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39 Open 314 Closed
39 Open 314 Closed
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Issues list

Terra to ENA workflow
#753 opened Feb 7, 2025 by AndrewLangvt
Freyja_FASTQ_PHB request - ability to provide GFF as input
#752 opened Feb 7, 2025 by kapsakcj
3
BioProject Accession Output Column for Terra_2_NCBI_PHB
#745 opened Feb 3, 2025 by frankambrosio3
1
[theiaProk] Combine shovill_se and shovill_pe into a single task shovill that can handle both input types
#738 opened Jan 24, 2025 by cimendes
[TheiaProk] Update mlst task to use docker image incl. Providencia spp. scheme & DB
#714 opened Jan 8, 2025 by kapsakcj
1
Dorado basecalling workflow enhancements
#713 opened Jan 8, 2025 by fraser-combe
2
@fraser-combe
2
[feature request - TheiaProk] output fastp JSON report
#698 opened Dec 18, 2024 by kapsakcj
[TheiaProk_ONT] Artic 1.5.1 onwards no longer supports medaka & moved to clair3
#697 opened Dec 18, 2024 by Michal-Babins
1
@Michal-Babins
[TheiaProk wfs] upgrade StxTyper version when available & ensure all OPERON output types are captured appropriately
#694 opened Dec 16, 2024 by kapsakcj
1
@fraser-combe
5
[Freyja] Remove lineage file if not SARS-CoV-2
#688 opened Dec 11, 2024 by Michal-Babins
2
Update BUSCO to v5.8.2 to avoid potential errors with missing reference files
#687 opened Dec 10, 2024 by sam-baird
@sage-wright
2
Increase min depth of coverage for Flu assembly using IRMA
#676 opened Nov 19, 2024 by molly-hetheringtonrauth
1
@sage-wright
7
[theiaprok] upgrade amrfinderplus to latest version that includes stxtyper & db update
#672 opened Nov 7, 2024 by kapsakcj
6
[feature request] add support for SRS accession and other kinds of accessions in SRA_Fetch workflow
#664 opened Oct 30, 2024 by kapsakcj
GAMBIT misclassified genome Klebsiella/E. coli
#663 opened Oct 30, 2024 by michellescribner
1
[TheiaProk] upgrade ANI database to RGDv3 to match PN2.0 enhancement This issue is a new feature or request standby This issue is waiting for resources to be worked on
#649 opened Oct 17, 2024 by kapsakcj
4 tasks
1
[Terra_2_NCBI] Fail workflow if so samples are successful
#645 opened Oct 9, 2024 by cimendes
1
[TheiaProk - Kleborate] Only run for Klebsiella pneumoniae
#632 opened Sep 27, 2024 by cimendes
1
[New workflow] TheiaEuk_ONT
#625 opened Sep 18, 2024 by cimendes
1
@cimendes @Michal-Babins
[TheiaProk] Add QC threshold functionality to export_taxon_tables optional task enhancement This issue is a new feature or request
#620 opened Sep 16, 2024 by kapsakcj
1
[TheiaProk] Output salmonella serogroup as additional column (SISTR)
#618 opened Sep 13, 2024 by kapsakcj
2
[theiaprok & theiaeuk] output GAMBIT distance & distance threshold to Terra data table
#613 opened Sep 11, 2024 by kapsakcj
2
[PHB - TheiaProk_ONT - DragonFlye ] Move away from wrapped tools for complex tasks such assembly bug This issue is a bug: something doesn't work right enhancement This issue is a new feature or request work on me! This issue can be worked on and needs assignment
#565 opened Jul 31, 2024 by cimendes
1
@fraser-combe
2
Make new workflow compatible with Illumina VSP (Viral Surveillance Panel)
#553 opened Jul 24, 2024 by sage-wright
1
@cimendes @sage-wright
[TheiaProk and TheiaMeta] Add CheckM for assembly QC (completeness and contamination)
#476 opened May 17, 2024 by cimendes
ProTip! Exclude everything labeled bug with -label:bug.