What’s changed:

Bug Fixes

• This patch release fixes an overly-ambitious attempt to prevent silent errors that actually caused a silent error in TheiaProk_ONT:
  • When Illumina reads were provided for TheiaProk_ONT assembly polishing, the workflow would fail in the bwa_all task due to a silent error in how we captured the versioning information for BWA. This has been fixed, so you can now polish your ONT assemblies with Illumina data to your heart’s content.
• A bug in Dorado_Basecalling (when the number of chunks equaled the number of POD5 files) has been fixed.
• Ash O’Farrell fixed a bug in the the tbp-parser task that prevents division by zero when a sample has extremely low coverage. Thanks, Ash!
• The tbp_parser_min_frequency and tbp_parser_min_percent_coverage variables are appropriately Floats and not Integers. You can provide as many decimals as you want now (but only one per value, in accordance with the rules of math).

Future Proofing

• We’ve made a few changes to our workflows to permit compatibility with Terra changing to use the Google Batch API (see the details regarding these changes from Terra here).
  • Please note: We’ve noticed a few task failures due to memory when using the Google Batch API that previously succeeded with the LifeSciences API (the current version of Terra). If you are testing Terra with Google Batch and run into unanticipated errors, please let us know.
• We have ended developmental support for the Nullarbor_PHB workflow. This workflow will be available for PHB v3.0.0 and below in perpetuity but will no longer be updated.

Other Updates

• The AMR_Search task has been added to the TheiaProk and TheiaEuk workflows! To run AMR_Search, set the new input parameter run_amr_search to True.
  • Please note: AMR_Search will only be run if the sample is one of the following organisms (determined either by the user with expected_taxon or by GAMBIT taxon identification):
• The following Docker images have been updated:
  • AMRFinderplus → us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:4.0.19-2024-12-18.1
  • MLST → us-docker.pkg.dev/general-theiagen/staphb/mlst:2.23.0-2024-12-31
  • tbp-parser → us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.4.5
  • Pangolin → us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.33
• Various documentation updates have been made and broken links fixed.

User instructions:

• Change version to v3.0.1!
• Click “Use defaults” on the Outputs tab.

We treat patch releases just the same as major releases. You can feel confident knowing that we carefully validate the results to make sure there’s no unintended differences between versions.