GATK4 conda failures
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bug
CI-issue
conda-fail
tests
- Dominant language
- Nextflow
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- Avg merge
- 1d 6h
- Merged PRs (30d)
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Description
All gatk4 modules were updated in #9033.
However, the PR was force merged @maxulysse, with approval from @nf-core/maintainers with some standing conda issues for the gakt4/createreadcountpanelofnormals module.
This was seemingly caused by an underlying spark dependency, which didn't jive with conda.
Docker/Singularity tests pass without any issues.
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
Inspect the gatk4/createreadcountpanelofnormals module and its Spark-related conda dependency. Compare the failing conda path with the passing Docker and Singularity tests. Done means the module's conda tests pass without regressing the other reported test paths.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- spark
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100