mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
c5235a983d
* Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
48 lines
1.9 KiB
Text
48 lines
1.9 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process MOSDEPTH {
|
|
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::mosdepth=0.3.2' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0"
|
|
} else {
|
|
container "quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(bai)
|
|
path bed
|
|
val window_size
|
|
|
|
output:
|
|
tuple val(meta), path('*.global.dist.txt') , emit: global_txt
|
|
tuple val(meta), path('*.region.dist.txt') , emit: regions_txt
|
|
tuple val(meta), path('*.summary.txt') , emit: summary_txt
|
|
tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed
|
|
tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi
|
|
tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed
|
|
tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi
|
|
path '*.version.txt' , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def interval = window_size ? "--by ${window_size}" : "--by ${bed}"
|
|
"""
|
|
mosdepth \\
|
|
$interval \\
|
|
$options.args \\
|
|
$prefix \\
|
|
$bam
|
|
echo \$(mosdepth --version 2>&1) | sed 's/^.*mosdepth //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|