Pipeline linting test `pipeline_if_empty_null` can be extremely slow in some contexts
Open
A pull request for this has already been merged.
- #3820 by @jmuhlich — merged
bug
linting
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
When I run time nf-core pipelines lint locally (VSCode, Ubuntu 24.04) with a conda installed nf-core tools, the whole test takes
real 3m58.398s
user 3m45.035s
sys 0m22.198s
Taking a particualrly long time on pipeline_if_empty_null
If I run with same branch on gitpod
real 0m57.994s
user 0m36.490s
sys 0m45.334s
Command used and terminal output
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
Start by running nf-core pipelines lint and isolate the pipeline_if_empty_null test, comparing the local and Gitpod timings described in the issue. Trace the test's setup and execution to identify why it becomes slow in some contexts; done means the cause is addressed and the test completes without the reported excessive delay.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- devtools, testing-qa
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100