mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
34 lines
1.1 KiB
Text
34 lines
1.1 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process BWA_INDEX {
|
|
tag "$fasta"
|
|
label 'process_high'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
|
|
|
conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
|
|
} else {
|
|
container "biocontainers/bwa:v0.7.17_cv1"
|
|
}
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "${fasta}.*" , emit: index
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
bwa index $options.args $fasta
|
|
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|