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37 lines
1 KiB
Text
37 lines
1 KiB
Text
process BAMUTIL_TRIMBAM {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' :
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'quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1' }"
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input:
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tuple val(meta), path(bam), val(trim_left), val(trim_right)
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output:
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tuple val(meta), path("*.bam"), emit: bam
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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 ?: "${meta.id}"
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"""
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bam \\
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trimBam \\
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$bam \\
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${prefix}.bam \\
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$args \\
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-L $trim_left \\
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-R $trim_right
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bamutil: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
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END_VERSIONS
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"""
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}
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