Hey everyone! Just an update on my side, 1.2.0 PR has been finalised earlier this week and for the main dev - > master PR is waiting reviews - I posted in #C08K66XCZSL . You are absolutely welcome to have a look, your review would be hugely appreciated! During testing and CI I encountered

conda

issues some of which I addressed with a smaller PR with some module updates and conda CI conda channels (in an attempt to fix

conda

CI). That said, all Docker/Singularity tests work perfectly. I see in the previous release the

conda

CI passed because

conda

runs were deleted from the CI workflow, so it wasn't actually tested. Conda CI tests got re-introduced however with the v3.4.1 template update. Perhaps worth discussing whether from here on we do provide

conda

support with the pipeline or whether conda CI is required to get a green badge for testing. I've taken it as far as I could, now it's in the hands of the reviewers, and happy to take the lead back on once those are in 😄

Thank you @Ira Iosub. Apologies for not getting to it sooner. I know I also owe an update on RiboCode but its just been so hard to carve out time. I have added this to my To Do.

fantastic. Just to mention it briefly here we are making great progress with the implementation of Plastid and RiboDetector (I’ll leave the details to Sebastian), but they will also only be ready for the next release - in the new year?

Thanks everyone! Once this release is out, I’m happy to help with reviews/testing. And great to hear the updates🎉

Looks like I removed the Conda last time round: https://github.com/nf-core/riboseq/pull/99

Thank you very much!

I think this should fix the Conda thing: https://github.com/nf-core/riboseq/pull/120

Approved! I believe it will fix it too. Feel free to merge:)

Hmm, still broken, but differently so!

strange..not sure why ribo-tish complains 🤔

I know why, pr incoming...

thanks! all clear

You have my approval @Ira Iosub, but you'll need another. There's just one minor thing you should fix about the conditional before you merge.

Great catch!! Thanks for that. I’ll follow with a PR with the fixes and will try to get another review

You know I'm not sure. But I don't see that anyone will complain if you do.

Thank you @Jonathan Manning ! Getting back to this on Monday. Re the 2nd reviewer asking for updating the FASTQC_QC_TRIM_FILTER_SETSTRANDEDNESS - which now contains ribodetector and bowtie2. Since you are actively working on this in #125 how do you think it’s best to address this review? Update the subworkflow or simply try to change the input locally for now?

I'd disregard because it will go away by itself when we merge 125. I'm going to have a quick go to finish 125, if it's easy, otherwise it'll happen later next week

Hey @Jonathan Manning, just so this release (and

dev

branch) isn’t blocked by broken functionality, I settled on a compromise: updated the affected subworkflow to a recent sha tag that fixes the issue, but doesn’t yet include the ribodetector/bowtie2 overhaul. See here: https://github.com/nf-core/riboseq/pull/126