`modules lint --fix` changes more entries in the meta.yml than expected
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- Dominant language
- Python
- Stars
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- Avg merge
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- Merged PRs (30d)
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Description
Description of the bug
See also this Dicussion on the PR: https://github.com/nf-core/modules/pull/7201#discussion_r1888543191
Running linting with the --fix flag leads to the meta.yml being changed a lot while only one output pattern would have needed to be changed. Instead the whole output section of the meta.yml is affected. Changes look like:
Seems as if the pattern part is moved up to the meta map and the type of the actual file output is changed to map and its description changed to the meta description.
Command used and terminal output
nf-core modules lint --fix custom/matrixfilter
System information
will be supplied by @nschcolnicov
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 by reproducing nf-core modules lint --fix custom/matrixfilter and inspect the affected meta.yml output section. Compare the changes with the PR discussion at https://github.com/nf-core/modules/pull/7201#discussion_r1888543191. Done means --fix changes only the intended output pattern rather than unrelated output entries.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100