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45 lines
1.4 KiB
Text
45 lines
1.4 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process GATK4_MERGEBAMALIGNMENT {
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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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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id: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(aligned)
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path unmapped
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path fasta
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path dict
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output:
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tuple val(meta), path('*.merged.bam'), emit: bam
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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}" : "${meta.id}"
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"""
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gatk MergeBamAlignment \\
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ALIGNED=$aligned \\
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UNMAPPED=$unmapped \\
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R=$fasta \\
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O=${prefix}.merged.bam \\
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$options.args
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gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
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"""
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}
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