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80 lines
2.6 KiB
Text
80 lines
2.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } 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=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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tuple val(meta) , path(input) , path(input_index) , 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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val interval_label
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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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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${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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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 ${interval_label} --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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"""
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gatk 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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-O ${prefix}.vcf.gz \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(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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