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process {
withName: 'DEEPTOOLS_COMPUTEMATRIX' {
ext.args = [
'reference-point',
'--referencePoint TSS',
'-b 1000',
'-a 500',
'--binSize 10',
'--missingDataAsZero',
'--skipZeros',
'--smartLabels'
].join(' ').trim()
}
withName: 'MACS3_CALLPEAK' {
ext.args = [
'--keep-dup 1',
'--format BAM',
'--nomodel',
'--shift -15',
'--extsize 30',
'--call-summits',
'--cutoff-analysis',
params.narrow_peak ? '' : "--broad --broad-cutoff ${params.broad_cutoff}",
params.save_macs_pileup ? '--bdg --SPMR' : '',
params.macs_fdr ? "--qvalue ${params.macs_fdr}" : '',
params.aligner == "chromap" ? "--format BAM" : ''
].join(' ').trim()
}
}
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