@mashehu I am a bit lost with the order of the 3 PRs. Is there any error in a PR that would be fixed by merging another PR?

sorry, i keep getting side-tracked by other things while trying to work on this. I would first merge this one https://github.com/nf-core/cageseq/pull/90 (with all the linting failing for now). I would then actually try to get the latest template update in, so we have nf-test to run testing with. and then can add your module updates. I marked my local module conversion as draft, because I haven't finished everything there yet.

thanks, #90 merged I'll leave you to work on #89 . let me know if I can help with anything there