Clinical-Genomics / cg / 13516627620

86%

Build Type

push

github

Committed by web-flow

Commit Message

remove reference genome tomte (#4224)(minor)

Part of #4218 
Remove the possibility of specifying a reference genome in Tomte from an order. The value for the reference genome will always be set to `hg38`. The value will not be saved in the database for each sample, but set as constant in the `TomteAnalysisAPI`.

## NOTE
This has to be merged together with https://github.com/Clinical-Genomics/clinical-genomics-ui/pull/701

### Added

- `get_genome_build` method in the `TomteAnalysisAPI` that overrides the parent method and returns HG38

### Changed

- Update `upload_rna_genome_build_to_scout` without calling the get_genome_build from the deleted module but using directly HG38

### Fixed

- The function `get_genome_build` in the parent class `NFAnalysisAPI` contained only the logic for Tomte, as this method is overridden in all the NF-Pipelines. Its logic was removed and now it raises a `NotImplementedError`.
- Remove `cg/meta/workflow/utils/genome_build_helpers.py` as contained functions used to fetch the reference genome for tomte cases from the database
- Removed `reference_genome` in the `TomteSample` in the ordering models
- Remove reference_genome from Tomte Fixtures

Run Details

5 of 6 new or added lines in 3 files covered. (83.33%)

1 existing line in 1 file now uncovered.

26076 of 30445 relevant lines covered (85.65%)

0.86 hits per line