I discovered a new bug for our test run: github.com/nf-core/riboseq/pull/220

Am I the only one who still gets confused when you’ve got 14 windows open with PRs and development things across 6 workflows and analysis projects?

The nf-core modules merge queue seems to be broken for every merge against master. Issue filed here: github.com/nf-core/modules/issues/12457

Just fyi, the workflow so far is fantastic! I am curently preparing two more PRs or feature requests to make it an even better 🌟 workflow - I hope to have everything by this afternoon/p.m.

Can we talk about @Sebastian Uhrig’s output structure suggestion? Thoughts? github.com/nf-core/riboseq/pull/206

I also thought it might be a good idea to tackle an open issue someone posted about experiments with mixed UMI status: github.com/nf-core/riboseq/pull/223 github.com/nf-core/riboseq/issues/146

I’m rapidly running out of Friday hours, will try to take a look over the weekend, sorry

Build ORF catalogue independently of StringTie now all green: github.com/nf-core/riboseq/pull/222

Here is one more for the ORF class vocabulary: github.com/nf-core/test-datasets/pull/2193

simple ORF cross caller merge test: github.com/nf-core/modules/pull/12495

FYI scottish bank holiday today, so I'll be back and dealing with these tomorrow

And last one for today: decouple ORF class from ORF length: github.com/nf-core/modules/pull/12498

github.com/nf-core/riboseq/pull/206 is now 🥬

I found a new bug when deltaTE was executed: github.com/nf-core/riboseq/pull/225

last one for today: github.com/nf-core/modules/pull/12599

Could I get a tick on this historic one? github.com/nf-core/riboseq/pull/151 Tiny but we still need it

Is there any verdict from the #CE8SSJV3N perspective as to whether the param changes for sortMeRNA are any use? I am happy to close it otherwise Edit: What I mean is, it was mentioned on the comments there that this was raised with regard to the RNA-seq pipeline too

This is the next one that unblocks work: update Ribo-TISH ORF classes github.com/nf-core/modules/pull/12613 (all tests passing)

I added a new mini Ribo-TISH test dataset: github.com/nf-core/test-datasets/pull/2208

This is the one I have been working towards for over a week, update on ORF classes: github.com/nf-core/riboseq/pull/226

increase default time and memory allocation for ORFMERGE (#C05785S3TMX) https://github.com/nf-core/riboseq/pull/229

This needs a re-review, changes applied: github.com/nf-core/riboseq/pull/228

increase default run-time for DESEQ2_DELTATE_ORF (#C05785S3TMX) github.com/nf-core/riboseq/pull/230

Quickly checking in here (@Jonathan Manning): I’ve got ~2 days left before going holiday - I think we should be pretty close to a new release of riboseq? Is there anything from my side that I can meaningfully do before? (for context, I may have access to a computer until then Sept 2nd, but no access until Sept. 19th). Thanks in advance if you manage to pull a new release (and an updated metro map 🚇 ) off during that time! And let me know if there is something I can do. 🙏

<!channel> could I get review on this release prep PR? github.com/nf-core/riboseq/pull/231. It's just the version bumps + credit updates. I've tried to update the credits appropriately, but if you feel changes are required now would be the time to shout! Also make sure any ORCID IDs etc are correct. Once someone approves this for me (and I've given you a day or two to make corrections), I'll be able to merge, make the big dev -> master release PR and start pestering folks for release reviews! I'll get the metro map sorted before the actual release happens.

<!channel> how do you feel about this as a new metro map? seqeralabs.github.io/nf-metro/dev/pipelines/riboseq_metro As always with these maps, I'm not going for faithful representation of the task graph, just a schematic overview of the logic.

morning all, i'm on leave today, but FYI i found a couple of bugs when reviewing the release PR myself. Fixes here: github.com/nf-core/riboseq/pull/235 ... but there's some issue with the CI on nf-core/modules i think

<!channel> can I get review on github.com/nf-core/riboseq/pull/235? Last PR before I ask for wider review of the main release PR and we get this puppy out the door 🙂

<!channel> the release has had two sets of eyes and comprehensive review, but I think Joon is OOO today for approval. Anyone fancy giving it a once-over and thumbs up so I can get it out the door? github.com/nf-core/riboseq/pull/234

.... aaand it's done. Well done team! github.com/nf-core/riboseq/…/2.0.0