Clinical-Genomics / cg_lims / 13837631941

59%

Build Type

push

github

Committed by web-flow

Commit Message

Add new EPP for fetching SMRT Cell sampled based sequencing metrics (#601)(minor)

### Added
- New models
    - cg_lims/EPPs/qc/models.py: CellSample, CellSampleSet
- New helper classes
    - cg_lims/EPPs/qc/sequencing_artifact_manager.py: SmrtCellSampleArtifacts, PacbioSequencingArtifactManager
    - cg_lims/EPPs/qc/sequencing_quality_checker.py: PacBioSequencingQualityChecker
- New common functions
    - cg_lims/get/artifacts.py: get_smrt_cell_sample_artifacts
- New EPP
    - cg_lims/EPPs/qc/pacbio_sequencing_quality_control.py: For fetching PacBio sequencing metrics and checking basic QC.
- New tests
    - tests/EPPs/qc/test_pacbio_sequencing_artifact_manager.py
    - tests/EPPs/qc/test_pacbio_sequencing_quality_checker.py
- New fixtures
    - tests/conftest.py: For PacBio sample sequencing metrics
    - tests/fixtures/revio_demux_run/: Demultiplex Revio Run step fixture

### Changed
- Renamed several files and functions to discern between PacBio and Illumina sequencing results

### Fixed
- Missing docstrings
- Spelling mistakes
- cg_lims/scripts/prepare_fixture.py

Run Details

157 of 211 new or added lines in 11 files covered. (74.41%)

1 existing line in 1 file now uncovered.

5249 of 8767 relevant lines covered (59.87%)

0.6 hits per line