mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
dce27b8102
* Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
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 BOWTIE_BUILD {
|
|
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), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1'
|
|
} else {
|
|
container 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1'
|
|
}
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path 'bowtie' , emit: index
|
|
path '*.version.txt', emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
mkdir bowtie
|
|
bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
|
|
echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|