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https://github.com/MillironX/nf-core_modules.git
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b63b9f752d
* Fix for nested directories in tar archive * fix untar for tar with a single directory * prettier
64 lines
1.7 KiB
Text
64 lines
1.7 KiB
Text
process UNTAR {
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tag "$archive"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
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'ubuntu:20.04' }"
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input:
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tuple val(meta), path(archive)
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output:
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tuple val(meta), path("$untar"), emit: untar
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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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untar = archive.toString() - '.tar.gz'
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"""
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mkdir output
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## Ensures --strip-components only applied when top level of tar contents is a directory
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## If just files or multiple directories, place all in output
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if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
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tar \\
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-C output --strip-components 1 \\
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-xzvf \\
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$args \\
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$archive \\
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$args2
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else
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tar \\
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-C output \\
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-xzvf \\
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$args \\
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$archive \\
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$args2
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fi
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mv output ${untar}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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untar: \$(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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stub:
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untar = archive.toString() - '.tar.gz'
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"""
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touch $untar
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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untar: \$(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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