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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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[TheiaMeta] Populate midas outputs to data table
#308
cimendes
opened
7 months ago
0
restore vadr_num_alerts string output to theiacov_fasta workflow
#307
kapsakcj
closed
7 months ago
0
vadr_num_alerts not output in TheiaCoV_FASTA
#306
sage-wright
closed
7 months ago
0
theiacov_fasta wf logic change for flu
#305
kapsakcj
closed
7 months ago
6
TheiaCoV_Fasta_PHB failing when flu_subtype input is blank
#304
jrotieno
closed
7 months ago
0
Samples_To_Ref_Tree_PHB: changed "organism" input to "nextclade_dataset_name"
#303
jrotieno
closed
7 months ago
3
Changing the "Samples_To_Ref_Tree_PHB" `organism` input to `nextclade_dataset_name`
#302
jrotieno
closed
7 months ago
0
Maximum estimated genome size
#301
andrewjpage
closed
3 months ago
1
[PR Template Update] Updating template per identified dev process improvements
#300
kelseykropp
closed
7 months ago
0
[PR Template Update] Update template per identified dev process improvements
#299
kelseykropp
closed
7 months ago
1
Kraken2 report output variable type breaks export taxon table task
#298
cimendes
closed
7 months ago
0
[TheiaProk suite] Patch fix: change type of kraken2_report to be string in taxon_table task
#297
cimendes
closed
7 months ago
0
[PHB Release 1.3.0] update version and docker tags (nexclade sc2, pangolin, tbp-parser 1.1.7)
#296
cimendes
closed
8 months ago
5
Adding flu and RSV to TheiaCoV fastq workflows (VADR)
#295
kevinlibuit
closed
5 months ago
3
Add Spoligotyping from TBProfiler to TheiaProk Outputs
#294
frankambrosio3
opened
8 months ago
0
update docker to version tag 2.23.0-2024-01
#293
cimendes
closed
8 months ago
3
Update Gambit database files to version 1.3.0
#292
kevinlibuit
closed
8 months ago
5
Shared variants tasks and QC improvements for kSNP3 and Snippy
#291
michellescribner
closed
5 months ago
11
Use the organism parameter workflow in all TheiaCoV workflows
#290
sage-wright
closed
6 months ago
0
update default freyja docker image to 1.4.8 for multiple tasks
#289
kapsakcj
closed
8 months ago
0
TheiaCoV_ONT: prevent failure by coercing files into strings
#288
sage-wright
closed
8 months ago
0
[feature request] add new output columns for Freyja QC values
#287
kapsakcj
closed
6 months ago
1
[TheiaProk Workflows] Add Kraken2 as optional module
#286
cimendes
closed
8 months ago
4
Add hicap outputs to TheiaProk_ONT
#285
michellescribner
closed
2 months ago
0
Make workflow to prepare metadata and files for CZGenEpi
#284
sage-wright
closed
8 months ago
0
Merge TB changes into main
#283
sage-wright
closed
8 months ago
0
Add FastQC as an optional module
#282
sage-wright
closed
8 months ago
0
Move TheiaValidate into its own repository
#281
sage-wright
closed
8 months ago
0
Make Plasmidfinder optional, on by default
#280
michellescribner
closed
5 months ago
4
[TheiaProk] Add Kraken2 as optional module
#279
cimendes
closed
8 months ago
0
[Kraken2 Standalone] Substitute kronatools by krakentools for Krona report visualisation
#278
cimendes
opened
8 months ago
0
Use of GAMBIT image with DB
#277
kevinlibuit
closed
8 months ago
1
TBProfiler tNGS workflow
#276
sage-wright
closed
4 months ago
0
output unaligned FASTQ files TheiaCov_Illumina PE and SE
#275
kapsakcj
closed
6 months ago
5
[TheiaCoV_Fasta_Batch] Substitute FASTA concatenating task to ensure proper sample_id propagation
#274
cimendes
closed
8 months ago
1
virulencefinder is not triggered for Shigella sonnei
#273
kapsakcj
closed
1 month ago
1
TBProfiler_tNGS_PHB: Introduction of tNGS workflow for TB
#272
sage-wright
closed
4 months ago
0
[TheiaCoV_ONT] workflow fails when assembly cannot be produced
#271
emmadoughty
closed
1 month ago
5
TheiaCoV_ONT workflow fails to complete when read screening fails
#270
emmadoughty
closed
8 months ago
0
[SRA_Fetch] Ensure that the SRA Lite format IS NOT being downloaded
#269
cimendes
closed
6 months ago
3
Update task_augur_refine iqd back to 4
#268
jrotieno
closed
8 months ago
0
[New Utility] Workflow to rename FASTQ files (non-destructive)
#267
cimendes
closed
8 months ago
1
[Utilities] Add workflow to rename FASTQ files in a non-destructive manner
#266
cimendes
closed
8 months ago
0
[Freyja] update docker image to 1.4.8
#265
sage-wright
closed
8 months ago
0
TheiaValidate: Compare file contents
#264
sam-baird
closed
7 months ago
2
[AMRFinderPlus] Update database to latest version by next release
#263
cimendes
closed
8 months ago
1
[MLST] Update MLST database for next release
#262
cimendes
closed
8 months ago
1
[TheiaCoV_FASTA_Batch] FASTA header not matching sample name
#261
sage-wright
closed
8 months ago
1
FastQC added as an optional module in all Illumina_PE and Illumina_SE workflows
#260
sage-wright
closed
8 months ago
1
[New workflow] Workflow to create Terra table after data upload to Google bucket
#259
emmadoughty
closed
2 months ago
0
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