is nanopolish removable from bacass? this is seen as something that shouldn’t be used now - I’ve been chatting with Nanopore on that.

Theoretically yes: Medaka is default, nanopolish an option, see https://nf-co.re/bacass/2.4.0/parameters/#polish_method. I tend to prefer choices over removal, but if nanopolish is indeed not good practice any more (I dont now), then its fine to remove it, in my opinion.