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Ran 23 Jun 2025 11:58AM UTC

Files 835

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Committed 23 Jun 2025 11:56AM UTC coverage: 85.752% (-0.07%) from 85.824%

Job # 15823539042.1

Build Type

push

github

Committed by

web-flow

Commit Message

Fix(Start query) Harmonize cases to start query (#4443)(minor)

## Description
This PR harmonises the logic for getting which cases should be analysed. I removes all the special logic for Balsamic and MIP-DNA and centralises the logic to the database layer.

### Important changes:
- microSALT is now explicitly treated as an exception, and is the only pipeline that will start automatically if allready analysed but new data is added.

- The start-available command no longer performs the SeqeuencingQC check. Instead it just queries the `case.aggregated_sequencing_qc` column in the database. The command `cg sequencing-qc` runs the same logic on a timer, so the will be performed by this command instead.

### Changed

- Sequencing QC removed from start-available
- Sequencing QC added as a query filter in start-available
- Removed special `is_case_ready_for_analysis` from MIP-DNA and Balsamic
- Removed the extra `_is_case_to_be_analyzed` check in read.py

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