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https://github.com/MillironX/nf-core_modules.git
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eeda4136c0
* fix cat stub * add test * commit suggestions Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
62 lines
2 KiB
Text
62 lines
2 KiB
Text
process CAT_CAT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
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'quay.io/biocontainers/pigz:2.3.4' }"
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input:
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tuple val(meta), path(files_in)
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output:
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tuple val(meta), path("${prefix}"), emit: file_out
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def file_list = files_in.collect { it.toString() }
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// | input | output | command1 | command2 |
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// |-----------|------------|----------|----------|
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// | gzipped | gzipped | cat | |
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// | ungzipped | ungzipped | cat | |
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// | gzipped | ungzipped | zcat | |
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// | ungzipped | gzipped | cat | pigz |
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// Use input file ending as default
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prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
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out_zip = prefix.endsWith('.gz')
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in_zip = file_list[0].endsWith('.gz')
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command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
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command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
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"""
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$command1 \\
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$args \\
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${file_list.join(' ')} \\
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$command2 \\
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> ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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stub:
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def file_list = files_in.collect { it.toString() }
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prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
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"""
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touch $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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