Bump staging to f654f6

[github-actions]

@maverbiest wants to update the staging deployment from pathoplexus/pathoplexus@8b8f81a to pathoplexus/pathoplexus@f654f62.

Commit date: 2026-09-18T11:34:43Z

Changelog

• feat: enable raw reads on Pathoplexus pathoplexus#1105
• feat: enable s3, add sealed secrets pathoplexus#1147
• Update Loculus version to 4d0ce6 pathoplexus#1148
• Revert "feat: enable files on PPX, add embl annotation files, reprocess everything" pathoplexus#1146
• feat: enable files on PPX, add embl annotation files, reprocess everything pathoplexus#1142
• Update Loculus version to c8edd2 pathoplexus#1144

Comparison

pathoplexus/pathoplexus@8b8f81a...f654f62

Pre-merge checklists

Before merging this PR and bumping the staging version, clone the production database to staging and confirm this was successful:

• DB clone: ssh bastion "cd pathoplexus/scripts/db-clone/ && ./clone-prod-to-staging.sh"
• Restart staging backend: kubectl rollout restart deployment/loculus-backend -n staging
• Run regressions tests to confirm staging is now identical to production (you will need to wait for SILO pods to import any new data)

Post-merge checklists

After merging this PR, work through these checks (or provide justification for anything that was skipped) to confirm functionality and data integrity of Pathoplexus under the new version.

Standard checklist:

• Run regression tests, highlight any observed differences and discuss why they are expected. If the new version includes new preprocessing pipeline versions: wait for reprocessing to finish and for all new SILO pods to come up first
• Confirm submit/revise/revoke flow works (also pay close attention to the UI, document anything out of the ordinary):
  • Submit test data to the staging preview
    • Confirm submission goes through (paste AccessionVersion(s) here)
  • Revise a test sequence (paste AccessionVersion here)
    • Confirm revision goes through
  • Revoke a test sequence (paste AccessionVersion here)
    • Confirm revocation goes through

Rollout-specific checklist:

Document any checks that were performed to test newly added features, database surgeries, etc. here.

[maverbiest]

Closing so we can roll out pathoplexus/pathoplexus#1151 as well