FilterMutectCalls --stats parameter

Hi,
First of all, thank you so much for developing and maintaining this excellent tool!

I’m currently using Sarek 3.8.1 and tried to run mutect2, and I noticed that the .stats file does not appear to be passed to FilterMutectCalls. In the module ~/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/filtermutectcalls/main.nf, the .stats file is listed as an input, but it doesn’t seem to be included in the parameters passed to FilterMutectCalls.

...

input:
    tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)
    tuple val(meta2), path(fasta)
    tuple val(meta3), path(fai)
    tuple val(meta4), path(dict)

...

FilterMutectCalls \\
--variant $vcf \\
--output ${prefix}.vcf.gz \\
--reference $fasta \\
$orientationbias_command \\
$segmentation_command \\
$estimate_command \\
$table_command \\
--tmp-dir . \\
$args

...

As a workaround, I overrode ext.args by adding the --stats argument in my sys.config, which resolved the issue on my end.

withName: 'FILTERMUTECTCALLS.*' {
    ext.args = { "--stats ${meta.id}.mutect2.vcf.gz.stats" }
}

I’m not sure whether omission of --stats is intentional or perhaps an oversight, so I thought I’d check.
Thanks again!

Start in modules/nf-core/gatk4/filtermutectcalls/main.nf, where stats is declared as an input but is absent from the FilterMutectCalls command. Compare the existing command arguments with the reported ext.args workaround. Done means the stats file is passed through the module without requiring a config override; verify using the relevant Sarek Mutect2 workflow run.