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42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process UNTAR {
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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 ? "conda-forge::sed=4.7" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
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} else {
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container "biocontainers/biocontainers:v1.2.0_cv1"
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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 "$untar" , emit: untar
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path "versions.yml", emit: version
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script:
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def software = getSoftwareName(task.process)
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untar = archive.toString() - '.tar.gz'
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"""
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tar \\
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-xzvf \\
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$options.args \\
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$archive
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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}
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