mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
dce27b8102
* Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
36 lines
1.2 KiB
Text
36 lines
1.2 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
def VERSION = '2.2.0'
|
|
|
|
process HISAT2_EXTRACTSPLICESITES {
|
|
tag "$gtf"
|
|
label 'process_medium'
|
|
publishDir "${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::hisat2=2.2.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
|
|
} else {
|
|
container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
|
|
}
|
|
|
|
input:
|
|
path gtf
|
|
|
|
output:
|
|
path "*.splice_sites.txt", emit: txt
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
|
|
echo $VERSION > ${software}.version.txt
|
|
"""
|
|
}
|