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3c4eaec52b
* added output channel for stats file, updated meta yml with description and test yml with check for stats file * Update modules/gatk4/mutect2/main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
77 lines
2.5 KiB
Text
77 lines
2.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GATK4_MUTECT2 {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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}
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input:
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tuple val(meta) , path(bam) , path(bai) , val(which_norm)
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val run_single
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val run_pon
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path fasta
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path fastaidx
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path dict
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path germline_resource
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path germline_resource_idx
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path panel_of_normals
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path panel_of_normals_idx
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output:
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tuple val(meta), path("*.vcf.gz") , emit: vcf
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tuple val(meta), path("*.tbi") , emit: tbi
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tuple val(meta), path("*.stats") , emit: stats
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tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def inputsList = []
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def normalsList = []
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def inputsCommand = ''
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def panelsCommand = ''
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def normalsCommand = ''
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bam.each() {a -> inputsList.add(" -I " + a ) }
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inputsCommand = inputsList.join( ' ')
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if(run_pon) {
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panelsCommand = ''
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normalsCommand = ''
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} else if(run_single) {
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panelsCommand = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals"
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normalsCommand = ''
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} else {
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panelsCommand = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals --f1r2-tar-gz ${prefix}.f1r2.tar.gz"
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which_norm.each() {a -> normalsList.add(" -normal " + a ) }
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normalsCommand = normalsList.join( ' ')
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}
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"""
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gatk Mutect2 \\
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-R ${fasta} \\
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${inputsCommand} \\
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${normalsCommand} \\
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${panelsCommand} \\
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-O ${prefix}.vcf.gz \\
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$options.args
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echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt
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"""
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}
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