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e01a98a704
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add unzip module * Remove missing TODOs update mtea * Apply changes after code-review from @grst * Account for user trying to supply two input archives * Remove debugging test * Update modules/unzip/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Correct output path Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
43 lines
1.4 KiB
Text
43 lines
1.4 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process UNZIP {
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tag "$archive"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::p7zip=15.09" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4"
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} else {
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container "quay.io/biocontainers/p7zip:15.09--h2d50403_4"
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}
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input:
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path archive
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output:
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path "${archive.baseName}/" , emit: unzipped_archive
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
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"""
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7za \\
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e \\
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-o"${archive.baseName}"/ \\
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$options.args \\
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$archive
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echo \$(7za --help) | grep Version | sed 's/.*p7zip Version//; s/(.*//' 1> ${software}.version.txt
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"""
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}
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