nf-core_modules/modules/macs2/callpeak/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

53 lines
1.9 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1"
} else {
container "quay.io/biocontainers/macs2:2.2.7.1--py38h0213d0e_1"
}
input:
tuple val(meta), path(ipbam), path(controlbam)
val macs2_gsize
output:
tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
tuple val(meta), path("*.xls") , emit: xls
path "versions.yml" , emit: versions
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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def format = meta.single_end ? 'BAM' : 'BAMPE'
def control = controlbam ? "--control $controlbam" : ''
"""
macs2 \\
callpeak \\
$options.args \\
--gsize $macs2_gsize \\
--format $format \\
--name $prefix \\
--treatment $ipbam \\
$control
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(macs2 --version | sed -e "s/macs2 //g")
END_VERSIONS
"""
}