issues
search
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
34
stars
16
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
theiacov_fasta wf logic change for flu
#305
kapsakcj
closed
6 months ago
6
TheiaCoV_Fasta_PHB failing when flu_subtype input is blank
#304
jrotieno
closed
6 months ago
0
Samples_To_Ref_Tree_PHB: changed "organism" input to "nextclade_dataset_name"
#303
jrotieno
closed
6 months ago
3
Changing the "Samples_To_Ref_Tree_PHB" `organism` input to `nextclade_dataset_name`
#302
jrotieno
closed
6 months ago
0
Maximum estimated genome size
#301
andrewjpage
closed
2 months ago
1
[PR Template Update] Updating template per identified dev process improvements
#300
kelseykropp
closed
6 months ago
0
[PR Template Update] Update template per identified dev process improvements
#299
kelseykropp
closed
6 months ago
1
Kraken2 report output variable type breaks export taxon table task
#298
cimendes
closed
6 months ago
0
[TheiaProk suite] Patch fix: change type of kraken2_report to be string in taxon_table task
#297
cimendes
closed
6 months ago
0
[PHB Release 1.3.0] update version and docker tags (nexclade sc2, pangolin, tbp-parser 1.1.7)
#296
cimendes
closed
6 months ago
5
Adding flu and RSV to TheiaCoV fastq workflows (VADR)
#295
kevinlibuit
closed
3 months ago
3
Add Spoligotyping from TBProfiler to TheiaProk Outputs
#294
frankambrosio3
opened
6 months ago
0
update docker to version tag 2.23.0-2024-01
#293
cimendes
closed
6 months ago
3
Update Gambit database files to version 1.3.0
#292
kevinlibuit
closed
6 months ago
5
Shared variants tasks and QC improvements for kSNP3 and Snippy
#291
michellescribner
closed
4 months ago
11
Use the organism parameter workflow in all TheiaCoV workflows
#290
sage-wright
closed
5 months ago
0
update default freyja docker image to 1.4.8 for multiple tasks
#289
kapsakcj
closed
6 months ago
0
TheiaCoV_ONT: prevent failure by coercing files into strings
#288
sage-wright
closed
7 months ago
0
[feature request] add new output columns for Freyja QC values
#287
kapsakcj
closed
5 months ago
1
[TheiaProk Workflows] Add Kraken2 as optional module
#286
cimendes
closed
6 months ago
4
Add hicap outputs to TheiaProk_ONT
#285
michellescribner
closed
1 month ago
0
Make workflow to prepare metadata and files for CZGenEpi
#284
sage-wright
closed
6 months ago
0
Merge TB changes into main
#283
sage-wright
closed
7 months ago
0
Add FastQC as an optional module
#282
sage-wright
closed
6 months ago
0
Move TheiaValidate into its own repository
#281
sage-wright
closed
7 months ago
0
Make Plasmidfinder optional, on by default
#280
michellescribner
closed
4 months ago
4
[TheiaProk] Add Kraken2 as optional module
#279
cimendes
closed
6 months ago
0
[Kraken2 Standalone] Substitute kronatools by krakentools for Krona report visualisation
#278
cimendes
opened
7 months ago
0
Use of GAMBIT image with DB
#277
kevinlibuit
closed
6 months ago
1
TBProfiler tNGS workflow
#276
sage-wright
closed
3 months ago
0
output unaligned FASTQ files TheiaCov_Illumina PE and SE
#275
kapsakcj
closed
5 months ago
5
[TheiaCoV_Fasta_Batch] Substitute FASTA concatenating task to ensure proper sample_id propagation
#274
cimendes
closed
7 months ago
1
virulencefinder is not triggered for Shigella sonnei
#273
kapsakcj
closed
1 week ago
1
TBProfiler_tNGS_PHB: Introduction of tNGS workflow for TB
#272
sage-wright
closed
3 months ago
0
[TheiaCoV_ONT] workflow fails when assembly cannot be produced
#271
emmadoughty
closed
2 weeks ago
5
TheiaCoV_ONT workflow fails to complete when read screening fails
#270
emmadoughty
closed
7 months ago
0
[SRA_Fetch] Ensure that the SRA Lite format IS NOT being downloaded
#269
cimendes
closed
4 months ago
3
Update task_augur_refine iqd back to 4
#268
jrotieno
closed
7 months ago
0
[New Utility] Workflow to rename FASTQ files (non-destructive)
#267
cimendes
closed
7 months ago
1
[Utilities] Add workflow to rename FASTQ files in a non-destructive manner
#266
cimendes
closed
7 months ago
0
[Freyja] update docker image to 1.4.8
#265
sage-wright
closed
6 months ago
0
TheiaValidate: Compare file contents
#264
sam-baird
closed
6 months ago
2
[AMRFinderPlus] Update database to latest version by next release
#263
cimendes
closed
7 months ago
1
[MLST] Update MLST database for next release
#262
cimendes
closed
6 months ago
1
[TheiaCoV_FASTA_Batch] FASTA header not matching sample name
#261
sage-wright
closed
7 months ago
1
FastQC added as an optional module in all Illumina_PE and Illumina_SE workflows
#260
sage-wright
closed
6 months ago
1
[New workflow] Workflow to create Terra table after data upload to Google bucket
#259
emmadoughty
closed
2 weeks ago
0
Enhanced quality control metrics for Snippy and TheiaEuk
#258
michellescribner
closed
4 months ago
0
Expose midas secondary genus absolute coverage
#257
michellescribner
closed
5 months ago
1
HOSTILE: For TheiaCoV_Illumina_PE_PHB and TheiaCoV_ONT_PHB
#256
jrotieno
closed
7 months ago
0
Previous
Next