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

nf-core

Hi, I opened <https://github.com/nf-core/sarek/pull/2361|github.com/nf-core/sarek/pull/2361> TMB with pyTMB on Mutect2 calls annotated with snpEff, towards <https://github.com/nf-core/sarek/issues/495|github.com/nf-core/sarek/issues/495> and picking up <https://github.com/nf-core/sarek/pull/616|github.com/nf-core/sarek/pull/616>. It is my first sarek PR, so the CI runs need a maintainer's approval. Happy to change the approach if it should be done differently. Thanks!

It should work without. are you a member of the nf-core org?

if not, please go to <#CEB982K2T> to be added :slightly_smiling_face:

Thanks Rike! Joined the org now, and CI is green apart from Sentieon (no secrets on forks). No rush at all on my PR, whenever someone has time to look.

the PR looks pretty good at first glance. I will do a bit deeper review tmrw. The annotation stream has a few particularities, so just want to make sure all the right things are included/excluded in the channel wiring

Thanks a lot for tackleing this, it’s been an ancient request