Pass a list of modules/subworkflows(files) to nf-core modules lint
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- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
I was working on https://github.com/nf-core/modules/pull/6286 last week.
I really wanted to avoid using path-filter and having the whole separate step logic for the linting.
I think we could offload the changed files to pre-commit, and create pre-commit hooks for nf-core/tools. I think it would be pretty slick for pipelines as well(I know I don't run nf-core lint often enough personally)
The only issue I had was the way pre-commit passes files. It will pass nf-core modules lint modules/nf-core/bowtie/align/main.nf modules/nf-core/bowtie/build/main.nf modules/nf-core/fastqc/main.nf ... which currently doesn't work.
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 the nf-core modules lint CLI entry point and inspect how it handles the module and subworkflow paths passed by pre-commit hooks. Reproduce the command with the listed changed-file arguments; done means those paths are accepted for linting, with the behavior verified by the relevant existing tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, tooling
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100