A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Cleaning up some mutectcaller bits <https://github.com/nf-core/sarek/pull/2348|github.com/nf-core/sarek/pull/2348> i think then we can merge  <https://github.com/nf-core/sarek/pull/2180|github.com/nf-core/sarek/pull/2180> nd I can fast follow a PR that fully integrates the filtering

ok I think I had some weird local settings from playing around sth else around verbosity and surpressing logs

agents might be running nextflow and nf-test in agents mode, and don't get all output the right way

yeah I am trying to figure ot if I can force it not to use those flags, it's very annoying

do you want to review this one: <https://github.com/nf-core/sarek/pull/2180/changes|github.com/nf-core/sarek/pull/2180/changes> I reviewed a few times, but now I also contributed quite a bit to it

moving discussion here: I don't think we should merge the subworkflows because parabricks has no scatter/gathering logic and doesn't support a number of thins mutect does like joint calling

I was more thinking merge the 2 pb_mutect 2 subworkflows in one

I do not want to cram pb_mutect2 and mutect2 in one subworkflow, apart from the one we have to do all variant calling

My aim here is just avoiding code duplication

ok this is easy, so will add it to the PR. I am in parallel exploring the filtering where it may get more complicated again, but I will handle that on the filtering PR