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Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls
PR checklist
Closes #XXX
- [x] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the module conventions in the contribution docs
- [ ] If necessary, include test data in your PR.
- [ ] Remove all TODO statements.
- [x] Emit the
versions.yml
file. - [x] Follow the naming conventions.
- [x] Follow the parameters requirements.
- [x] Follow the input/output options guidelines.
- [ ] Add a resource
label
- [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
- [x]
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
- [ ]
PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
- [ ]
PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
- [x]
There is an error related to Conda that I am unsure on how to fix or if it is necessary to fix it:
Caused by: Failed to create Conda environment command: conda create --mkdir --yes --quiet --prefix /home/runner/pytest_workflow_3j9p2vgr/picard_liftovervcf_test_picard_liftovervcf_stubs/work/conda/env-aa7c3f17b3e9b256fbd55d1bfa076bd8 bioconda::picard=2.27.1 status : 1 message: PaddingError: Placeholder of length '80' too short in package /home/runner/pytest_workflow_3j9p2vgr/picard_liftovervcf_test_picard_liftovervcf_stubs/work/conda/env-aa7c3f17b3e9b256fbd55d1bfa076bd8/bin/Rscript. The package must be rebuilt with conda-build > 2.0.
@FriederikeHanssen @ramprasadn . The tests now pass, I think this is good for merging.