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29 Open 197 Closed
29 Open 197 Closed
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Issues list

New version of AMRFinder database and software high High priority improvement
#382 opened Jan 17, 2025 by samuell General pipeline
@ryanjameskennedy
Add spa-type analysis to Nanopore track improvement medium Medium priority
#375 opened Nov 25, 2024 by Emkago Nanopore
@Emkago
Cleanup config files and duplicated code improvement medium Medium priority
#365 opened Nov 5, 2024 by ryanjameskennedy General pipeline
@ryanjameskennedy
Add FoHM mutations to TBProfiler high High priority improvement
#363 opened Oct 29, 2024 by ryanjameskennedy TB
@ryanjameskennedy
Add postal code entry to "sample_list" file and provide in output improvement medium Medium priority
#356 opened Oct 16, 2024 by hrydbeck General pipeline
@ryanjameskennedy
Create subrun command to partially run jasen modules improvement medium Medium priority
#355 opened Oct 3, 2024 by ryanjameskennedy General pipeline
@ryanjameskennedy
Download medaka models improvement medium Medium priority
#341 opened Aug 22, 2024 by Emkago Nanopore
@samuell @Emkago @ryanjameskennedy
1
Add pHierCC module for Enterobase related actions improvement medium Medium priority
#339 opened Aug 15, 2024 by ryanjameskennedy Ecoli
@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 General pipeline
@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
Add profile for Enterococcus faecalis new analysis
#302 opened May 21, 2024 by samuell
@samuell
Check compatibility with Nanopore high High priority
#301 opened May 17, 2024 by Emkago Nanopore
@Emkago
2
Add species Neisseria gonorrhoeae low Low priority new analysis
#291 opened Apr 25, 2024 by fwa93
@ryanjameskennedy
4
Add general gram negative workflow improvement medium Medium priority
#286 opened Apr 11, 2024 by ryanjameskennedy General pipeline
@ryanjameskennedy
Add plasmid detection improvement medium Medium priority
#281 opened Apr 4, 2024 by ryanjameskennedy General pipeline
@ryanjameskennedy
Add trim adapters optional module improvement medium Medium priority
#280 opened Apr 4, 2024 by ryanjameskennedy General pipeline
@samuell @ryanjameskennedy
Prodigal training files are moved in Makefile but not in config files bug Something isn't working low Low priority
#279 opened Mar 26, 2024 by samuell General pipeline
@samuell
1
Create .fsa virulence gene file for K pneumoniae for virulencefinder_db to use improvement low Low priority
#208 opened Nov 1, 2023 by ryanjameskennedy Klebsiella pneumoniae
@samuell
Ensuring simultaneous JASEN runs don't collide re chewBBACA bug Something isn't working low Low priority
#191 opened Oct 10, 2023 by ryanjameskennedy Pipeline efficiency
@ryanjameskennedy
Intraspecies contamination check improvement medium Medium priority
#183 opened Sep 21, 2023 by LordRust Pipeline efficiency
@ryanjameskennedy
1
Update README to contain Nanopore medaka model table improvement low Low priority
#175 opened Sep 5, 2023 by ryanjameskennedy Nanopore
@Emkago
Add sanity checks in order to prevent pipeline termination errors bug Something isn't working good first issue Good issue to tackle for new contributors medium Medium priority
#161 opened Jul 11, 2023 by LordRust Pipeline efficiency
@ryanjameskennedy
ProTip! Exclude everything labeled bug with -label:bug.