nf-core_modules/modules/mosdepth/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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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']) }
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conda (params.enable_conda ? 'bioconda::mosdepth=0.3.2' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0"
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} else {
container "quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0"
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}
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 "versions.yml" , emit: versions
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script:
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
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
END_VERSIONS
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"""
}