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Download monthly annotations#9

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MattWellie merged 5 commits intomainfrom
download_monthly_annotations
Jan 13, 2026
Merged

Download monthly annotations#9
MattWellie merged 5 commits intomainfrom
download_monthly_annotations

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@MattWellie MattWellie commented Jan 9, 2026

Purpose

  • Coupled with Update mitoreport to v1.2.3 images#270
  • Uncoupled - the latest version of mitoreport has some VCGS/MCRI-specific integrations which prevent us upgrading, this solution will work on the older software version

Proposed Changes

  • While we're updating the MitoReport image, we can remove the once-on-build annotation update from the image, and move that into a monthly process
  • This PR proposes a generic location "gs://cpg-common-main/mitoreport_ref/YYYY-MM/mito_map_annotations.json"
  • Each time the workflow runs, this first step will trigger if the file doesn't exist for the current month. The Stage will generate and upload a new reference bundle, and that will be passed into the MitoReport job.

n.b. if we pursue this we should remove the annotation download from the base image, push version 1.2.3, then update the default config file here. optional - this would override/ignore the default location anyway, so no explicit removal would be required

Checklist

  • Related GitHub Issue created
  • Tests covering new change
  • Linting checks pass

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@EddieLF EddieLF left a comment

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Approving after tests.

Run where Mitomap annotations needed downloading for the first time:
https://batch.hail.populationgenomics.org.au/batches/1124000

Run where Mitomap annotations were re-used:
https://batch.hail.populationgenomics.org.au/batches/1124002

@MattWellie MattWellie merged commit efdfc85 into main Jan 13, 2026
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@MattWellie MattWellie deleted the download_monthly_annotations branch January 13, 2026 00:02
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2 participants