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409af2f27c
* feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
60 lines
2 KiB
Text
60 lines
2 KiB
Text
process GATK4_MUTECT2 {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(intervals)
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path fasta
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path fai
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path dict
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path germline_resource
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path germline_resource_tbi
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path panel_of_normals
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path panel_of_normals_tbi
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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 "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def inputs = input.collect{ "--input $it"}.join(" ")
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def interval_command = intervals ? "--intervals $intervals" : ""
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def pon_command = panel_of_normals ? "--panel-of-normals $panel_of_normals" : ""
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def gr_command = germline_resource ? "--germline-resource $germline_resource" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" Mutect2 \\
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$inputs \\
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--output ${prefix}.vcf.gz \\
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--reference $fasta \\
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$pon_command \\
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$gr_command \\
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$interval_command \\
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--tmp-dir . \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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