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Published 20 hours ago • verified publisher icon nf-core

Add skani round 2

Open CarsonJM opened this issue 1 year ago • 3 comments

PR checklist

Re-opens #5502

  • [ ] This comment contains a description of changes (with reason).
  • [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - have you followed the module conventions in the contribution docs
  • [ ] If necessary, include test data in your PR.
  • [ ] Remove all TODO statements.
  • [ ] Emit the versions.yml file.
  • [ ] Follow the naming conventions.
  • [ ] Follow the parameters requirements.
  • [ ] Follow the input/output options guidelines.
  • [ ] Add a resource label
  • [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • [ ] nf-core modules test <MODULE> --profile docker
      • [ ] nf-core modules test <MODULE> --profile singularity
      • [ ] nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile conda

CarsonJM avatar Apr 29 '24 21:04 CarsonJM

@jfy133 back in action part2. I'm still experimenting with the best way to add the -l option, but will let you know when I'm ready for another review!

CarsonJM avatar Apr 29 '24 21:04 CarsonJM

@CarsonJM , can you make the adjustments suggested here?

SPPearce avatar May 13 '24 14:05 SPPearce

Yes I can! I am in the middle of a wet-lab onslaught at the moment and have fallen behind on nf-core stuff, but am hoping to be back at it soon!

CarsonJM avatar May 13 '24 16:05 CarsonJM

Bumpity bump

SPPearce avatar May 29 '24 19:05 SPPearce

Bumpity bump. The environment.yml files will need changing to meet the recent changes (remove name and defaults).

SPPearce avatar Sep 07 '24 12:09 SPPearce

@CarsonJM ?

SPPearce avatar Mar 05 '25 20:03 SPPearce

Carson might not be able to get back to this any time soon, he told us life situation meant he would have very little time for a long time

jfy133 avatar Mar 06 '25 05:03 jfy133

Carson might not be able to get back to this any time soon, he told us life situation meant he would have very little time for a long time

Ok, thanks for letting me know James. I've made the minor changes, bumped the version, and updated the meta and environment to be up-to-date. Can you or @nvnieuwk take another look and get this merged in?

SPPearce avatar Mar 06 '25 06:03 SPPearce