Hi. Is there any plan to integrate

parabricks

for mapping to the pipeline similar to

sarek

?

I don't think that's on the roadmap for now but you could start with BAMs; we are feeding it DRAGEN alignments as a starting point, for example.

Hi @Ömer An adding to Oliver, with the different aligners out there we prefer to focus on downstream from BAM/CRAM. There is a mapping step for connivance/end-to-end pipeline purposes but it is by no means meant to be complete. If you end up making a wrapper workflow with parabricks please feel free to let us know and we can add to the documentation