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ee5f59705f
* Adding new module gfaffix. * add missing entry to pytest_modules.yml * update to 0.1.4--hec16e2b_0 * fixup after prettier * add when section * update md5sum * Change to process_single as discussed Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Simon Heumos <simon.heumos@qbic.uni-tuebingen.de>
36 lines
1 KiB
Text
36 lines
1 KiB
Text
process GFAFFIX {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gfaffix:0.1.4--hec16e2b_0' :
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'quay.io/biocontainers/gfaffix:0.1.4--hec16e2b_0' }"
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input:
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tuple val(meta), path(gfa)
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output:
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tuple val(meta), path("*.gfa"), emit: gfa
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tuple val(meta), path("*.txt"), emit: affixes
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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 ?: "${meta.id}"
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"""
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gfaffix \\
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$args \\
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$gfa \\
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-o ${prefix}.gfaffix.gfa > ${prefix}.affixes.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gfaffix: \$(gfaffix --version 2>&1 | grep -o 'gfaffix .*' | cut -f2 -d ' ')
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END_VERSIONS
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"""
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}
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