mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
e3cf4c822c
* Update dsh-bio modules to version 2.0.4 * update docker tag * update md5 checksums * Update software/dshbio/filtergff3/main.nf * Update software/dshbio/splitgff3/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process DSHBIO_SPLITBED {
|
|
tag "${meta.id}"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.4" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.4--hdfd78af_0"
|
|
} else {
|
|
container "quay.io/biocontainers/dsh-bio:2.0.4--hdfd78af_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bed)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bed.gz"), emit: bed
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
dsh-bio \\
|
|
split-bed \\
|
|
$options.args \\
|
|
-p $prefix \\
|
|
-s '.bed.gz' \\
|
|
-i $bed
|
|
|
|
echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt
|
|
"""
|
|
}
|