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Migrate `gget/gget` to nf-test

Open jvfe opened this issue 9 months ago • 4 comments

PR checklist

Closes #7588

  • [x] This comment contains a description of changes (with reason).
  • [x] 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.
  • [x] 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:
      • [x] nf-core modules test <MODULE> --profile docker
      • [x] 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

jvfe avatar Mar 24 '25 18:03 jvfe

Maybe your conda issues go away if you update gget to the latest version :) https://anaconda.org/bioconda/gget (0.29.0)

famosab avatar Mar 25 '25 09:03 famosab

I would update the branch - hard to see which tests are belongig to you :) also I am confused are there other modules gget/... ? Because if only this exists I think you can just call it gget

famosab avatar Mar 25 '25 16:03 famosab

I would update the branch - hard to see which tests are belongig to you :) also I am confused are there other modules gget/... ? Because if only this exists I think you can just call it gget

Yeah I'm not sure why it's called gget/gget, since it's the only module. But given I'm just migrating the test cases, not sure I should change the modules name. I've updated the containers but I'm still getting a few errors.

jvfe avatar Mar 25 '25 16:03 jvfe

For some reason I'm not being able to generate the full snapshot, every time it's failing because of connection issues.

jvfe avatar Mar 25 '25 19:03 jvfe

When I clone your repo I run into the same problems with not being able to run the tests - no idea why. I am closing this in favor of a new PR https://github.com/nf-core/modules/pull/8518/

famosab avatar May 20 '25 12:05 famosab