[request] Lint for a potential runtime error with nf-test and github actions
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
Currently we have faced issues with nf-test in github actions that has led to a consistent runtime error because the test took longer than 2h see this github actions run for PR #12421 in nf-core modules.
The error only occured during nf-test with github actions and could not be reproduced locally.
Fix
It was fixed by including a config to limit cpu's, memory and runtime, as seen for commit 7e95850.
Request
Matthias H. mentioned that it might be best to lint for this issue.
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 reviewing the linked GitHub Actions run for PR #12421 and commit 7e95850 to understand the runtime failure and the configuration that fixed it. Then inspect the repository's existing linting entry points and determine how to detect missing CPU, memory, and runtime limits; done means the case is reported reliably by linting.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- github-actions, python
- Domain
- ci-cd, tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 45/100