nf-core_modules/modules/gubbins/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GUBBINS {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::gubbins=2.4.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gubbins:2.4.1--py38h197edbe_1"
} else {
container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
}
input:
path alignment
output:
path "*.fasta" , emit: fasta
path "*.gff" , emit: gff
path "*.vcf" , emit: vcf
path "*.csv" , emit: stats
path "*.phylip" , emit: phylip
path "*.recombination_predictions.embl" , emit: embl_predicted
path "*.branch_base_reconstruction.embl", emit: embl_branch
path "*.final_tree.tre" , emit: tree
path "*.node_labelled.final_tree.tre" , emit: tree_labelled
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
run_gubbins.py \\
--threads $task.cpus \\
$options.args \\
$alignment
echo \$(run_gubbins.py --version 2>&1) > ${software}.version.txt
"""
}