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Commits on Mar 4, 2026

• [Zip_Column_Content] Resolve overwriting of identical filenames (#1009)

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• [AMRsearch] Parse Resistance Outputs (#1002)

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• [Snippy_Streamline] Expose snp_dist resource inputs (#1012)

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Commits on Mar 3, 2026

• [Microreact] Adding New Workflow, Microreact_Export (#937)

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Commits on Mar 2, 2026

• [iVar Version] Include iVar Consensus Version in assembly_method (#1011)

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Commits on Feb 17, 2026

• update stxtyper to 1.0.45 (#1004)

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• [KSNP4] Increase Memory to 16 GB (#1010)

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Commits on Feb 3, 2026

• [Pilon] Expose Pilon Version (#1001)

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Commits on Jan 29, 2026

• set nextclade outputs to be generic (#997)

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Commits on Jan 28, 2026

• [Flu Track] Expose and deinterleave IRMA aligned reads (#990)

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• [Basespace_Fetch] Extending grep -E to project ID track (#981)

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Commits on Jan 5, 2026

• [IQ-TREE] Specificity of Parameters (#979)

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Commits on Nov 24, 2025

• [Morgana_Magic] Include missing value propagation (#955)

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Commits on Nov 18, 2025

• [Morgana_Magic] Exposing inputs from characterization tasks (#954)

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Commits on Nov 12, 2025

• [TheiaViral_Panel] Create a panel compatible viral assembly pipeline for species level identification and extraction utilizing TheiaViral_Illumina_PE (#920)

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Commits on Nov 6, 2025

• [Morgana_Magic] Implementation of Morgana Magic into TheiaCov Workflows (#931)

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Commits on Nov 3, 2025

• [Basespace_Fetch] Bolstering Grep Functionality (#934)

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Commits on Oct 1, 2025

• [Basespace_Fetch] Add handling to Basespace_Fetch when separators are discrepant (#929)

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Commits on Sep 12, 2025

• [Bakta] Change Boolean Input to Correct File Designation (#918)

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Commits on Sep 3, 2025

• [ECTyper] Update to 2.0.0 with added outputs and documentation updates (#847)

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Commits on Aug 26, 2025

• [Nextclade] Update Nextclade to v3.16.0 and update dataset tags (#907)

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Commits on Aug 20, 2025

• [Mercury_Prep_N_Batch] Updating Mercury Version; Exposing Bankit files and changing metadata to a TSV (#904)

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Commits on Aug 19, 2025

• [AMRFinderPlus] Update to database version 2025-07-16.1 (#902)

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Commits on Aug 14, 2025

• [AMRFinderPlus] Alphabetize gene outputs for AMRFinderPlus string outputs (#897)

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Commits on Jul 17, 2025

• doc update (#880)

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Commits on Jul 16, 2025

• [Versioning] Updating PHB Version (#876)

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• [Taxon Tables] Sync Taxon Tables (#877)

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Commits on Jul 15, 2025

• [TS_MLST] Refactor of E coli, A baumannii secondary scheme selection and scheme override (#873)

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Commits on Jul 2, 2025

• [TS_MLST] Bug fix - Error in concatenation when file missing (#867)

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Commits on Jun 27, 2025

• [TheiaProk] Additions to TheiaProk requested during OH onboarding (#846)

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Commits on Jun 17, 2025

• [IRMA] Allow for soft failure of IRMA when assembly isn't created (#857)

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• [Nextclade & Measles] Adding Measles functionality to TheiaCov (#855)

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Commits on Jun 12, 2025

• [AMRFinder] AMRFinder update to v4.0.23 and database v2025-06-03.1 (#854)

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Commits on Jun 10, 2025

• [Nextclade] Version and DS tag update (#850)

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Commits on Jun 2, 2025

• stxtyper docker update with doc update (#840)

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