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36 lines
1.2 KiB
Text
36 lines
1.2 KiB
Text
process BIOBAMBAM_BAMMARKDUPLICATES2 {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
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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.txt"), emit: metrics
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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 ?: "${meta.id}"
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"""
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bammarkduplicates2 \\
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$args \\
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I=$bam \\
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O=${prefix}.bam \\
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M=${prefix}.metrics.txt \\
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tmpfile=$prefix \\
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markthreads=$task.cpus
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bammarkduplicates2: \$(echo \$(bammarkduplicates2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
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END_VERSIONS
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"""
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}
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