Capture `.nf-core.yml` errors and give a useful message
Open
Nobody has claimed this yet.
bug
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
Context on Slack: https://nfcore.slack.com/archives/CE5LG7WMB/p1747295666065149
TODO:
- Capture the traceback and print a useful error message
- Print the key that throws the error
- Link to the lint error docs
Command used and terminal output
nf-core modules update
AssertionError: Config file '.nf-core.yml' is invalid
lint: Input should be a valid boolean
input: ['README.md', 'main.nf']
System information
No response
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
Reproduce the failure with nf-core modules update and the invalid .nf-core.yml shown in the report, then trace the configuration-validation error path. Done means the traceback is captured, the failing key is identified, and the message links to the nf-core lint error documentation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100