Support running gatk4/cnnscorevariants over Conda
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Description
gatk4/cnnscorevariants doesn't support conda because the gatk4 Conda package doesn't include the right dependencies.
@FriederikeHanssen tried adding gatktool (#1786) but that didn't work either (error message: https://github.com/nf-core/modules/pull/1786#issuecomment-1332772235).
An issue has been created on the gatk repository: https://github.com/broadinstitute/gatk/issues/7811
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 with modules/nf-core/gatk4/cnnscorevariants/main.nf at lines 5-8 and review the failed gatktool attempt in #1786. Check the linked GATK issue #7811 for the dependency status. Done means the module can run gatk4/cnnscorevariants with Conda and includes the required dependencies.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100