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[TheiaProk - ANI] Make any fault resistant to when there are multiple top hits with the exact same score
#529
opened Jul 3, 2024 by
cimendes
[TheiaCoV SE] Implement human scrubbing of reads with HRRT to mirror TheiaCoV PE
#528
opened Jul 3, 2024 by
cimendes
[feature request] for Flu samples with no AA_dels or subs; output None instead of NA
#523
opened Jun 27, 2024 by
kapsakcj
[TheiaCoV] Update kraken2 viral database to fix weird RSV-B nomenclature
#520
opened Jun 24, 2024 by
cimendes
[Documentation] Major update and polishing on Augur documentation in preparation for next release
documentation
This issue asks for documentation changes
#509
opened Jun 18, 2024 by
cimendes
Create Terra_2_NCBI metadata formatter for Wastewater biosample package
#495
opened May 31, 2024 by
michellescribner
[TheiaCoV and TheiaMeta] Implement HOSTILE and Check resource usage for hostile-pe
#486
opened May 24, 2024 by
andrewjpage
[SRA-Fetch] Add additional check for SRA-Lite format when reads are marked as "reject"
#480
opened May 22, 2024 by
cimendes
[SRA-Fetch] Reimplement using fasterq-dump directly to avoid SRA-Lite file download
#479
opened May 22, 2024 by
cimendes
[TheiaProk and TheiaMeta] Add CheckM for assembly QC (completeness and contamination)
#476
opened May 17, 2024 by
cimendes
[New workflow - Internal] Gambit fastq for internal testing and evaluation
#472
opened May 16, 2024 by
cimendes
[feature request] output fastq-scan JSONs in all workflows that include it
#471
opened May 13, 2024 by
kapsakcj
[TheiaProk_ONT] Read QC Trim runtime parameters not exposed on Terra
#470
opened May 13, 2024 by
cimendes
[TheiaProk_ONT] Tun Tiptofts on downsampled samples instead of raw reads
#467
opened May 8, 2024 by
cimendes
output VADR annotations (esp. for Flu) & upgrade to VADR docker w/ new Flu model files
#464
opened May 7, 2024 by
kapsakcj
[SRA-Fetch] Output what version of the workflow was run, similar to TheiaCoV, TheiaProk, TheiaEuk
#451
opened May 2, 2024 by
cimendes
Prokka-Like Genome Annotation for Virus Genomes in the TheiaCoV Workflows
#450
opened May 2, 2024 by
jrotieno
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