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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>
38 lines
1.3 KiB
Text
38 lines
1.3 KiB
Text
process DEEPARG_DOWNLOADDATA {
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label 'process_single'
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conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
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'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
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/*
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We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
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Original report: https://github.com/nf-core/funcscan/issues/23
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*/
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containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
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input:
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output:
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path "db/" , emit: db
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def VERSION='1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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deeparg \\
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download_data \\
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$args \\
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-o db/
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deeparg: $VERSION
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END_VERSIONS
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"""
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}
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