pypgx/runngspipeline

[Jorisvansteenbrugge]

PR checklist

Closes #5987 This PR adds a new module: pypgx/runngspipeline

• [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!
• [x] If you've added a new tool - have you followed the module conventions in the contribution docs
• [x] Remove all TODO statements.
• [x] Emit the versions.yml file.
• [x] Follow the naming conventions.
• [x] Follow the parameters requirements.
• [x] Follow the input/output options guidelines.
• [x] Add a resource label
• [x] 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

[Jorisvansteenbrugge]

For some reason the conda based tests are not working..

[famosab]

Can you run the test locally with the conda profile? nf-core modules test pypgx/runngspipeline --profile conda -u

[Jorisvansteenbrugge]

Can you run the test locally with the conda profile? nf-core modules test pypgx/runngspipeline --profile conda -u

@famosab Thank you for taking a look! I get the same error unfortunately.. I wonder if this is the same issue as #4234 opened by @edmundmiller .

I see this error appears when running tests for subworkflows. Could be that we need to add a name to environment.yml? If two modules in a subworkflow have exactly the same environment.yml I suspect the environment names may clash

While this is not a subworkflow, the nf-test for this module is chained with other modules that use the exact same environment.yml. I am however not sure what the solution is.

[famosab]

In theory that should not happen with nf-test anymore as noted down here: https://github.com/nf-core/modules/issues/5836

They seemed to have thought about a fix: https://github.com/nf-core/modules/issues/6664

Maybe it is worth asking in the slack since this issue came up a few times :)

[Jorisvansteenbrugge]

@famosab Thanks :)

It seems like we are waiting for https://github.com/nextflow-io/nextflow/pull/5489 to get merged. Which should fix the issue (https://github.com/nextflow-io/nextflow/issues/5485)

[Jorisvansteenbrugge]

Thanks for the contribution. I'm just a bit concerned on how the output is given back. Is there a need for it to be in a zip format ?

@LouisLeNezet The zip files are simply what the tool outputs, it is not something I added myself

[LouisLeNezet]

Thanks for the contribution. I'm just a bit concerned on how the output is given back. Is there a need for it to be in a zip format ?

@LouisLeNezet The zip files are simply what the tool outputs, it is not something I added myself

That's fine for me then.