I'm running the ChIP-Seq pipeline and wanted to change a couple of parameters, which I'm assuming are to be provided by a config file. Is this the correct way to provide additional arguments?

process {
    withName: 'BOWTIE2_ALIGN' {
        ext.args = {
            [
                meta.read_group ? "--rg-id ${meta.id} --rg SM:${meta.id - ~/_T\\d+$/} --rg PL:ILLUMINA --rg LB:${meta.id} --rg PU:1" : '',
                params.seq_center ? "--rg CN:${params.seq_center}" : '',
                '-X 1000'
            ].join(' ').trim()
        }
    }

    withName: 'BAMTOOLS_FILTER' {
        ext.args = {
            [
                meta.single_end ? '-F 0x004' : '-F 0x004 -F 0x0008 -f 0x001',
                params.keep_dups ? '' : '-F 0x0400',
                params.keep_multi_map ? '' : '-q 30'
            ].join(' ').trim()
        }
    }

yes, put it in a

custom.config

and supply it with the

-c

argument. In case you have further chipseq pipeline specific questions, don't hesitate to ask in #CFP55NZ5G