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39 Open 212 Closed
39 Open 212 Closed
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Issues list

Kraken disk/network overload improvement
#425 opened May 5, 2025 by LordRust
Dubious ownership error when updating databases managed as submodules bug Something isn't working high High priority
#424 opened Apr 28, 2025 by mhkc Version 1.1.0
1
@ryanjameskennedy
Take another look at pubmlst updating script bug Something isn't working high High priority
#422 opened Apr 14, 2025 by ryanjameskennedy Version 1.2.0
add variant caller suitable for LR
#420 opened Mar 28, 2025 by Emkago Version 1.2.0
@Emkago
1
adapt prp to report results from LR analysis improvement WIP Work in progress
#419 opened Mar 28, 2025 by Emkago
2 of 4 tasks
Version 1.2.0
@Emkago
Change args to Virulancefinder medium Medium priority
#416 opened Mar 18, 2025 by Emkago Version 1.2.0
@Emkago
3
Make args to Flye species specific improvement medium Medium priority
#415 opened Mar 18, 2025 by Emkago
Add Gambit to streptococcus pipeline high High priority improvement
#413 opened Mar 18, 2025 by ryanjameskennedy Version 1.1.0
1
@ryanjameskennedy
Change kpneumoniae cgmlst scheme to pasteur scheme improvement medium Medium priority
#405 opened Feb 18, 2025 by ryanjameskennedy Version 1.4.0
@ryanjameskennedy
Add kleborate to kpneumoniae workflow medium Medium priority new analysis
#404 opened Feb 18, 2025 by ryanjameskennedy Version 1.4.0
@ryanjameskennedy
Separate everything into subworkflows improvement medium Medium priority
#402 opened Feb 17, 2025 by ryanjameskennedy Version 1.1.0
1
@ryanjameskennedy
Create one base config whereby user specified configs can be imported to via profiles improvement medium Medium priority
#401 opened Feb 16, 2025 by ryanjameskennedy Version 1.1.0
1
@ryanjameskennedy
Add module/method that takes in kraken results and appends relevant species files for streptoccocus improvement medium Medium priority
#400 opened Feb 14, 2025 by ryanjameskennedy Version 2.0.0
@ryanjameskennedy
Move configs to separate repo improvement
#393 opened Feb 3, 2025 by mhkc Version 1.4.0
@ryanjameskennedy
1
New version of AMRFinder database and software high High priority improvement
#382 opened Jan 17, 2025 by samuell Version 1.3.0
@ryanjameskennedy
Cleanup config files and duplicated code improvement medium Medium priority
#365 opened Nov 5, 2024 by ryanjameskennedy Version 1.1.0
1
@ryanjameskennedy
Add FoHM mutations to TBProfiler high High priority improvement
#363 opened Oct 29, 2024 by ryanjameskennedy Version 1.3.0
@ryanjameskennedy
Create subrun command to partially run jasen modules improvement medium Medium priority
#355 opened Oct 3, 2024 by ryanjameskennedy Version 1.4.0
@ryanjameskennedy
Download medaka models improvement medium Medium priority
#341 opened Aug 22, 2024 by Emkago Version 1.5.0
@samuell @Emkago @ryanjameskennedy
1
Add pHierCC module for Enterobase related actions improvement medium Medium priority
#339 opened Aug 15, 2024 by ryanjameskennedy Version 1.3.0
@ryanjameskennedy
Add profile for Borrelia new analysis
#328 opened Jun 26, 2024 by ryanjameskennedy
@ryanjameskennedy
Makefile core usage argument improvement low Low priority
#326 opened Jun 14, 2024 by sylvinite
@samuell @sylvinite
Add profile for Pseudomonas aeruginosa new analysis
#306 opened May 21, 2024 by samuell
@samuell
Add profile for Acinetobacter baumannii new analysis
#305 opened May 21, 2024 by samuell
@samuell
Add profile for Enterococcus faecium new analysis
#303 opened May 21, 2024 by samuell
@samuell
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