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https://github.com/MillironX/nf-core_modules.git
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f469045a95
* fix: remove left-over unnecessary code * Adds --fakeroot option for singularity usage with DeepARG as workaround for broken conda dependency * Update modules/deeparg/downloaddata/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Update modules/deeparg/predict/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Apply suggestions from code review * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Go back to original logic Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
39 lines
1.2 KiB
Text
39 lines
1.2 KiB
Text
def VERSION='1.0.2'
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process DEEPARG_DOWNLOADDATA {
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label 'process_low'
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conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
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'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
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/*
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We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
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This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
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*/
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containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
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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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"""
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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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