nf-core_modules/software/macs2/callpeak/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
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process MACS2_CALLPEAK {
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) }
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conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0"
} else {
container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0"
}
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input:
tuple val(meta), path(ipbam), path(controlbam)
val macs2_gsize
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output:
tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
tuple val(meta), path("*.xls") , emit: xls
path "*.version.txt" , emit: version
tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
tuple val(meta), path("*.bed") , optional:true, emit: bed
tuple val(meta), path("*.bdg") , optional:true, emit: bdg
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def format = meta.single_end ? 'BAM' : 'BAMPE'
def control = controlbam ? "--control $controlbam" : ''
"""
macs2 \\
callpeak \\
$options.args \\
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--gsize $macs2_gsize \\
--format $format \\
--name $prefix \\
--treatment $ipbam \\
$control
macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
"""
}