For the freebayes implementation: Is there a reason why this specific line was added: https://github.com/nf-core/sarek/blob/9b85c0f04b5d7f279f407125a8cad6bcc2d801f5/conf/modules/freebayes.config#L69 It seems to me that

--pooled-discrete

overwrites

--pooled-continuous

we originally had this in the old modules.config file:

if (params.tools && params.tools.split(',').contains('freebayes')) {
        withName: '.*:PAIR_VARIANT_CALLING:RUN_FREEBAYES_SOMATIC:FREEBAYES' {
            ext.args       = "--pooled-continuous \
                            --pooled-discrete \
                            --genotype-qualities \
                            --report-genotype-likelihood-max \
                            --allele-balance-priors-off \
                            --min-alternate-fraction 0.03 \
                            --min-repeat-entropy 1 \
                            --min-alternate-count 2 "
        }
    }

I encounter very bad results for freebayes with my benchmarking that is why I am investigating 🙂

coming from old sarek: https://github.com/SciLifeLab/Sarek/blob/master/somaticVC.nf#L244-L256

the freebayes docs are also not that big and a little confusing