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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
44 lines
1.7 KiB
Text
44 lines
1.7 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GUBBINS {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::gubbins=2.4.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gubbins:2.4.1--py38h197edbe_1"
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} else {
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container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
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}
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input:
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path alignment
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output:
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path "*.fasta" , emit: fasta
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path "*.gff" , emit: gff
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path "*.vcf" , emit: vcf
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path "*.csv" , emit: stats
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path "*.phylip" , emit: phylip
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path "*.recombination_predictions.embl" , emit: embl_predicted
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path "*.branch_base_reconstruction.embl", emit: embl_branch
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path "*.final_tree.tre" , emit: tree
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path "*.node_labelled.final_tree.tre" , emit: tree_labelled
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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run_gubbins.py \\
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--threads $task.cpus \\
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$options.args \\
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$alignment
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echo \$(run_gubbins.py --version 2>&1) > ${software}.version.txt
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"""
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}
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