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Ran 15 Aug 2024 01:49PM UTC

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Committed 15 Aug 2024 01:47PM UTC coverage: 84.729% (+0.1%) from 84.607%

Job # 10404839673.1

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push

github

Committed by

web-flow

Commit Message

feature(dev-branch-pacbio) (#3453)(minor)

## Description
This PR introduces a new structure for the run devices post-processing:

### Added

- CLI command `cg post-process run <run-name>` which currently works with PacBio SMRT cells but will work for any run in the future
- Abstract interfaces for the classes described in the diagram above, suitable for overriding with the proper classes for each device
- Classes for the PacBio post-processing
- CRUD functions to create and read PacBio DB entries
- Util functions
- Test functions, fixtures and fixture files

### Changed

- Function `store_fastq_path_in_housekeeper` in housekeeper modified into `create_bundle_and_add_file_with_tags` so that it works in a more general way (not only for fastqs)


Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se>

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