2021-03-26 23:25:40 +00:00
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// Import generic module functions
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2021-09-27 08:41:24 +00:00
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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2021-03-26 23:25:40 +00:00
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params.options = [:]
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options = initOptions(params.options)
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process GATK4_MARKDUPLICATES {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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2021-04-09 16:23:56 +00:00
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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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2021-03-26 23:25:40 +00:00
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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)
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.metrics"), emit: metrics
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2021-09-27 08:41:24 +00:00
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path "versions.yml" , emit: version
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2021-03-26 23:25:40 +00:00
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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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"""
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gatk MarkDuplicates \\
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--INPUT $bam \\
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--METRICS_FILE ${prefix}.metrics \\
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--TMP_DIR . \\
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--ASSUME_SORT_ORDER coordinate \\
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--CREATE_INDEX true \\
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--OUTPUT ${prefix}.bam \\
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$options.args
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2021-09-27 08:41:24 +00:00
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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2021-09-27 21:10:37 +00:00
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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2021-09-27 08:41:24 +00:00
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END_VERSIONS
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2021-03-26 23:25:40 +00:00
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"""
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}
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