Hi, trying again: if someone can take a look on https://github.com/nf-core/rnaseq/pull/1746 and review: small enhancement to check contamination rnaseq also in raw (unaligned) files.

Hey! Jon is out of office this week, @Jonathan Manningfor when you are back . Maybe cross post to #C06303N1ZBP 🙂

Hi Elad, could you had something to the PR description as to why you want to do this please?

Yes, I wrote : "If you want to check contamination in kraken on raw data (only trimmed)" evaluating contamination in raw data before alignment

The PR description is actually empty, and i'd be interested in the rationale for this to justify the increased complexity/ run times

what do you mean PR description?

Ahh, you put a sentence in the checklist, that's normally left alone and I ignore it.

when evaluating kraken + bbsplit -> the unmapped reads of BBSplit are the first aligner