pypgx/runngspipeline

[Jorisvansteenbrugge]

PR checklist

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

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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    • 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: #5836

They seemed to have thought about a fix: #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 nextflow-io/nextflow#5489 to get merged. Which should fix the issue (nextflow-io/nextflow#5485)