We have both the bamfiltering_genomicbamfilterflag and the bamfiltering_retainunmappedgenomicbam flags.

If I remember right, the idea at the beginning was to make the flag generic and restrain from named flags (e.g. set to 5 to remove unpaired reads and unmapped as desired).

However, we now have the situation that the bamfiltering_genomicbamfilterflag is conditioned on the bamfiltering_retainunmappedgenomicbam.

(in modules.conf)
withName: SAMTOOLS_VIEW_BAM_FILTERING {
        tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}" }
        ext.args = [
            "-q ${params.bamfiltering_mappingquality}",
            params.bamfiltering_retainunmappedgenomicbam ? '' : "-F ${params.bamfiltering_genomicbamfilterflag}",
        ].join(' ').trim()
        ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}_filtered" }
        publishDir = [
            [
                // data
                path: { "${params.outdir}/read_filtering/filtered_bams/data/" },
                mode: params.publish_dir_mode,
                pattern: '*.bam',
                enabled: params.bamfiltering_savefilteredbams
            ]
        ]
    }

Problem

The bamfilter workflow will not behave as expected!

• If the filter flag is 1 (filter unpaired) but retain_unmapped is set, filtering will just not happen
• If the filter flag is 1 and retain_unmapped is not set, filtering will happen, but unmapped will still be retained.

Solutions

1. Drop the filter-flag option (if its only used for mapped/unmapped)
2. Update the filterflag based on the retain_unmapped flag (add 4 to if retain_unmapped is false) and only filter by flag
3. make them independent (filter -F4 if not retain_unmapped and additionally -F filterflag) to allow for filtering weird flags like vendor-failed (etc.)

I think independent filtering would work best :)