sageproteomics/sage

[dgemperline-lilly]

PR checklist

Closes #XXX

• 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

[dgemperline-lilly]

addressed via commit

[FloWuenne]

Hey @dgemperline-lilly is this ready to be reviewed? If yes, I would update the branch, do a final pass and then approve if everything checks out!

[dgemperline-lilly]

Hey @dgemperline-lilly is this ready to be reviewed? If yes, I would update the branch, do a final pass and then approve if everything checks out!

Yes good to go I think?

[dgemperline-lilly]

@adamrtalbot I addressed the proposed changes via additional commit. Any way you can approve?

[FloWuenne]

We are just having a discussion about this in the maintainers team whether putting the file directly here is ok or whether you need to put it somewhere else. Does this file exist somewhere on github already?

[dgemperline-lilly]

Yes it does - originally had it linked on github publicly. We can revert if that is what is recommended.

[FloWuenne]

@dgemperline-lilly I have added some review comments to fix remaining linting warnings.
The last thing we need to wait on before merging is where to put the test file. I will get back to you here once we have decided whether including it in the modules folder is ok or not!

[FloWuenne]

@dgemperline-lilly The result from discussions between the maintainers team was pretty clear that test files cannot be in modules directly. Can you please make a PR to : https://github.com/nf-core/test-datasets/tree/modules with your test data? Feel free to ping me to review and approve!

[FloWuenne]

Finally, please remove the file from this repo and move it to test-datasets. Sorry for the confusion!

[dgemperline-lilly]

@FloWuenne Opened pull request here: nf-core/test-datasets#1234 with the new file added. Will add in another commit once pull request goes through.

[FloWuenne]

@dgemperline-lilly Just approved the PR on test-datasets. Should be able to query that data in here now 😃 ! Thanks for adding the data to test-datasets David!

[dgemperline-lilly]

Added key to test_dataset.config. Need approval here:

#5803

[FloWuenne]

OK last thing is to remove the old test file and make the two changes I suggested and we are good! 👍🏻

[FloWuenne]

LGTM now ⭐ !