here is another "good" one (67 files): github.com/nf-core/proteinfamilies/pull/205 Since we have a breaking release coming, it was a good opportunity to find useless or mergeable input parameters and duplicate/inconsistent outputs. Going from 44 to 33 input pipeline params, and a much more beautiful and intuitive output folders/files architecture. CONTRIBUTING.md doc has also been updated so new contributors and their bots can be taught how to thematically name their params now to fit in the pipeline