mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
a70abc236b
* added files * edited files * edited files * edited file * test(sequenzautils): Remove md5sum Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
40 lines
1.4 KiB
Text
40 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process SEQUENZAUTILS_GCWIGGLE {
|
|
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), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2"
|
|
} else {
|
|
container "quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
|
|
output:
|
|
tuple val(meta), path("*.wig.gz"), emit: wig
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
sequenza-utils \\
|
|
gc_wiggle \\
|
|
$options.args \\
|
|
--fasta $fasta \\
|
|
-o ${prefix}.wig.gz
|
|
|
|
echo \$(sequenzautils --version 2>&1) | sed 's/^.*sequenzautils //; s/Using.*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|