nf-core / nf-core/genomeassembler
Improve test coverage
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Description
Description of feature
Current CI tests cover the core functionality of the pipeline (assembly), but fall a bit short on the later stages, which has led to bugs being noticed only during runs of the full_test on AWS (cp #226).
Ideally, this should be improved with more fine-grained nf-test tests. Properly testing the pipeline is not completely trivial, due to the parameterisation at the sample level, which should be incorporated in tests, i.e. switching of certain params at the sample-level.
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 existing nf-test coverage for the pipeline’s assembly stage and the full_test run on AWS. Extend coverage to the later pipeline stages, including sample-level parameter switching, and verify that the new tests exercise those runs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- aws
- Domain
- bioinformatics, testing
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100