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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>
48 lines
2.4 KiB
Text
48 lines
2.4 KiB
Text
process DEEPBGC_PIPELINE {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1':
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'quay.io/biocontainers/deepbgc:0.1.30--pyhb7b1952_1' }"
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input:
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tuple val(meta), path(genome)
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path(db)
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output:
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tuple val(meta), path("${genome.baseName}/README.txt") , optional: true, emit: readme
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tuple val(meta), path("${genome.baseName}/LOG.txt") , emit: log
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tuple val(meta), path("${genome.baseName}/${genome.baseName}.antismash.json") , optional: true, emit: json
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tuple val(meta), path("${genome.baseName}/${genome.baseName}.bgc.gbk") , optional: true, emit: bgc_gbk
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tuple val(meta), path("${genome.baseName}/${genome.baseName}.bgc.tsv") , optional: true, emit: bgc_tsv
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tuple val(meta), path("${genome.baseName}/${genome.baseName}.full.gbk") , optional: true, emit: full_gbk
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tuple val(meta), path("${genome.baseName}/${genome.baseName}.pfam.tsv") , optional: true, emit: pfam_tsv
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tuple val(meta), path("${genome.baseName}/evaluation/${genome.baseName}.bgc.png") , optional: true, emit: bgc_png
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tuple val(meta), path("${genome.baseName}/evaluation/${genome.baseName}.pr.png") , optional: true, emit: pr_png
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tuple val(meta), path("${genome.baseName}/evaluation/${genome.baseName}.roc.png") , optional: true, emit: roc_png
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tuple val(meta), path("${genome.baseName}/evaluation/${genome.baseName}.score.png") , optional: true, emit: score_png
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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 prefix = task.ext.prefix ?: "${meta.id}"
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"""
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export DEEPBGC_DOWNLOADS_DIR=${db}
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deepbgc \\
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pipeline \\
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$args \\
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$genome
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deepbgc: \$(echo \$(deepbgc info 2>&1 /dev/null/ | grep 'version' | cut -d " " -f3) )
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prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
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END_VERSIONS
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"""
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}
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