mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process COOLER_DIGEST {
|
|
tag '$fasta'
|
|
label 'process_medium'
|
|
publishDir "${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::cooler=0.8.11" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
|
|
} else {
|
|
container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
|
|
}
|
|
|
|
input:
|
|
path fasta
|
|
path chromsizes
|
|
val enzyme
|
|
|
|
output:
|
|
path "*.bed" , emit: bed
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
cooler digest \\
|
|
$options.args \\
|
|
-o "${fasta.baseName}_${enzyme.replaceAll(/[^0-9a-zA-Z]+/, "_")}.bed" \\
|
|
$chromsizes \\
|
|
$fasta \\
|
|
$enzyme
|
|
|
|
echo \$(cooler --version 2>&1) | sed 's/cooler, version //' > ${software}.version.txt
|
|
"""
|
|
}
|