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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>
29 lines
907 B
Text
29 lines
907 B
Text
process AMRFINDERPLUS_UPDATE {
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tag "update"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
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'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
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output:
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path "amrfinderdb.tar.gz", emit: db
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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mkdir amrfinderdb
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amrfinder_update -d amrfinderdb
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tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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amrfinderplus: \$(amrfinder --version)
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END_VERSIONS
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"""
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}
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