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Clinical-Genomics / cg / 16644338343
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DEFAULT BRANCH: master
Ran 31 Jul 2025 08:49AM UTC
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Files 874
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31 Jul 2025 08:46AM UTC coverage: 100.0% (+14.2%) from 85.764%
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DEV - Start Taxprofiler analyses using pipeline integration flow (#4509)(patch)

## Description
Development branch for integrating Taxprofiler to the new AnalysisStarter flow
To be merged with https://github.com/Clinical-Genomics/servers/pull/1676

### Added

- Class TaxprofilerParamsFileCreator
- Base model TaxprofilerParameters inheriting from WorkflowParameters (empty as no extra parameters are needed)
- Taxprofiler to configurator factory and to analysis starter factory
- Dev cli commands:
  - dev_config_case
  - dev_run
  - dev_start
  - dev_start_available
- Tests for new cli commands

### Changed

- Move the constructor from the child classes to the parent ParamsFileCreator. This constructor receives only the servers params file path. Override only in raredisease as it needs store and LIMS

### Fixed

- Enhance tests and fixtures of analysis start workflow

Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se>

81 of 81 new or added lines in 11 files covered. (100.0%)

2 of 2 relevant lines covered (100.0%)

13919.5 hits per line

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ID Job ID Ran Files Coverage
1 16644338343.1 31 Jul 2025 08:49AM UTC 874
85.81
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