Release 2.2.1 #662
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Release 2.2.1 #662
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* Added PORTAL_RELEASE.md * Added automated_pipeline.drawio * Added Star Alignment, Oncoanalyser and TSO ctDNA how to * Improved Tumor/Normal, Transcriptome, umccrise, RNAsum how to * Updated and sync OpenAPI swagger docs * Bumped localstack v3 * Improved README and IAM docs
Updated documentation
Updated PORTAL_RELEASE.md documentation
* Enforced BSSH Run ID and Instrument Run ID requirement as Lambda payload contract * Deprecated singular linkage service method between LibraryRun <> Workflow i.e. `libraryrun_srv.link_library_runs_with_workflow(library_id: str, workflow: Workflow)` * Refactored to use SequenceRun cross over method for linkage `link_library_runs_with_x_seq_workflow(...)` * Adjusted and improved affected integration test cases * Removed redundant assertions from star_alignment handler
Improved TSO ctDNA Lambda handler
* Reduced required fields to allow more use cases
* Improved automated_pipeline.drawio * Added Lab Metadata Tracking new sheet process
Updated documentation
* Do not submit transcriptome workflow job just alone with metadata into the channel. Guard corresponding FastqListRow must not empty. * Guarded the use case with unit test * Improved integration tests Resolved #655
* Pull up high level Q/A notes on what automation do with topup and rerun library, PTC/NTC samples, Lab Metadata new sheet procedure, ctTSO run dir dependency caveat.
* Bumped minor dev dependencies * Resolved https://github.com/umccr/data-portal-apis/security/dependabot/44
Fixed transcriptome orchestration step skip if FastqListRow empty
Improved Pipeline Automation documentation
Bumped dependencies
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See milestone 2.2.1