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@clingen-sthlm clingen-sthlm released this 23 Jun 11:56
v71.2.0
0a46624

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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