Why does nf-core/atacseq use MAPQ ≥1 rather than a stricter cutoff such as MAPQ ≥30 before peak calling? Does MAPQ ≥1 truly restrict the BAM to uniquely mapped reads? @Jose Espinosa-Carrasco

withName: 'BAMTOOLS_FILTER' {

ext.args  = {

[

meta.single_end ? '-F 0x004' : '-F 0x004 -F 0x0008 -f 0x001',

params.keep_dups ? '' : '-F 0x04 @00',

params.keep_multi_map ? '' : '-q 1'

].join(' ').trim()

}