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Ran 13 Mar 2025 02:54PM UTC

Files 226

Run time 63min

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Committed 13 Mar 2025 02:53PM UTC coverage: 59.872% (+0.4%) from 59.426%

Job # 13837631941.1

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

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