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v4.0.0: Async indexing, service token

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@OrdiNeu OrdiNeu released this 05 Mar 20:56
· 131 commits to develop since this release
02c1c93

Summary of Changes

  • Indexing changed to asynchronous task
  • Adds service token support for Query
  • Switched to hg38 for integration tests
  • Query beacon results only return authorized results now

What's Changed

  • DIG-1382, DIG-1384: query uses a service token with htsget by @daisieh in #282
  • Switch hg37 to hg38 for the integration tests by @OrdiNeu in #283
  • DIG-1459: Async indexing by @daisieh in #285
  • DIG-1376 :Update GH Action to improve PR title and description by @mshadbolt in #286
  • DIG-1463: Verify existence of genomic files by @daisieh in #287
  • Reverting #239: Remove variantfile's optional genomic_id field by @daisieh in #288
  • Fix Dispatch Action by @mshadbolt in #289
  • DIG-1486, DIG-1487: Informative handling of indexing failures by @daisieh in #290
  • Wait for indexing before continuing the test_index_variantfile test by @OrdiNeu in #291
  • bug fix: when forcing indexing, mark the indexed bit as 0 by @daisieh in #292
  • hotfix: biosampleId includes cohort, as documented in beacon yaml by @daisieh in #294
  • DIG-1404: add variants and reads to sample by @daisieh in #293
  • DIG-1511: Query beacon results should only return authorized results by @daisieh in #295

New Contributors

Full Changelog: v3.1.0...v4.0.0