Hi. I am running tests with sarek 3.8.1 (w Sentieon inside) and I noticed that the pipeline is performing base quality recalibration with gatk. Is there a way to force it to switch to sentieon-bqsr? This is the command:

Hey! Sention BQSR is not implemented at the moment: https://nf-co.re/sarek/3.8.1/docs/usage/#qualcal-bqsr mostly because so far there wasn't a whole lot of interest in adding it. We have the modules though in nf-core/modules so could add it in at some point