Batch module updates - Fall 2024 #5828
Description
Warning
Please open PRs against the batch_update_staging branch. Then we can have small, easy to review, atomic PRs but also merge all batch updates to the modules repo in one go.
Note
[Edit - @ewels]: I've split into two groups, those that will require changes from pipeline developers (other than just pulling in updated modules as normal) and those that will not (those that will require changes to pipeline code).
Anything that doesn't need changes to pipeline code can be done iteratively if we wish, rather than batched.
### ✅ Will not require pipeline updates ✅ ✅ ✅ ✅ ✅
- [ ] https://github.com/nf-core/modules/issues/4983
- [ ] https://github.com/nf-core/modules/issues/5830
- [ ] https://github.com/nf-core/modules/issues/5831
- [ ] https://github.com/nf-core/modules/issues/5829
- [ ] https://github.com/nf-core/modules/issues/5835
- [ ] https://github.com/nf-core/modules/issues/5836
- [ ] https://github.com/nf-core/modules/issues/5848
- [ ] https://github.com/nf-core/modules/issues/4570
- [ ] https://github.com/nf-core/modules/issues/6001
- [ ] https://github.com/nf-core/modules/issues/6454
- [ ] https://github.com/nf-core/modules/issues/6226
- [ ] https://github.com/nf-core/modules/issues/6504
- [ ] https://github.com/nf-core/modules/issues/6505
- [ ] https://github.com/nf-core/modules/issues/6650
### ⚡ Will require pipeline updates ⚡⚡⚡⚡⚡⚡⚡⚡
- [ ] https://github.com/nf-core/modules/issues/4517
- [ ] https://github.com/nf-core/modules/issues/5834
- [ ] https://github.com/nf-core/modules/issues/5832
- [ ] https://github.com/nf-core/modules/issues/5833
Just a heads up for bulk changes: there is a strict matrix limit of 256 tests in a test strategy on github, so that is the max number of module changes in a PR. @mashehu #2738