mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
def options = initOptions(params.options)
|
||
|
|
|
||
|
|
process BISMARK_GENOME_PREPARATION {
|
||
|
|
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::bismark==0.23.0" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/bismark:0.23.0--0"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
path fasta, stageAs: "BismarkIndex/*"
|
||
|
|
|
||
|
|
output:
|
||
|
|
path "BismarkIndex" , emit: index
|
||
|
|
path "*.version.txt", emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
"""
|
||
|
|
bismark_genome_preparation \\
|
||
|
|
$options.args \\
|
||
|
|
BismarkIndex
|
||
|
|
|
||
|
|
echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|