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90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
44 lines
1.1 KiB
Text
44 lines
1.1 KiB
Text
process GUNZIP {
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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("$gunzip"), emit: gunzip
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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gunzip = archive.toString() - '.gz'
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"""
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gunzip \\
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-f \\
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$args \\
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$archive
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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stub:
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gunzip = archive.toString() - '.gz'
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"""
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touch $gunzip
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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}
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