Bad check on pipelines `modules.json`
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- Dominant language
- Python
- Stars
- 322
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- 255
- Avg merge
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- Merged PRs (30d)
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Description
I removed the multiqc module from nf-core from my pipeline to install my own for development purposes. Now, I get this error for no valid reason :
The error disappear once I reinstall the multiqc module from nf-core.
I believe this behavior from the lint test is not the one expected, nor wanted. It is caused by this line in the modules.json lint test, that checks that all repositories listed install modules, which is now not the case for my nf-core after uninstalling multiqc (only subworkflows). I also don't think it's a requirement that makes sense to be enforced.
I'll try to propose a quick PR to fix this if I end up having some time.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at nf_core/pipelines/lint/modules_json.py line 29, where the modules.json lint check requires every listed repository to install modules. Reproduce the lint with an nf-core repository containing only subworkflows, then verify the check accepts it while still validating repositories that install modules.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 45/100