mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
dce27b8102
* Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
44 lines
1.7 KiB
Text
44 lines
1.7 KiB
Text
// 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
|
|
"""
|
|
}
|