Heads-up: I have the UMI thing in my sights. I want to factor the logic out of rnaseq (there are some improvments coming there), and then I'll apply here as a subworkflow. We also have improvements in preprocessing I'll deploy here too. For next week!

That’s great to hear, Jon! Regarding the UMI bug, @Ira Iosub might also be working on it already

hey! my changes wouldn't include the re-factoring as subworflows from rnaseq, just a quick fix. so I am ok to hold off w my changes as what @Jonathan Manning proposed seems more robust 🙂

Maybe you can do the quick fix in parallel @Ira Iosub?

ofc, opened a PR, suggested both of you as reviewers :)

The changes look good to me, I have now approved the PR. We will try to run a test after lunch

Yes, I'm afraid that's what we have to do. We could patch the module on the workflow level, but if it makes sense there it probably makes sense to apply to the module for everyone

OK, will do.

Yep. No releases as such, so no need for dev

Thanks. I have made this one instead: https://github.com/nf-core/modules/pull/7145

took the liberty of updating

RIBOTRICER_PREPAREORFS

with @Felix Krueger’s updated resources module https://github.com/nf-core/riboseq/pull/77, using

nf-core modules update ribotricer/prepareorfs

The above PR (https://github.com/nf-core/riboseq/pull/77) has failing tests, and we don’t exactly know where they are from. Can someone please take a look? @Jonathan Manning @Maxime Garcia? Thanks!

Will do- also need to fix the branch protections I think, to require test passes

great, this worked now. thanks!

No worries, we'll need to revert it when the 'proper fix' is ready https://nfcore.slack.com/archives/C04QR0T3G3H/p1733312474302079

yeah, I'm checking this closely