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53 lines
1.7 KiB
Text
53 lines
1.7 KiB
Text
process MACS2_CALLPEAK {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' :
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'quay.io/biocontainers/macs2:2.2.7.1--py38h4a8c8d9_3' }"
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input:
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tuple val(meta), path(ipbam), path(controlbam)
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val macs2_gsize
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output:
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tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
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tuple val(meta), path("*.xls") , emit: xls
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
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tuple val(meta), path("*.bed") , optional:true, emit: bed
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tuple val(meta), path("*.bdg") , optional:true, emit: bdg
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def args_list = args.tokenize()
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def format = meta.single_end ? 'BAM' : 'BAMPE'
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def control = controlbam ? "--control $controlbam" : ''
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if(args_list.contains('--format')){
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def id = args_list.findIndexOf{it=='--format'}
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format = args_list[id+1]
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args_list.remove(id+1)
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args_list.remove(id)
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}
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"""
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macs2 \\
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callpeak \\
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${args_list.join(' ')} \\
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--gsize $macs2_gsize \\
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--format $format \\
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--name $prefix \\
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--treatment $ipbam \\
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$control
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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macs2: \$(macs2 --version | sed -e "s/macs2 //g")
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END_VERSIONS
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"""
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}
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