Clinical-Genomics / cg / 8723821188

86%

Build Type

push

github

Committed by web-flow

Commit Message

Refactor of Sequencing metrics module (#3137)(patch)

Now that we only have one bcl converter, much of the nested structure in the sequencing metrics module can be simplified. This PR refactors the Sequencing metrics module based on renaming modules, models and directories.

### Changed
- Removed directories `models` and `parsers` in `cg/apps/sequencing_metrics_parser`. The `bcl_convert` modules were moved one folder up, at the same level as the API, so now we have a flat structure.
- Renamed `BclConvertMetricsParser` to `MetricsParser`
- Renamed `BclConvertQualityMetrics` to `SequencingQualityMetrics`
- Renamed `BclConvertDemuxMetrics` to `DemuxMetrics`
- Moved function `get_flow_cell_id` to `g/utils/flow_cell.py` so that it is accessible to all the code in a nice dependence tree
- Removed bcl2fastq demultiplexed flow cell fixture and its data

Run Details

42 of 42 new or added lines in 4 files covered. (100.0%)

13 existing lines in 1 file now uncovered.

12608 of 15207 relevant lines covered (82.91%)

1.28 hits per line