theiagen public_health_bioinformatics issues

theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

GNU General Public License v3.0

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issues

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[experimental] Adds stxtyper to merlin_magic and TheiaProk wfs

#525 kapsakcj opened 21 hours ago
0
[TheiaProk] Add emmtyper task for Streptococcus pyogenes

#524 sam-baird opened 1 day ago
0
[feature request] for Flu samples with no AA_dels or subs; output None instead of NA

#523 kapsakcj opened 1 day ago
0
Enable H5N1 in TheiaCoV & Augur

#522 AndrewLangvt opened 2 days ago
0
update default pangolin docker (pdata 1.27) & nextclade dataset tags for SC2, Flu, Mpox

#521 kapsakcj closed 4 days ago
2
[TheiaCoV] Update kraken2 viral database to fix weird RSV-B nomenclature

#520 cimendes opened 5 days ago
0
Fix typo in Terra_2_NCBI Wastewater metadata

#519 michellescribner closed 5 days ago
0
theiameta output krona plots showing incorrect taxids

#518 kapsakcj opened 1 week ago
0
[all workflows] upgrade PHB version to 2.1.0

#517 kapsakcj closed 4 days ago
2
[TheiaProk] upgrade mlst docker image to 2024-06-01 staphb build; reduced runtime parameters; enable preemptible

#516 kapsakcj closed 4 days ago
2
[TheiaMeta] krona bugfix for NCBI taxon IDs & reduce compute resources

#515 kapsakcj opened 1 week ago
0
[TheiaProk] Update amrfinderplus to v3.12.8; DB: v2024-05-02.2; reduce compute resources

#514 kapsakcj closed 4 days ago
1
update versioning task to v2.1.0

#513 kapsakcj closed 4 days ago
0
[SRA-Fetch] Detect SRA-Lite when it's low quality file

#512 cimendes opened 1 week ago
0
[Release] Update amrfinderplus database for June 2024

#511 cimendes closed 4 days ago
4
[Release] Update mlst database for June 2024

#510 cimendes closed 4 days ago
0
[Documentation] Major update and polishing on Augur documentation in preparation for next release

#509 cimendes opened 1 week ago
1
[TheiaProk] expose hicap outputs in theiaprok_fasta and theiaprok_ont

#508 cimendes closed 1 week ago
1
add `percentage_mapped_reads` output to TheiaCoV wfs

#507 kapsakcj opened 2 weeks ago
0
[Mercury_Prep_N_Batch] Enable flu compatibility and move Mercury into its own GitHub repository

#506 sage-wright opened 2 weeks ago
0
[AMRFinderPlus] parse BETA-LACTAM genes and subclasses into individual output columns

#505 sage-wright closed 1 week ago
1
Beta-Lactam Parsing

#504 sage-wright closed 1 week ago
0
Augur_PHB: Set sample_metadata_tsvs input to optional

#503 jrotieno closed 1 week ago
4
[TheiaCoV_Illumina_PE & _ONT] Create sub-workflow for flu-specific modules

#502 sage-wright closed 1 week ago
3
[TheiaCoV] Enable user to run TheiaCoV with an unsupported organism

#501 sage-wright closed 2 weeks ago
2
allow for non-standardized organisms in TheiaCoV wfs & organism_parameters subwf

#500 kapsakcj closed 2 weeks ago
1
Add mutation context to Augur_PHB for Mpox

#499 emily-smith1 opened 3 weeks ago
2
Automatically convert spaces to dashes in workflows that accept strings

#498 AndrewLangvt closed 2 weeks ago
4
[Reorder Matrix Task] Remove A1 cell for compatibility with MicrobeTrace

#497 cimendes closed 3 weeks ago
0
[kSNP3] fix behaviour when phandango colouring is set to false

#496 cimendes closed 3 weeks ago
1
Create Terra_2_NCBI metadata formatter for Wastewater biosample package

#495 michellescribner opened 4 weeks ago
0
[Internal] Updating runtime parameters

#494 sage-wright closed 3 weeks ago
4
Make MIDAS optional in TheiaProk

#493 andrewjpage closed 3 weeks ago
2
Make busco preemptible

#492 andrewjpage closed 3 weeks ago
0
Update check-reads to use less CPUs

#491 andrewjpage closed 3 weeks ago
0
Check cg-pipeline CPUs used

#490 andrewjpage closed 3 weeks ago
0
Reduce Gambit task resource requirements

#489 andrewjpage closed 3 weeks ago
0
Check RAM Midas uses

#488 andrewjpage closed 3 weeks ago
1
ksnp3 doesn't have CPUs passed in

#487 andrewjpage closed 3 weeks ago
1
Check resource usage for hostile-pe

#486 andrewjpage opened 1 month ago
0
shovill-pe CPUs not set in task

#485 andrewjpage closed 3 weeks ago
0
Refine memory and cpus for frequent tasks

#484 andrewjpage closed 1 month ago
2
Change version_capture container

#483 andrewjpage closed 3 weeks ago
0
[Freyja_Dashboard] fix typo in freyja_dashboard output File variable name

#482 AndrewLangvt closed 1 month ago
1
Add RSV to the Augur workflow

#481 jrotieno closed 3 weeks ago
0
[SRA-Fetch] Add additional check for SRA-Lite format when reads are marked as "reject"

#480 cimendes opened 1 month ago
0
[SRA-Fetch] Reimplement using fasterq-dump directly to avoid SRA-Lite file download

#479 cimendes opened 1 month ago
1
Augur Updates for RSV-A and RSV-B

#478 jrotieno closed 3 weeks ago
1
Snippy_Variants: Calculate % reads aligned

#477 emmadoughty opened 1 month ago
0
[TheiaProk and TheiaMeta] Add CheckM for assembly QC (completeness and contamination)

#476 cimendes opened 1 month ago
0