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theiagen
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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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[TheiaProk] Have standalone abricate module with updated VFDB database
#430
cimendes
closed
2 months ago
1
[TheiaProk] Add abricate module for vibrio characterization
#429
cimendes
closed
1 week ago
5
[tbp-parser] update version
#428
sage-wright
closed
2 months ago
0
[TheiaProk] tbprofiler optimizations
#427
kapsakcj
opened
2 months ago
0
[TheiaCoV_ONT] adds the assembly_mean_coverage metrics for influenza HA and NA in the TheiaCoV_ONT
#426
cimendes
closed
1 month ago
0
[TheiaEuk] revert busco container to busco:v5.3.2_cv1 for theiaeuk
#425
cimendes
closed
2 months ago
0
[BUSCO] memory issue
#424
sage-wright
opened
2 months ago
0
[Kraken2] Expose what database was used on output table for SE, PE and ONT
#423
cimendes
closed
1 month ago
0
[Freyja_Dashboard] fix typo in freyja_dashboard output File variable name
#422
kapsakcj
closed
1 month ago
0
pangolin_update wf: hide unused input params for vadr
#421
kapsakcj
closed
2 months ago
0
[kSNP3] output SNP matrix headers
#420
frankambrosio3
closed
4 weeks ago
3
[Cauris_Cladetyper] Cladetyper outputs renaming
#419
frankambrosio3
opened
2 months ago
0
setting vadr_skip_length via organism_parameters subworkflow as this …
#418
kapsakcj
closed
2 months ago
3
theiacov_illumina_pe kraken output name change
#417
kapsakcj
closed
2 months ago
4
[Merlin_Magic] Expose all docker containers so they are available to be edited by the user
#416
cimendes
opened
2 months ago
0
pangolin_update wf bug fix and hiding one input param related to Flu and organism_parameters subwf
#415
kapsakcj
closed
2 months ago
3
update to latest nextclade_dataset release for SC2 `2024-04-15--15-08-22Z`
#414
kapsakcj
closed
2 months ago
1
[TheiaProk] Add emmtyper tool to GAS TheiaProk track
#413
cimendes
closed
2 days ago
3
[TheiaCoV] IRMA task runs out of disk space due to default TMP directory
#412
kapsakcj
closed
2 weeks ago
1
[PHB v2.0.0] update CI
#411
cimendes
closed
2 months ago
2
[PHB] Update version in preparation for next release
#410
cimendes
closed
2 months ago
0
[TheiaCoV] Isolate nextclade_v3 task for flu so that we can have outputs for HA and NA segments clearly identified
#409
cimendes
closed
1 week ago
0
Ensure compliance with the PHA4GE Best Practices
#408
sage-wright
closed
2 months ago
0
Comply with the PHA4GE Best Practices document!
#407
sage-wright
closed
2 months ago
0
add Flu NA Nextclade outputs to theiacov_illumina_pe
#406
kapsakcj
closed
2 months ago
5
Nextclade Flu NA outputs not populated to Terra data table
#405
kapsakcj
closed
2 months ago
0
Added output
#404
frankambrosio3
closed
2 months ago
1
TBProfiler add coverage report output file
#403
frankambrosio3
closed
2 months ago
0
[Kraken2] rename task call to just `kraken2` to harmonise inputs across all workflows
#402
cimendes
opened
2 months ago
0
update BUSCO to v5.7.1 and small tweaks to WDL task
#401
kapsakcj
closed
2 months ago
7
[Nextclade] consider adding back optional input "input-pcr-primers" for nextclade v3 task
#400
kapsakcj
opened
3 months ago
0
[Mercury_Prep_N_Batch] add state to country
#399
sage-wright
closed
2 months ago
2
[TheiaProk] Add abricate as optional module
#398
michellescribner
closed
1 month ago
0
[TheiaCoV] rework read screen task to no longer have organism-specific conditionals
#397
kapsakcj
closed
1 month ago
0
[Mercury_Prep_N_Batch] adjust GenBank parameter to say USA: [State] in accordance to new GenBank features
#396
sage-wright
closed
2 months ago
0
[TheiaProk] Add Vibrio cholerae sequence characterization for ONT
#395
michellescribner
closed
1 week ago
1
update default pangolin docker image to image with pangolin-data v1.26
#394
kapsakcj
closed
3 months ago
2
[Nextclade & TheiaCoV] remove tamiflu amino acid substitution detection since duplicated
#393
sage-wright
closed
3 months ago
3
Remove tamiflu outputs from nextclade
#392
sage-wright
closed
3 months ago
0
[TheiaProk] update ts_mlst docker image to latest release available (2024-03-11)
#391
cimendes
closed
3 months ago
1
update default pangolin docker prior to v2.0.0 release
#390
kapsakcj
closed
3 months ago
0
Set trimmomatic_args "-phred33" as default
#389
kapsakcj
closed
3 months ago
1
[QC Check] Squish bug when vadr_num_alerts is a String
#388
sage-wright
closed
3 months ago
1
[SRA_Fetch] Add task to detect if a file is SRA-Lite
#387
cimendes
closed
3 months ago
2
[TheiaCoV] Make the organism input mandatory in TheiaCoV workflow series
#386
cimendes
opened
3 months ago
0
bug fix to BaseSpace_Fetch_PHB
#385
kapsakcj
closed
3 months ago
1
Add VADR to flu and RSV TheiaCoV
#384
cimendes
closed
3 months ago
3
Fix dockstore yml for Find Shared Variants wf
#383
michellescribner
closed
3 months ago
0
adding option to remove reference sequence from alignment
#382
jrotieno
closed
3 months ago
2
option to exclude reference sequence from Augur_PHB
#381
jrotieno
closed
3 months ago
0
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