Expand nf-core modules test to allow testing of GPU based modules
Open
Nobody has claimed this yet.
enhancement
modules
nf-test
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
So far I only edited the tests/config/nf-test.config docker section to include
docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g) --gpus all'
but in theory this should be solved with the tag "gpu" in the nf.test file.
I would love to run
nf-core modules test parabricks/fq2bam
and the GPU additions to be resolved automatically.
Contributor guide
First steps
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with tests/config/nf-test.config and the nf.test files used by nf-core modules test. Run nf-core modules test parabricks/fq2bam and trace how the tag "gpu" is handled. Done means GPU-based modules receive the required GPU test settings automatically without manual Docker configuration.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- testing
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100