Cg

Changed

- Merged methods cases_to_mip_analyze and cases_to_balsamic_analyze, now called cases_to_analyze for any pipeline.
- Made method cases_to_deliver pipeline aware
- Made method cases_to_store pipeline aware
- Made method cases_to_clean pipeline aware
- Added option to apply read count threshold for cases_to_analyze based on panel in ClinicalDB
- Updated MIP and BALSAMIC workflows to utilize the new methods
- Added tests for new methods in balsamic workflow
- Removed class FastqAPI. FastqAPI was only used by BALSAMIC, and contained one method. The method is now moved to FastqHandler class.

Fixed
- Create crunchy pending path outside batch script

Fixed
- support current orderform RML-1604:9 again

Changed
- Use long description from setup.py on PyPI

Fixed
- Use another parameter in build and publish

Added
- Build and publish on pypi with github actions

[12]
Added
- Create a meta-API (BalsamicAnalysisAPI) to handle communication between balsamic and other cg applications. The API will handle the following:
- Calling BalsamicAPI to execute balsamic commands
- Query Lims and StatusDB to decide what arguments to pass to Balsamic
- Read (new version of) deliverables report generated by Balsamic and store bundle in Housekeeper + StatusDB
- More info in https://github.com/Clinical-Genomics/cg/pull/687

Changed
- Reduce number of options that can/should be passed to run the workflow. Most of the logic for determining the options will be handled by BalsamicAnalysisAPI.
- Every command now requires sample family name as argument.
- No longer support using sample_id to link files for sake of consistency.

[11]
Changed
- Removes all interactions with the beacon software