Use resource limits instead of setting process directives in nf-test configuration
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- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
Similar to https://github.com/nf-core/tools/pull/3037, we should set the maximum cpu, memory and time limit on nf-tests. This can be mostly done by the -profile test however it is beneficial to set a hard limit when using nf-tests so accidentally not using the test profile does not cause issues.
See https://github.com/nf-core/rnaseq/blob/99fb7efc9d2b17a7940f745570ff162c04548bc4/tests/nextflow.config#L23-L30 for current implementation in tests/nextflow.config:
// Impose sensible resource limits for testing
process {
withName: '.*' {
cpus = 2
memory = 3.GB
time = 2.h
}
}
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
Compare the requested behavior with nf-core/tools PR 3037 and the example in tests/nextflow.config from nf-core/rnaseq. Start by locating how nf-tests apply the -profile test configuration, then verify that CPU, memory, and time limits remain enforced when that profile is omitted.
Written by the indexing model from the issue text.
Assessment
- Domain
- testing
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100