nf-core_modules/software/bedtools/genomecov/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BEDTOOLS_GENOMECOV {
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::bedtools=2.30.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
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container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}
input:
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tuple val(meta), path(bams)
output:
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tuple val(meta), path("*.bed"), emit: coverage
path "*.version.txt", emit: version
script:
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def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools \\
genomecov \\
-ibam $bams \\
$options.args \\
> ${prefix}.bed
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}