDUPLICATES.out.versions) versions = versions.mix(INDEX_MARKDUPLICATES.out.versions) versions = versions.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.versions) diff --git a/subworkflows/local/bam_variant_calling_cnvkit/main.nf b/subworkflows/local/bam_variant_calling_cnvkit/main.nf index c6b93d33c9..161c2dc21a 100644 --- a/subworkflows/local/bam_variant_calling_cnvkit/main.nf +++ b/subworkflows/local/bam_variant_calling_cnvkit/main.nf @@ -9,11 +9,11 @@ include { CNVKIT_GENEMETRICS } from '../../../modules/nf-core/cnvkit/genemetrics workflow BAM_VARIANT_CALLING_CNVKIT { take: - cram // channel: [mandatory] cram - fasta // channel: [mandatory] fasta - fasta_fai // channel: [optional] fasta_fai - targets // channel: [mandatory] bed - reference // channel: [] cnn + cram // channel: [mandatory] meta, cram + fasta // channel: [mandatory] meta, fasta + fasta_fai // channel: [optional] meta, fasta_fai + targets // channel: [mandatory] meta, bed + reference // channel: [optional] meta, cnn main: versions = Channel.empty() diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf index 5989023adf..243b4d96c2 100644 --- a/subworkflows/local/bam_variant_calling_germline_all/main.nf +++ b/subworkflows/local/bam_variant_calling_germline_all/main.nf @@ -83,10 +83,10 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL { BAM_VARIANT_CALLING_CNVKIT( // Remap channel to match module/subworkflow cram.map{ meta, cram, crai -> [ meta, [], cram ] }, - fasta, - fasta_fai, - intervals_bed_combined, - [] + fasta.map{ it -> [[id:it[0].baseName], it] }, + fasta_fai.map{ it -> [[id:it[0].baseName], it] }, + intervals_bed_combined.map{ it -> [[id:it[0].baseName], it] }, + [[id:"null"], []] ) versions = versions.mix(BAM_VARIANT_CALLING_CNVKIT.out.versions) } @@ -181,8 +181,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL { if (tools.split(',').contains('manta')) { BAM_VARIANT_CALLING_GERMLINE_MANTA ( cram, - fasta, - fasta_fai, + fasta.map{ it -> [ [ id:'fasta' ], it ] }, + fasta_fai.map{ it -> [ [ id:'fasta_fai' ], it ] }, intervals_bed_gz_tbi_combined ) diff --git a/subworkflows/local/bam_variant_calling_germline_manta/main.nf b/subworkflows/local/bam_variant_calling_germline_manta/main.nf index 36cb957d6f..d27a999a68 100644 --- a/subworkflows/local/bam_variant_calling_germline_manta/main.nf +++ b/subworkflows/local/bam_variant_calling_germline_manta/main.nf @@ -10,8 +10,8 @@ include { MANTA_GERMLINE } from '../../../modules/nf-core/manta/germline/main' workflow BAM_VARIANT_CALLING_GERMLINE_MANTA { take: cram // channel: [mandatory] [ meta, cram, crai ] - fasta // channel: [mandatory] [ fasta ] - fasta_fai // channel: [mandatory] [ fasta_fai ] + fasta // channel: [mandatory] [ meta, fasta ] + fasta_fai // channel: [mandatory] [ meta, fasta_fai ] intervals // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi] or [ [], []] if no intervals; intervals file contains all intervals main: @@ -25,7 +25,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_MANTA { [it[0], it[1], it[2], bed_gz, bed_tbi] } - MANTA_GERMLINE(cram_intervals, fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] }, fasta_fai.map{ fasta_fai -> [ [ id:fasta_fai.baseName ], fasta_fai ] }) + MANTA_GERMLINE(cram_intervals, fasta, fasta_fai, []) small_indels_vcf = MANTA_GERMLINE.out.candidate_small_indels_vcf sv_vcf = MANTA_GERMLINE.out.candidate_sv_vcf diff --git a/subworkflows/local/bam_variant_calling_mpileup/main.nf b/subworkflows/local/bam_variant_calling_mpileup/main.nf index 412ba38619..663ed6a0bc 100644 --- a/subworkflows/local/bam_variant_calling_mpileup/main.nf +++ b/subworkflows/local/bam_variant_calling_mpileup/main.nf @@ -4,10 +4,10 @@ // For all modules here: // A when clause condition is defined in the conf/modules.config to determine if the module should be run -include { CAT_CAT as CAT_MPILEUP } from '../../../modules/nf-core/cat/cat/main' -include { BCFTOOLS_MPILEUP } from '../../../modules/nf-core/bcftools/mpileup/main' -include { SAMTOOLS_MPILEUP } from '../../../modules/nf-core/samtools/mpileup/main' -include { GATK4_MERGEVCFS as MERGE_BCFTOOLS_MPILEUP } from '../../../modules/nf-core/gatk4/mergevcfs/main' +include { BCFTOOLS_MPILEUP } from '../../../modules/nf-core/bcftools/mpileup/main' +include { CAT_CAT as CAT_MPILEUP } from '../../../modules/nf-core/cat/cat/main' +include { GATK4_MERGEVCFS as MERGE_BCFTOOLS_MPILEUP } from '../../../modules/nf-core/gatk4/mergevcfs/main' +include { SAMTOOLS_MPILEUP } from '../../../modules/nf-core/samtools/mpileup/main' workflow BAM_VARIANT_CALLING_MPILEUP { take: @@ -26,7 +26,7 @@ workflow BAM_VARIANT_CALLING_MPILEUP { // Run, if --tools mpileup keep_bcftools_mpileup = false - BCFTOOLS_MPILEUP(cram_intervals, fasta, keep_bcftools_mpileup) + BCFTOOLS_MPILEUP(cram_intervals, fasta.map{ it -> [[id:it[0].baseName], it] }, keep_bcftools_mpileup) //Only run, if --tools ControlFreec SAMTOOLS_MPILEUP(cram_intervals, fasta) diff --git a/subworkflows/local/bam_variant_calling_somatic_all/main.nf b/subworkflows/local/bam_variant_calling_somatic_all/main.nf index af2b8c1e2f..f561ea420c 100644 --- a/subworkflows/local/bam_variant_calling_somatic_all/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_all/main.nf @@ -118,10 +118,10 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL { BAM_VARIANT_CALLING_CNVKIT( // Remap channel to match module/subworkflow cram.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai -> [ meta, tumor_cram, normal_cram ] }, - fasta, - fasta_fai, - intervals_bed_combined, - [] + fasta.map{ it -> [[id:it[0].baseName], it] }, + fasta_fai.map{ it -> [[id:it[0].baseName], it] }, + intervals_bed_combined.map{ it -> [[id:it[0].baseName], it] }, + [[id:"null"], []] ) versions = versions.mix(BAM_VARIANT_CALLING_CNVKIT.out.versions) @@ -145,8 +145,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL { if (tools.split(',').contains('manta')) { BAM_VARIANT_CALLING_SOMATIC_MANTA( cram, - fasta, - fasta_fai, + fasta.map{ it -> [ [ id:'fasta' ], it ] }, + fasta_fai.map{ it -> [ [ id:'fasta_fai' ], it ] }, intervals_bed_gz_tbi_combined ) diff --git a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf index 7eb5e6687d..f6720c5406 100644 --- a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf @@ -9,8 +9,8 @@ include { MANTA_SOMATIC } from '../../../modules/nf-core/manta/somatic/main' workflow BAM_VARIANT_CALLING_SOMATIC_MANTA { take: cram // channel: [mandatory] [ meta, cram1, crai1, cram2, crai2 ] - fasta // channel: [mandatory] [ fasta ] - fasta_fai // channel: [mandatory] [ fasta_fai ] + fasta // channel: [mandatory] [ meta, fasta ] + fasta_fai // channel: [mandatory] [ meta, fasta_fai ] intervals // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi ] or [ [], [] ] if no intervals main: @@ -24,7 +24,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA { [it[0], it[1], it[2], it[3], it[4], bed_gz, bed_tbi] } - MANTA_SOMATIC(cram_intervals, fasta, fasta_fai) + MANTA_SOMATIC(cram_intervals, fasta, fasta_fai, []) candidate_small_indels_vcf = MANTA_SOMATIC.out.candidate_small_indels_vcf candidate_small_indels_vcf_tbi = MANTA_SOMATIC.out.candidate_small_indels_vcf_tbi diff --git a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf index d92b263b8a..31d968a245 100644 --- a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf +++ b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf @@ -85,10 +85,10 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL { BAM_VARIANT_CALLING_CNVKIT ( // Remap channel to match module/subworkflow cram.map{ meta, cram, crai -> [ meta, cram, [] ] }, - fasta, - fasta_fai, - [], - cnvkit_reference + fasta.map{ it -> [[id:it[0].baseName], it] }, + fasta_fai.map{ it -> [[id:it[0].baseName], it] }, + [[id:"null"], []], + cnvkit_reference.map{ it -> [[id:it[0].baseName], it] } ) versions = versions.mix(BAM_VARIANT_CALLING_CNVKIT.out.versions) @@ -141,9 +141,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL { BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA( cram, // Remap channel to match module/subworkflow - dict.map{ it -> [ [ id:'dict' ], it ] }, - fasta, - fasta_fai, + fasta.map{ it -> [ [ id:'fasta' ], it ] }, + fasta_fai.map{ it -> [ [ id:'fasta_fai' ], it ] }, intervals_bed_gz_tbi_combined ) diff --git a/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf index 10045c7356..38f5d4366c 100644 --- a/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf +++ b/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf @@ -10,9 +10,8 @@ include { MANTA_TUMORONLY } from '../../../modules/nf-core/manta/tumoronly/main' workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA { take: cram // channel: [mandatory] [ meta, cram, crai ] - dict // channel: [optional] [ meta, dict ] - fasta // channel: [mandatory] [ fasta ] - fasta_fai // channel: [mandatory] [ fasta_fai ] + fasta // channel: [mandatory] [ meta, fasta ] + fasta_fai // channel: [mandatory] [ meta, fasta_fai ] intervals // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi ] or [ [], [] ] if no intervals main: @@ -26,7 +25,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA { [it[0], it[1], it[2], bed_gz, bed_tbi] } - MANTA_TUMORONLY(cram_intervals, fasta, fasta_fai) + MANTA_TUMORONLY(cram_intervals, fasta, fasta_fai, []) small_indels_vcf = MANTA_TUMORONLY.out.candidate_small_indels_vcf candidate_sv_vcf = MANTA_TUMORONLY.out.candidate_sv_vcf diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml b/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml index 7a9fd10c4e..15d42da23f 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml @@ -59,3 +59,7 @@ authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@matthdsm" + - "@nvnieuwk" diff --git a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf index 2a875939de..3570a5b7c0 100644 --- a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf +++ b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf @@ -13,6 +13,7 @@ workflow VCF_ANNOTATE_SNPEFF { main: ch_versions = Channel.empty() + SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache) TABIX_BGZIPTABIX(SNPEFF_SNPEFF.out.vcf) diff --git a/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml b/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml index b3f10cae12..c8d5a635ee 100644 --- a/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml +++ b/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml @@ -36,3 +36,5 @@ output: Structure: [ path(versions.yml) ] authors: - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml index 144c681d79..2c93fed587 100644 --- a/tests/config/pytesttags.yml +++ b/tests/config/pytesttags.yml @@ -206,20 +206,20 @@ intervals: - tests/csv/3.0/fastq_single.csv - tests/test_intervals.yml -## gatk4_spark -gatk4_spark: +## gatk4spark +gatk4spark: - conf/modules/markduplicates.config - conf/modules/prepare_recalibration.config - conf/modules/recalibrate.config - - modules/nf-core/gatk4/applybqsrspark/main.nf - - modules/nf-core/gatk4/baserecalibratorspark/main.nf + - modules/nf-core/gatk4spark/applybqsr/main.nf + - modules/nf-core/gatk4spark/baserecalibrator/main.nf - modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf - - modules/nf-core/gatk4/markduplicatesspark/main.nf + - modules/nf-core/gatk4spark/markduplicates/main.nf - subworkflows/local/bam_applybqsr_spark/main.nf - subworkflows/local/bam_baserecalibrator_spark/main.nf - subworkflows/local/bam_markduplicates_spark/main.nf - tests/csv/3.0/fastq_single.csv - - tests/test_gatk4_spark.yml + - tests/test_gatk4spark.yml # variant calling diff --git a/tests/test_annotation_bcfann.yml b/tests/test_annotation_bcfann.yml index 78ec274431..93fa668c3d 100644 --- a/tests/test_annotation_bcfann.yml +++ b/tests/test_annotation_bcfann.yml @@ -1,5 +1,5 @@ - name: Run bcfann - command: nextflow run main.nf -profile test,test_cache,annotation --tools bcfann --outdir results --download_cache + command: nextflow run main.nf -profile test,test_cache,annotation --tools bcfann --outdir results tags: - annotation - bcfann @@ -7,4 +7,4 @@ - path: results/annotation/test/test_BCF.ann.vcf.gz # binary changes md5sums on reruns - path: results/annotation/test/test_BCF.ann.vcf.gz.tbi - md5sum: 2b6be791a106e60539892ddfc03eb47f + # binary changes md5sums on reruns diff --git a/tests/test_gatk4_spark.yml b/tests/test_gatk4spark.yml similarity index 97% rename from tests/test_gatk4_spark.yml rename to tests/test_gatk4spark.yml index 8dbc8fb974..7b6b42a3a5 100644 --- a/tests/test_gatk4_spark.yml +++ b/tests/test_gatk4spark.yml @@ -1,7 +1,7 @@ -- name: Run default pipeline with gatk4_spark +- name: Run default pipeline with gatk4spark command: nextflow run main.nf -profile test_cache,use_gatk_spark --outdir results tags: - - gatk4_spark + - gatk4spark - preprocessing files: - path: results/csv/markduplicates.csv @@ -48,10 +48,10 @@ # conda changes md5sums for test - path: results/preprocessing/mapped/ should_exist: false -- name: Run default pipeline with gatk4_spark and skipping all QC steps +- name: Run default pipeline with gatk4spark and skipping all QC steps command: nextflow run main.nf -profile test_cache,use_gatk_spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results tags: - - gatk4_spark + - gatk4spark - preprocessing - skip_qc files: @@ -84,7 +84,7 @@ - name: Run save_output_as_bam with gatk4 spark command: nextflow run main.nf -profile test_cache,use_gatk_spark --save_output_as_bam --outdir results tags: - - gatk4_spark + - gatk4spark - preprocessing - save_output_as_bam files: