We are considering to disable BQSR by default and reduce its impact to small variant calling only, not with the next release but with the one after: https://nfcore.slack.com/archives/C05V9FRJYMV/p1770369620766129?thread_ts=1770308396.103099&cid=C05V9FRJYMV . Would love some feedback if you are violently objecting to this. It should speed up the pipeline by a lot and from the developer side would contain a bunch of complexity