mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
ee90e7af77
* Add default output dir for modules that create indices * Change path for index module test output * Fix bowtie2/align tests * Fixing bowtie/align tests * Fix genomegenerate test * Fixing README linting
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BOWTIE2_BUILD {
|
|
tag "$fasta"
|
|
label 'process_high'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
|
|
|
|
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
|
|
} else {
|
|
container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
|
|
}
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path 'bowtie2' , emit: index
|
|
path '*.version.txt', emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
mkdir bowtie2
|
|
bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
|
|
echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|