mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-25 03:58:17 +00:00
460a3ed87b
* adding template for module groupreadsbyumi * update modules with code * strategy is required argument so moving it to input rather than options.args * tests successful committing yml * added meta to output Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
50 lines
1.7 KiB
Text
50 lines
1.7 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process FGBIO_GROUPREADSBYUMI {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
publishDir "${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::fgbio=1.4.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0"
|
|
} else {
|
|
container "quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(taggedbam)
|
|
val(strategy)
|
|
|
|
output:
|
|
tuple val(meta), path("*_umi-grouped.bam") , emit: bam
|
|
tuple val(meta), path("*_umi_histogram.txt"), emit: histogram
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
|
|
"""
|
|
mkdir tmp
|
|
|
|
fgbio \\
|
|
--tmp-dir=${PWD}/tmp \\
|
|
GroupReadsByUmi \\
|
|
-s $strategy \\
|
|
${options.args} \\
|
|
-i $taggedbam \\
|
|
-o ${prefix}_umi-grouped.bam \\
|
|
-f ${prefix}_umi_histogram.txt
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|