And here, in the wild expanses of the nf-core/rnas...
# request-review
j
And here, in the wild expanses of the nf-core/rnaseq repository, we observe a truly remarkable event. The Release Pull Request - Devicus mastericus rarum - has emerged from its den after months of patient gestation. At 330 commits and 546 files changed, this is one of the largest specimens we have ever documented. Experts agree the species would benefit from more frequent, smaller releases - but in captivity, the maintainer's feeding schedule has been... irregular. Note the extraordinary plumage: Parabricks GPU acceleration, prokaryotic RNA-seq support, multiple rRNA removal tools, tximport for RSEM, Sylph contamination detection - each adaptation more breathtaking than the last. But look more closely. Much of this creature's impressive bulk is, in fact, harmless padding. Modules updates. Subworkflow bumps. SHA changes in modules.json. Rather like a pufferfish inflating itself to deter predators - alarming at first glance, but fundamentally benign. Beneath the bluster, the actual pipeline logic is really quite manageable. The creature now faces a perilous journey. It must cross the treacherous master branch - and it cannot do so alone. It requires the rare and elusive Reviewer - a shy creature, easily startled by large diffs. Fear not, gentle Reviewer. We have prepared a guided safari. Each feature has been broken into individually-reviewed component PRs, catalogued by theme in the description. You need not traverse the entire savanna. Simply follow the trails we have marked. https://github.com/nf-core/rnaseq/pull/1717 Will this magnificent specimen survive the journey? That... is up to you. BBC theme intensifies
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m
+39,395 -33,757
546 files changed
That's a pretty big one, I'll have a look
I love a challenge
j
We did release just before xmas, I've just been too productive!
There's topics updates in there which basically modified every module
m
yeah, I figured, the blast radius was big
j
Also strict syntax, again, changes all over
m
Just back from lunch, and I can see that @Louis Le Nézet has already made nice comments
there seems to be 2 conda failure on the CI side
j
probably random, but i'll look into them
addressing the comments now
@Louis Le Nézet on your umitools comment, I added all those pins to harmonise results for ARM. That was kind of an rnaseq-specific concern, and we don't conventionally do a lot of pinning in the modules repo (at some point I think we'll have lock files for that), but here is the modules PR for your consideration: https://github.com/nf-core/modules/pull/10271
(and of course, all the conda is broken shakefist) Good now
... and the tx2gene snaphot fixes @Louis Le Nézet https://github.com/nf-core/rnaseq/pull/1725
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@mashehu when you're about I'd love to get those metro map fixes in before release- can work on further improvements for the next one 🙂 https://github.com/nf-core/rnaseq/pull/1714
Think I addressed all your points related to these changes @Louis Le Nézet (and noted a few unrelated ones for future action). Can I get your approval? CI being a bit flakey with Conda tests, working on it
approved with comments 1
Conda issue was
mkdir
thing, fix: https://github.com/nf-core/rnaseq/pull/1730
That animation bug was fun @mashehu 🙂, fixed https://github.com/nf-core/rnaseq/pull/1728
Could you clear your block on https://github.com/nf-core/rnaseq/pull/1730 @mashehu? Think the version thing is good now