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39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
process BAMCMP {
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label 'process_low'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' :
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'quay.io/biocontainers/bamcmp:2.2--h05f6578_0' }"
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input:
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tuple val(meta), path(sample), path(contaminant)
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output:
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tuple val(meta), path("*primary.bam") , emit: bam
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tuple val(meta), path("*contamination.bam"), emit: contamination_bam
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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bamcmp \\
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-1 $sample \\
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-2 $contaminant \\
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-A ${prefix}_primary.bam \\
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-B ${prefix}_contamination.bam \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bamcmp: $VERSION
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END_VERSIONS
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"""
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}
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