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64 lines
1.8 KiB
Plaintext
64 lines
1.8 KiB
Plaintext
process UNTAR {
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tag "$archive"
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label 'process_single'
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conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34"
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container "${ 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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'docker.io/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("$prefix"), emit: untar
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
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"""
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mkdir $prefix
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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 prefix
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if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
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tar \\
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-C $prefix --strip-components 1 \\
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-xavf \\
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$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 $prefix \\
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-xavf \\
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$args \\
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$archive \\
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$args2
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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stub:
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prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
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"""
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mkdir $prefix
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touch ${prefix}/file.txt
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cat <<-END_VERSIONS > versions.yml
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"${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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