nf-core_modules/software/mosdepth/main.nf
Jose Espinosa-Carrasco 572abb00b3
Remove def from module options definition in main (#270)
* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00

48 lines
1.8 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), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::mosdepth=0.3.1' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.1--ha7ba039_0"
} else {
container "quay.io/biocontainers/mosdepth:0.3.1--ha7ba039_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
"""
}