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Pull requests: theiagen/public_health_bioinformatics
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[Taxon_Table] resync taxon_tables inputs
#762
by xonq
was merged Feb 20, 2025
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10 of 15 tasks
[Documentation] improve new workflow template
#760
by sage-wright
was merged Feb 18, 2025
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3 of 8 tasks
[kSNP4] Add new task/workflow for phylogenetic/SNP analysis
#759
by MrTheronJ
was merged Feb 20, 2025
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8 of 11 tasks
Updates Flu Antiviral Resistance Detection Documentation
#758
by frankambrosio3
was merged Feb 14, 2025
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3 of 8 tasks
[TheiaProk] improve export taxon table functionality
#757
by sage-wright
was merged Feb 18, 2025
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9 of 11 tasks
[Read_Screen] BUG fix $ to ~ reference for workflow series
#754
by xonq
was merged Feb 7, 2025
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5 of 11 tasks
[Standardization] Standardizing the language behind percent identity and coverage
#751
by awh082834
was merged Feb 13, 2025
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11 tasks done
[NCBI Datasets] Add ability to download from ncbi viral datasets
#748
by Michal-Babins
was merged Feb 5, 2025
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5 of 11 tasks
[Merlin_magic; Sonneityping] harden workflow against failures due to sonnei typing disagreement
#747
by awh082834
was merged Feb 7, 2025
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5 of 11 tasks
[Freyja] Expose additional outputs and parse demixed output file for easy downstream concatenation
#746
by cimendes
was merged Feb 14, 2025
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5 of 11 tasks
[Snippy_Streamline] when
include_gbff
is true, use the GBFF file as the reference
#744
by sage-wright
was merged Feb 5, 2025
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11 tasks done
[Augur] Fix issue with empty clades.tsv file in augur_clades task
#742
by MrTheronJ
was merged Feb 6, 2025
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11 tasks done
[Taxon_Tables] Synchronize task_broad_terra_tools.wdl with current workflow outputs
#741
by xonq
was closed Feb 13, 2025
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9 of 15 tasks
[Bakta] update to latest version full and light db
#740
by fraser-combe
was merged Feb 11, 2025
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5 of 11 tasks
[Read_Screen] Comprehensively run QC checks regardless of failure status then output results
#736
by xonq
was merged Feb 6, 2025
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36 of 37 tasks
[Snippy Variants] Preserve current memory allocation & add error handling to prevent silent failures
#734
by MrTheronJ
was merged Jan 24, 2025
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10 of 11 tasks
[Reorder Matrix] Changed output file name to more general {cluster}_distance_matrix.csv
#733
by awh082834
was merged Jan 24, 2025
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5 of 11 tasks
[Documentation - Freyja] Update and revamp documentation to focus on non-SC2 organisms
#732
by cimendes
was merged Jan 27, 2025
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1 of 11 tasks
[Resource optimization] Set default Prokka resources to 4 CPUs and 16 GB Memory
#728
by awh082834
was merged Jan 17, 2025
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10 of 11 tasks
[TheiaEuk_Illumina_PE] Update to newest gambit fungal v1.0.0
#727
by Michal-Babins
was merged Feb 13, 2025
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5 of 11 tasks
[srst2_vibrio, merlin_magic] Removed instances of srst2_ from inputs
#726
by awh082834
was merged Jan 16, 2025
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11 tasks done
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