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Update UNTAR module
This commit is contained in:
parent
727291999b
commit
661cfbe012
3 changed files with 18 additions and 18 deletions
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@ -173,7 +173,7 @@
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},
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},
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"multiqc": {
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"multiqc": {
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"branch": "master",
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"branch": "master",
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"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
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"git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
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"installed_by": ["modules"]
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"installed_by": ["modules"]
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},
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},
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"porechop/porechop": {
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"porechop/porechop": {
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@ -214,7 +214,7 @@
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},
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},
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"untar": {
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"untar": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
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"installed_by": ["modules"]
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"installed_by": ["modules"]
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}
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}
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}
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}
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31
modules/nf-core/untar/main.nf
generated
31
modules/nf-core/untar/main.nf
generated
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@ -2,17 +2,17 @@ process UNTAR {
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tag "$archive"
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tag "$archive"
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label 'process_single'
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label 'process_single'
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conda "conda-forge::sed=4.7"
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conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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container "${ 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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'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
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'ubuntu:20.04' }"
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'docker.io/ubuntu:20.04' }"
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input:
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input:
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tuple val(meta), path(archive)
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tuple val(meta), path(archive)
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output:
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output:
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tuple val(meta), path("$untar"), emit: untar
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tuple val(meta), path("$prefix"), emit: untar
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path "versions.yml" , emit: versions
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path "versions.yml" , emit: versions
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -20,31 +20,29 @@ process UNTAR {
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script:
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script:
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def args2 = task.ext.args2 ?: ''
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untar = archive.toString() - '.tar.gz'
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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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"""
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mkdir output
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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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## 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 just files or multiple directories, place all in prefix
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if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
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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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tar \\
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-C output --strip-components 1 \\
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-C $prefix --strip-components 1 \\
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-xzvf \\
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-xavf \\
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$args \\
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$args \\
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$archive \\
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$archive \\
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$args2
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$args2
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else
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else
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tar \\
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tar \\
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-C output \\
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-C $prefix \\
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-xzvf \\
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-xavf \\
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$args \\
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$args \\
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$archive \\
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$archive \\
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$args2
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$args2
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fi
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fi
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mv output ${untar}
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
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untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
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@ -52,9 +50,10 @@ process UNTAR {
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"""
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"""
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stub:
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stub:
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untar = archive.toString() - '.tar.gz'
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prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
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"""
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"""
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touch $untar
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mkdir $prefix
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touch ${prefix}/file.txt
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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1
modules/nf-core/untar/meta.yml
generated
1
modules/nf-core/untar/meta.yml
generated
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@ -3,6 +3,7 @@ description: Extract files.
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keywords:
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keywords:
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- untar
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- untar
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- uncompress
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- uncompress
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- extract
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tools:
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tools:
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- untar:
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- untar:
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description: |
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description: |
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