@Mahesh Binzer-Panchal here is a docs update: https://github.com/nf-core/modules/pull/11587 Ran out of time to look into fixing the 'clean intermediates' bit, but I guess just the find command could be refined to not delete those. As a side note, I think maybe the other reason why it's a bit ugly is because I think Krakenuniq will autodownload taxdmp files for you if you don't supply them... so maybe taht's why the description was a bit odd (at first I just assumed someone could supply the ame thing downloaded outside, but I can't remember now)