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41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
process BIOBAMBAM_BAMMERGE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1':
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'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("${prefix}.bam") ,emit: bam
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tuple val(meta), path("${indexfilename}") ,optional:true, emit: bam_index
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tuple val(meta), path("${md5filename}") ,optional:true, emit: checksum
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path "versions.yml" ,emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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indexfilename = args.contains("indexfilename=") ? args =~ /indexfilename=([^\s]+)/ : ""
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md5filename = args.contains("md5filename=") ? args =~ /md5filename=([^\s]+)/ : ""
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def input_string = bam.join(" I=")
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"""
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bammerge \\
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I=${input_string} \\
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$args \\
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> ${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bammerge: \$( bammerge --version |& sed '1!d; s/.*version //; s/.\$//' )
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END_VERSIONS
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"""
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}
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