From 2e976204ee8c5fde72d2230d8ae69c90ea81268d Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 7 Jul 2023 15:11:41 +0200
Subject: [PATCH 1/2] update schema
---
docs/output.md | 12 +-
main.nf | 2 -
nextflow_schema.json | 318 +++++++++++++++++----------------------
workflows/raredisease.nf | 8 +-
4 files changed, 144 insertions(+), 196 deletions(-)
diff --git a/docs/output.md b/docs/output.md
index 856b0a79..bbbfa2cb 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -75,27 +75,27 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
##### Picard's MarkDuplicates
-[Picard MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) is used for marking PCR duplicates that can occur during library amplification. This is essential as the presence of such duplicates results in false inflated coverages, which in turn can lead to overly-confident genotyping calls during variant calling. Only reads aligned by Bwa-mem2 are processed by this tool.
+[Picard MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) is used for marking PCR duplicates that can occur during library amplification. This is essential as the presence of such duplicates results in false inflated coverages, which in turn can lead to overly-confident genotyping calls during variant calling. Only reads aligned by Bwa-mem2 are processed by this tool. By default, alignment files are published in bam format. If you would like to store cram files instead, set `--save_mapped_as_cram` to true.
Output files from Alignment
- `{outputdir}/alignment/`
- - `*.bam`: Bam file containing report containing quality metrics.
- - `*.bai`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+ - `*.bam|*.cram`: Alignment file in bam/cram format.
+ - `*.bai|*.crai`: Index of the corresponding bam/cram file.
- `*.txt`: Text file containing the dedup metrics.
##### Sentieon Dedup
-[Sentieon Dedup](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/#remove-or-mark-duplicates) is the algorithm used by Sentieon's driver to remove duplicate reads. Only reads aligned by Sentieon's implementation of bwa are processed by this algorithm.
+[Sentieon Dedup](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/#remove-or-mark-duplicates) is the algorithm used by Sentieon's driver to remove duplicate reads. Only reads aligned by Sentieon's implementation of bwa are processed by this algorithm. By default, alignment files are published in bam format. If you would like to store cram files instead, set `--save_mapped_as_cram` to true.
Output files from Alignment
- `{outputdir}/alignment/`
- - `*.bam`: Bam file containing report containing quality metrics.
- - `*.bai`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+ - `*.bam|*.cram`: Alignment file in bam/cram format.
+ - `*.bai|*.crai`: Index of the corresponding bam/cram file.
- `*.txt`: Text file containing the dedup metrics.
diff --git a/main.nf b/main.nf
index 47f00e53..0f31ba94 100644
--- a/main.nf
+++ b/main.nf
@@ -29,8 +29,6 @@ params.intervals_wgs = WorkflowMain.getGenomeAttribute(params,
params.intervals_y = WorkflowMain.getGenomeAttribute(params, 'intervals_y')
params.known_dbsnp = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp')
params.known_dbsnp_tbi = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp_tbi')
-params.known_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels')
-params.known_mills = WorkflowMain.getGenomeAttribute(params, 'known_mills')
params.ml_model = WorkflowMain.getGenomeAttribute(params, 'ml_model')
params.mt_fasta = WorkflowMain.getGenomeAttribute(params, 'mt_fasta')
params.reduced_penetrance = WorkflowMain.getGenomeAttribute(params, 'reduced_penetrance')
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 51b4586a..1fbdbf68 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -33,17 +33,19 @@
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
- "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+ "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
+ "hidden": true
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
- "fa_icon": "fas fa-file-signature"
+ "fa_icon": "fas fa-file-signature",
+ "hidden": true
}
}
},
- "reference_genome_options": {
- "title": "Reference genome options",
+ "reference_file_options": {
+ "title": "Reference file options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome related files and options required for the workflow.",
@@ -51,26 +53,30 @@
"bait_padding": {
"type": "number",
"default": 100,
- "fa_icon": "fas fa-greater-than",
+ "fa_icon": "fas fa-align-center",
"pattern": "^\\S+\\.bed(\\.gz)?$",
- "description": "The amount to pad each end of the target intervals to create bait intervals.",
- "hidden": true
+ "description": "The amount to pad each end of the target intervals to create bait intervals."
},
- "genome": {
+ "bwa": {
"type": "string",
- "description": "Name of iGenomes reference.",
- "fa_icon": "fas fa-book",
- "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
+ "format": "directory-path",
+ "description": "Directory for pre-built bwa index.",
+ "help_text": "If none provided, will be generated automatically from the FASTA reference.",
+ "fa_icon": "fas fa-folder-open"
},
- "fasta": {
+ "bwamem2": {
"type": "string",
- "format": "file-path",
- "exists": true,
- "mimetype": "text/plain",
- "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
- "description": "Path to FASTA genome file.",
- "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
- "fa_icon": "far fa-file-code"
+ "format": "directory-path",
+ "description": "Directory for pre-built bwamem2 index.",
+ "help_text": "If none provided, will be generated automatically from the FASTA reference.",
+ "fa_icon": "fas fa-folder-open"
+ },
+ "cadd_resources": {
+ "type": "string",
+ "format": "directory-path",
+ "fa_icon": "fas fa-file",
+ "description": "Path to the directory containing cadd annotations.",
+ "help_text": "This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
},
"fai": {
"type": "string",
@@ -78,46 +84,48 @@
"help_text": "If none provided, will be generated automatically from the FASTA reference",
"description": "Path to FASTA genome index file.",
"pattern": "^\\S+\\.fn?a(sta)?\\.fai$",
- "fa_icon": "far fa-file-code",
- "hidden": true
+ "fa_icon": "fas fa-file"
},
- "igenomes_base": {
+ "fasta": {
"type": "string",
- "format": "directory-path",
- "description": "Directory / URL base for iGenomes references.",
- "default": "s3://ngi-igenomes/igenomes",
- "fa_icon": "fas fa-cloud-download-alt",
- "hidden": true
+ "format": "file-path",
+ "exists": true,
+ "mimetype": "text/plain",
+ "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
+ "description": "Path to FASTA genome file.",
+ "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
+ "fa_icon": "fas fa-file"
},
- "igenomes_ignore": {
- "type": "boolean",
- "description": "Do not load the iGenomes reference config.",
- "fa_icon": "fas fa-ban",
- "hidden": true,
- "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+ "genome": {
+ "type": "string",
+ "description": "Name of iGenomes reference.",
+ "fa_icon": "fas fa-align-center",
+ "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.",
+ "default": "GRCh38"
},
- "bwa": {
+ "gens_gnomad_pos": {
"type": "string",
- "format": "directory-path",
- "description": "Directory for pre-built bwa index.",
- "help_text": "If none provided, will be generated automatically from the FASTA reference.",
- "fa_icon": "fas fa-folder-open",
+ "format": "file-path",
+ "fa_icon": "fas fa-file",
+ "description": "Path to a list of common SNP locations for Gens.",
+ "help_text": "Locations of gnomad SNPs with a high enough BAF.",
"hidden": true
},
- "bwamem2": {
+ "gens_interval_list": {
"type": "string",
- "format": "directory-path",
- "description": "Directory for pre-built bwamem2 index.",
- "help_text": "If none provided, will be generated automatically from the FASTA reference.",
- "fa_icon": "fas fa-folder-open",
+ "format": "file-path",
+ "fa_icon": "fas fa-file",
+ "description": "Path to interval list for Gens.",
+ "help_text": "This file contains the binning intervals used for CollectReadCounts.",
"hidden": true
},
- "cadd_resources": {
+ "gens_pon": {
"type": "string",
- "format": "directory-path",
+ "format": "file-path",
"fa_icon": "fas fa-file",
- "description": "Path to the directory containing cadd annotations.",
- "help_text": "This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
+ "description": "Path to panel of normals for Gens.",
+ "help_text": "The panel used to run DenoiseReadCounts.",
+ "hidden": true
},
"gnomad_af": {
"type": "string",
@@ -135,6 +143,19 @@
"description": "Path to the index file for the gnomad tab file with allele frequencies.",
"help_text": "Path to the index of gnomad tab file with CHR/START/REF,ALT/AF"
},
+ "igenomes_base": {
+ "type": "string",
+ "format": "directory-path",
+ "description": "Directory / URL base for iGenomes references.",
+ "default": "s3://ngi-igenomes/igenomes",
+ "fa_icon": "fas fa-cloud-download-alt"
+ },
+ "igenomes_ignore": {
+ "type": "boolean",
+ "description": "Do not load the iGenomes reference config.",
+ "fa_icon": "fas fa-ban",
+ "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+ },
"intervals_wgs": {
"type": "string",
"format": "path",
@@ -151,50 +172,39 @@
"description": "Path to the interval list of the Y chromosome.",
"help_text": "Path to the interval list of the Y chromosome. This is used to calculate coverage statistics for the Y chromosome."
},
- "mito_name": {
- "type": "string",
- "format": "path",
- "description": "Name of the mitochondrial contig in the reference fasta file",
- "help_text": "Used to extract relevant information from the references to analyse mitochondria"
- },
"known_dbsnp": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
+ "fa_icon": "fas fa-file",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
- "description": "Path to known dbSNP file.",
- "hidden": true
+ "description": "Path to known dbSNP file."
},
"known_dbsnp_tbi": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
+ "fa_icon": "fas fa-file",
"pattern": "^\\S+\\.vcf(\\.gz)?\\.tbi$",
- "description": "Path to known dbSNP file index.",
- "hidden": true
+ "description": "Path to known dbSNP file index."
},
- "known_indels": {
+ "local_genomes": {
"type": "string",
- "format": "path",
- "fa_icon": "fas fa-chart-bar",
- "pattern": "^\\S+\\.vcf(\\.gz)?$",
- "description": "Path to known indels file.",
- "hidden": true
+ "format": "directory-path",
+ "fa_icon": "fas fa-map-marker-alt",
+ "description": "Local directory base for genome references that map to the config.",
+ "help_text": "This folder is a flat structure with file names that map to the config."
},
- "known_mills": {
+ "mito_name": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
- "pattern": "^\\S+\\.vcf(\\.gz)?$",
- "description": "Path to known Mills file.",
- "hidden": true
+ "description": "Name of the mitochondrial contig in the reference fasta file",
+ "help_text": "Used to extract relevant information from the references to analyse mitochondria",
+ "fa_icon": "fas fa-align-center"
},
"ml_model": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
- "description": "Path to sentieon machine learning model file.",
- "hidden": true
+ "fa_icon": "fas fa-file",
+ "description": "Path to sentieon machine learning model file."
},
"mt_fasta": {
"type": "string",
@@ -202,90 +212,80 @@
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to mitochondrial FASTA genome file.",
- "fa_icon": "far fa-file-code"
+ "fa_icon": "fas fa-file"
},
"reduced_penetrance": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
- "description": "File with gene ids that have reduced penetrance. For use with genmod",
- "hidden": true
+ "fa_icon": "fas fa-file-csv",
+ "description": "File with gene ids that have reduced penetrance. For use with genmod"
+ },
+ "save_reference": {
+ "type": "boolean",
+ "description": "If generated by the pipeline save the required indices/references in the results directory.",
+ "help_text": "The saved references can be used for future pipeline runs, reducing processing times.",
+ "fa_icon": "fas fa-save"
},
"score_config_snv": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
- "description": "SNV rank model config file for genmod.",
- "hidden": true
+ "fa_icon": "fas fa-file",
+ "description": "SNV rank model config file for genmod."
},
"score_config_sv": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
- "description": "SV rank model config file for genmod.",
- "hidden": true
+ "fa_icon": "fas fa-file",
+ "description": "SV rank model config file for genmod."
},
"sequence_dictionary": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
+ "fa_icon": "fas fa-file",
"pattern": "^\\S+\\.dict$",
- "description": "Genome dictionary file",
- "hidden": true
+ "description": "Path to the genome dictionary file"
},
- "vep_filters": {
+ "svdb_query_dbs": {
"type": "string",
- "format": "path",
- "fa_icon": "fas fa-chart-bar",
- "description": "File containing HGNC_IDs of interest on separate lines.",
- "hidden": true
+ "format": "file-path",
+ "description": "Databases used for structural variant annotation.",
+ "fa_icon": "fas fa-file-csv",
+ "help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation."
},
"target_bed": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-bezier-curve",
+ "fa_icon": "fas fa-file",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"description": "Path to directory for target bed file.",
- "help_text": "If you would like to limit your analysis to specific regions of the genome, you can pass those regions in a bed file using this option",
- "hidden": true
- },
- "svdb_query_dbs": {
- "type": "string",
- "format": "file-path",
- "description": "Databases used for structural variant annotation.",
- "fa_icon": "far fa-file-code",
- "help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation."
+ "help_text": "If you would like to limit your analysis to specific regions of the genome, you can pass those regions in a bed file using this option"
},
"variant_catalog": {
"type": "string",
"format": "file-path",
"description": "Path to variant catalog file",
"help_text": "Used with ExpansionHunter and if no catalogue is passed, then a default will be used.",
- "fa_icon": "far fa-file-code",
- "hidden": true
+ "fa_icon": "fas fa-file"
},
"vcfanno_resources": {
"type": "string",
- "description": "Text file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.",
+ "description": "Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.",
"help_text": "If no file is passed, default configurations will be used according to genome build within the context of the pipeline.",
- "fa_icon": "fas fa-folder-open",
- "hidden": true
+ "fa_icon": "fas fa-file"
},
"vcfanno_toml": {
"type": "string",
"description": "Path to the vcfanno toml file.",
"pattern": "^\\S+\\.toml$",
"help_text": "If no toml is passed, default configurations will be used according to genome build within the context of the pipeline.",
- "fa_icon": "fas fa-file-csv",
- "hidden": true
+ "fa_icon": "fas fa-file"
},
"vcfanno_lua": {
"type": "string",
"description": "Path to the vcfanno lua file.",
"pattern": "^\\S+\\.lua$",
"help_text": "Custom operations file (lua). For use when the built-in ops don't supply the needed reduction.",
- "fa_icon": "fas fa-file-code",
- "hidden": true
+ "fa_icon": "fas fa-file"
},
"vep_cache": {
"type": "string",
@@ -293,47 +293,14 @@
"help_text": "If no directory path is passed, vcf files will not be annotated by vep.",
"fa_icon": "fas fa-folder-open"
},
- "save_reference": {
- "type": "boolean",
- "description": "If generated by the pipeline save the required indices/references in the results directory.",
- "help_text": "The saved references can be used for future pipeline runs, reducing processing times.",
- "fa_icon": "fas fa-save"
- },
- "local_genomes": {
- "type": "string",
- "format": "directory-path",
- "fa_icon": "fas fa-map-marker-alt",
- "description": "Local directory base for genome references that map to the config.",
- "help_text": "This folder is a flat structure with file names that map to the config."
- },
- "gens_interval_list": {
- "type": "string",
- "format": "file-path",
- "default": null,
- "fa_icon": "fas fa-bezier-curve",
- "description": "Path to interval list for Gens.",
- "help_text": "This file contains the binning intervals used for CollectReadCounts.",
- "hidden": true
- },
- "gens_pon": {
- "type": "string",
- "format": "file-path",
- "default": null,
- "fa_icon": "far fa-file-code",
- "description": "Path to panel of normals for Gens.",
- "help_text": "The panel used to run DenoiseReadCounts.",
- "hidden": true
- },
- "gens_gnomad_pos": {
+ "vep_filters": {
"type": "string",
- "format": "file-path",
- "default": null,
- "fa_icon": "far fa-bezier-curve",
- "description": "Path to a list of common SNP locations for Gens.",
- "help_text": "Locations of gnomad SNPs with a high enough BAF.",
- "hidden": true
+ "format": "path",
+ "fa_icon": "fas fa-file-csv",
+ "description": "Path to the file containing HGNC_IDs of interest on separate lines."
}
- }
+ },
+ "required": ["fasta", "intervals_wgs", "intervals_y"]
},
"analysis_options": {
"title": "Analysis options",
@@ -345,44 +312,39 @@
"type": "string",
"default": "wgs",
"description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
- "fa_icon": "fas fa-book",
+ "fa_icon": "fas fa-align-center",
"enum": ["wgs", "wes", "mito"]
},
"save_mapped_as_cram": {
"type": "boolean",
- "default": false,
"description": "Specifies whether to generate and publish alignment files as cram instead of bam",
- "fa_icon": "fas fa-book"
+ "fa_icon": "fas fa-toggle-on"
},
"skip_snv_annotation": {
"type": "boolean",
- "default": false,
"description": "Specifies whether or not to skip annotate SNV subworkflow.",
- "fa_icon": "fas fa-book"
+ "fa_icon": "fas fa-toggle-on"
},
"skip_sv_annotation": {
"type": "boolean",
- "default": false,
"description": "Specifies whether or not to skip annotate structural variant subworkflow.",
- "fa_icon": "fas fa-book"
+ "fa_icon": "fas fa-toggle-on"
},
"skip_mt_analysis": {
"type": "boolean",
- "default": false,
"description": "Specifies whether or not to skip the subworkflow that analyses mitochondrial genome separate from the nuclear genome.",
- "fa_icon": "fas fa-book"
+ "fa_icon": "fas fa-toggle-on"
},
"gens_switch": {
"type": "boolean",
- "default": false,
"description": "Specifies whether or not to run gens preprocessing subworkflow.",
- "fa_icon": "fas fa-book"
+ "fa_icon": "fas fa-toggle-on"
},
"platform": {
"type": "string",
"default": "illumina",
"description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
- "fa_icon": "fas fa-book",
+ "fa_icon": "fas fa-align-center",
"enum": ["illumina"]
}
}
@@ -397,15 +359,13 @@
"type": "string",
"default": "bwamem2",
"description": "Specifies the alignment algorithm to use - available options are 'bwamem2' and 'sentieon'.",
- "fa_icon": "fas fa-map-signs",
+ "fa_icon": "fas fa-align-center",
"enum": ["bwamem2", "sentieon"]
},
"rmdup": {
"type": "boolean",
- "default": false,
"description": "Specifies whether duplicates reads should be removed prior to variant calling.",
- "fa_icon": "fas fa-map-signs",
- "hidden": true
+ "fa_icon": "fas fa-toggle-on"
}
}
},
@@ -418,28 +378,26 @@
"call_interval": {
"type": "string",
"format": "path",
- "fa_icon": "fas fa-chart-bar",
- "description": "Interval in the reference that will be used in the software",
- "hidden": true
+ "fa_icon": "fas fa-align-center",
+ "description": "Interval in the reference that will be used in the software"
},
"pcr_amplification": {
"type": "boolean",
- "default": false,
"description": "Indicates whether the sample library is amplified using PCR or not. Set to false for PCR Free samples.",
- "fa_icon": "fas fa-map-signs"
+ "fa_icon": "fas fa-toggle-on"
},
"variant_type": {
"type": "string",
"default": "snp",
"description": "Specifies the variant types for sentieon variant caller.",
- "fa_icon": "fas fa-map-signs",
+ "fa_icon": "fas fa-align-center",
"enum": ["snp", "indel", "snp,indel"]
},
"variant_caller": {
"type": "string",
"default": "deepvariant",
"description": "Specifies the variant caller to use - available options are 'deepvariant' and 'sentieon'.",
- "fa_icon": "fas fa-map-signs",
+ "fa_icon": "fas fa-random",
"enum": ["deepvariant", "sentieon"]
}
}
@@ -452,9 +410,9 @@
"properties": {
"vep_cache_version": {
"type": "integer",
- "default": "107",
+ "default": 107,
"description": "Specify the version of the VEP cache provided to the `--vep_cache` option.",
- "fa_icon": "fas fa-book",
+ "fa_icon": "fas fa-align-center",
"enum": [107]
}
}
@@ -553,14 +511,12 @@
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
- "default": false,
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
- "default": false,
"hidden": true
},
"publish_dir_mode": {
@@ -584,7 +540,6 @@
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
- "default": false,
"hidden": true
},
"max_multiqc_email_size": {
@@ -599,7 +554,6 @@
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
- "default": false,
"hidden": true
},
"hook_url": {
@@ -625,7 +579,8 @@
"multiqc_methods_description": {
"type": "string",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
- "fa_icon": "fas fa-cog"
+ "fa_icon": "fas fa-cog",
+ "hidden": true
},
"validate_params": {
"type": "boolean",
@@ -638,7 +593,6 @@
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
- "default": false,
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
@@ -646,7 +600,6 @@
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
- "default": false,
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
@@ -654,7 +607,6 @@
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
- "default": false,
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
}
@@ -666,7 +618,7 @@
"$ref": "#/definitions/input_output_options"
},
{
- "$ref": "#/definitions/reference_genome_options"
+ "$ref": "#/definitions/reference_file_options"
},
{
"$ref": "#/definitions/analysis_options"
diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
index 7256c568..edf5a6ac 100644
--- a/workflows/raredisease.nf
+++ b/workflows/raredisease.nf
@@ -28,8 +28,6 @@ def checkPathParamList = [
params.intervals_y,
params.known_dbsnp,
params.known_dbsnp_tbi,
- params.known_indels,
- params.known_mills,
params.ml_model,
params.mt_fasta,
params.multiqc_config,
@@ -37,14 +35,14 @@ def checkPathParamList = [
params.score_config_snv,
params.score_config_sv,
params.sequence_dictionary,
- params.target_bed,
params.svdb_query_dbs,
+ params.target_bed,
params.variant_catalog,
- params.vep_filters,
params.vcfanno_lua,
params.vcfanno_resources,
params.vcfanno_toml,
- params.vep_cache
+ params.vep_cache,
+ params.vep_filters
]
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
From f14a62a21195a771f80338304bfb8b54a2d73a65 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 7 Jul 2023 15:22:30 +0200
Subject: [PATCH 2/2] order
---
nextflow_schema.json | 48 ++++++++++++++++++++++----------------------
1 file changed, 24 insertions(+), 24 deletions(-)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3e11602d..dce94330 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -336,6 +336,18 @@
"fa_icon": "fas fa-align-center",
"enum": ["wgs", "wes", "mito"]
},
+ "gens_switch": {
+ "type": "boolean",
+ "description": "Specifies whether or not to run gens preprocessing subworkflow.",
+ "fa_icon": "fas fa-toggle-on"
+ },
+ "platform": {
+ "type": "string",
+ "default": "illumina",
+ "description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
+ "fa_icon": "fas fa-align-center",
+ "enum": ["illumina"]
+ },
"save_mapped_as_cram": {
"type": "boolean",
"description": "Specifies whether to generate and publish alignment files as cram instead of bam",
@@ -346,6 +358,11 @@
"description": "Specifies whether or not to skip CNV calling.",
"fa_icon": "fas fa-book"
},
+ "skip_mt_analysis": {
+ "type": "boolean",
+ "description": "Specifies whether or not to skip the subworkflow that analyses mitochondrial genome separate from the nuclear genome.",
+ "fa_icon": "fas fa-toggle-on"
+ },
"skip_snv_annotation": {
"type": "boolean",
"description": "Specifies whether or not to skip annotate SNV subworkflow.",
@@ -355,23 +372,6 @@
"type": "boolean",
"description": "Specifies whether or not to skip annotate structural variant subworkflow.",
"fa_icon": "fas fa-toggle-on"
- },
- "skip_mt_analysis": {
- "type": "boolean",
- "description": "Specifies whether or not to skip the subworkflow that analyses mitochondrial genome separate from the nuclear genome.",
- "fa_icon": "fas fa-toggle-on"
- },
- "gens_switch": {
- "type": "boolean",
- "description": "Specifies whether or not to run gens preprocessing subworkflow.",
- "fa_icon": "fas fa-toggle-on"
- },
- "platform": {
- "type": "string",
- "default": "illumina",
- "description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
- "fa_icon": "fas fa-align-center",
- "enum": ["illumina"]
}
}
},
@@ -412,19 +412,19 @@
"description": "Indicates whether the sample library is amplified using PCR or not. Set to false for PCR Free samples.",
"fa_icon": "fas fa-toggle-on"
},
- "variant_type": {
- "type": "string",
- "default": "snp",
- "description": "Specifies the variant types for sentieon variant caller.",
- "fa_icon": "fas fa-align-center",
- "enum": ["snp", "indel", "snp,indel"]
- },
"variant_caller": {
"type": "string",
"default": "deepvariant",
"description": "Specifies the variant caller to use - available options are 'deepvariant' and 'sentieon'.",
"fa_icon": "fas fa-random",
"enum": ["deepvariant", "sentieon"]
+ },
+ "variant_type": {
+ "type": "string",
+ "default": "snp",
+ "description": "Specifies the variant types for sentieon variant caller.",
+ "fa_icon": "fas fa-align-center",
+ "enum": ["snp", "indel", "snp,indel"]
}
}
},