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88 Open 257 Closed
88 Open 257 Closed
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Issues list

[Bug - task_ivar_variant_call] Fix potential places for failure
#716 opened Jan 9, 2025 by Michal-Babins
@Michal-Babins
[TheiaProk] Update mlst task to use docker image incl. Providencia spp. scheme & DB
#714 opened Jan 8, 2025 by kapsakcj
Dorado basecalling workflow enhancements
#713 opened Jan 8, 2025 by fraser-combe
small docs typo
#711 opened Jan 6, 2025 by kapsakcj
1
[New Workflow] Clair3_variants
#707 opened Dec 30, 2024 by Michal-Babins
1
@Michal-Babins
[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
[TheiaProk wfs] (eventually) upgrade StxTyper version when available & ensure all OPERON output types are captured appropriately
#694 opened Dec 16, 2024 by kapsakcj
2
TheiaProk reports success on clean_check_reads but it has failed
#691 opened Dec 13, 2024 by andrewjpage
TheiaProk read screen reports success when it fails
#690 opened Dec 13, 2024 by andrewjpage
1
[Freyja] Remove lineage file if not SARS-CoV-2
#688 opened Dec 11, 2024 by Michal-Babins
Update BUSCO to v5.8.2 to avoid potential errors with missing reference files
#687 opened Dec 10, 2024 by sam-baird
2
make skip screen actually skip the task
#677 opened Nov 26, 2024 by sage-wright
1
@sage-wright
Increase min depth of coverage for Flu assembly using IRMA
#676 opened Nov 19, 2024 by molly-hetheringtonrauth
@sage-wright
1
[theiaprok] upgrade amrfinderplus to latest version that includes stxtyper & db update
#672 opened Nov 7, 2024 by kapsakcj
[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
[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
[All workflows] Create tasks to summarise version-control results such as docker and software version
#639 opened Oct 2, 2024 by cimendes
[TheiaMeta] Improve documentation
#638 opened Oct 1, 2024 by cimendes
@cimendes
1
[Augur wf] Potential bug with augur_clades call block conditional run_traits
#633 opened Sep 27, 2024 by kapsakcj
6
[TheiaProk - Kleborate] Only run for Klebsiella pneumoniae
#632 opened Sep 27, 2024 by cimendes
[TheiaProk] Update Kleborate to v3
#631 opened Sep 27, 2024 by cimendes
[New workflow] Rabies analysis workflow
#626 opened Sep 18, 2024 by michellescribner
@cimendes
ProTip! What’s not been updated in a month: updated:<2024-12-11.