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44 Open 315 Closed
44 Open 315 Closed
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Issues list

basespace_fetch enhancement - set default for api_server input
#775 opened Mar 13, 2025 by kapsakcj
Expose seqsero2 "Potential inter-serotype contamination" to the data table
#774 opened Mar 13, 2025 by cimendes
Standalone Workflow for Centroid
#773 opened Mar 13, 2025 by michellescribner
Raise Salmonella serogroup to table-level output
#772 opened Mar 12, 2025 by ArieDash
1
Updates to non-SC2 pathogen list and barcodes location
#770 opened Mar 11, 2025 by ss43
snippy_streamline expose optional runtime parameters; increase default ram on 1 task
#765 opened Feb 26, 2025 by kapsakcj
Terra to ENA workflow
#753 opened Feb 7, 2025 by AndrewLangvt
@Michal-Babins
Freyja_FASTQ_PHB request - ability to provide GFF as input
#752 opened Feb 7, 2025 by kapsakcj
1
@awh082834
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
2
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
[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
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