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@v-rocheleau v-rocheleau commented May 8, 2025

Remove the DRS bridge volume from Gohan, as required for object storage.

Note that this still works with DRS/Drop-Box in local or S3 mode.

Rather than exchanging files from shared persistent volumes, gohan now downloads and uploads the files it needs over the network only.

Gohan's /ingest endpoint now accepts Drop-Box object paths:

  1. Downloads the VCF to a temp location: /app/vcfs/<name>.vcf.gz
  2. Generates a tabix file to a temp location: /app/vcfs/<name>.vcf.gz.tbi
  3. Upload files to DRS (bridge-less)
  4. Process VCFs
  5. Remove temp files

Other changes

  1. fix: vcf ingestion WDL workflow returns non zero code if an ingestion status has an error, fixes silent workflow errors
  2. tests: drop-box is now part of the integration tests

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@davidlougheed davidlougheed left a comment

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lgtm!

@v-rocheleau v-rocheleau merged commit 55deb25 into master Sep 2, 2025
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3 participants