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f5d5926516
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
80 lines
2.5 KiB
Text
80 lines
2.5 KiB
Text
process GATK4_MUTECT2 {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
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input:
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tuple val(meta) , path(input) , path(input_index) , path(intervals), val(which_norm)
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val run_single
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val run_pon
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val run_mito
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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 panels_command = ''
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def normals_command = ''
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def inputs_command = '-I ' + input.join( ' -I ')
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def interval = intervals ? "-L ${intervals}" : ""
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if(run_pon) {
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panels_command = ''
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normals_command = ''
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} else if(run_single) {
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panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals"
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normals_command = ''
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} else if(run_mito){
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panels_command = "-L ${intervals} --mitochondria-mode"
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normals_command = ''
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} else {
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panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals --f1r2-tar-gz ${prefix}.f1r2.tar.gz"
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normals_command = '-normal ' + which_norm.join( ' -normal ')
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}
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" Mutect2 \\
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-R ${fasta} \\
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${inputs_command} \\
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${normals_command} \\
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${panels_command} \\
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${interval} \\
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-O ${prefix}.vcf.gz \\
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$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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