Comments (1)
lheisler
commented on August 19, 2024
This took quite a bit of testing to implement, but all seems to be in place. All tests passed at this point, it is possible that there are other parts of the code that need to be accounted for and will keep this in mind with further development. These corrections will allow better extensibility, and implementation of new pipelines.
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Related Issues (20)
- Consolidate test data files?
- Tests for janus.py command line script HOT 1
- Investigate mutation test warnings
- Intermittent CAP mutation test error
- Refactor calls to shell
- Inconsistent _concat.txt suffix in output
- Cross-check sample names in config
- Replace get_tgca.r HOT 1
- Clean up preProcCNA.r HOT 1
- Dependency (if any) between pipeline config files HOT 1
- Fix or suppress numpy warning at runtime
- Move deprecated code into a "legacy" package
- Document & validate study config HOT 4
- Reinstate "colours" for cancer type HOT 1
- Add vcf2maf dependency in janus module
- Get fasta reference from environment module HOT 1
- Environment variables for mutation pipeline HOT 3
- Make mutation tests faster
- Non-CAP mutation scripts do not generate metadata
- Ensure pipeline R scripts and data files are installed by setup.py HOT 2
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