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AustralianBioCommons / atol-canopy Public

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feat: update reporting process for qc reads and assembly pipelines (rebased)#29

Merged

emilylm merged 16 commits into

mainAustralianBioCommons/atol-canopy:mainfrom

update-reporting-process-rebaseAustralianBioCommons/atol-canopy:update-reporting-process-rebaseCopy head branch name to clipboard

Jun 9, 2026

Conversation Commits16 (16)Checks Files changed

Merged

feat: update reporting process for qc reads and assembly pipelines (rebased)#29
emilylm merged 16 commits into
mainfrom
update-reporting-process-rebase

Commits

Commits on Jun 9, 2026

feat: add assembly_run abstraction, referencing unique github_repo + git_commit pair
emilylm
committed
feat: add source reads to qc_reads
emilylm
committed
feat: add source reads to qc_reads
emilylm
committed
feat: add source reads to qc_reads
emilylm
committed
feat: add source_read_file_checksums to qc_reads, validating this and bpa_package_id
emilylm
committed
fix: fix migration, specimen lookup and add logging
emilylm
committed
style: linting
emilylm
committed
feat: update qc_read_file fields
emilylm
committed
fix: fix migration
emilylm
committed
feat: make assembly runs unique on github_repo + git_commit, and improve debugging
emilylm
committed
feat: make assembly runs unique on github_repo + git_commit, and improve debugging
emilylm
committed
feat: add taxon_info rows iff ncbi fetch succeeds, log ncbi failures in taxon_info/bulk-insert
emilylm
committed
feat: updates assembly stage run to rmv "status" and rename "stats" to "data"
emilylm
committed
feat: refactor migrations
emilylm
committed
feat: remove external_run_id from stage_runs
emilylm
committed
feat: returns meaningful error for duplicate reports - same stage and assembly run
emilylm
committed

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