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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] Kraken2 inputs duplicated due to PR #286
#337
cimendes
closed
3 months ago
0
Add FastQC & FastP reports as TheiaProk outputs
#336
emily-smith1
closed
3 months ago
0
TheiaValidate: Compare file contents (#264)
#335
sage-wright
closed
5 months ago
7
Upgrade AMRFinderPlus to version 3.12.8 and DB to version 2024-01-31.1
#334
cimendes
closed
4 months ago
3
V. cholerae O1/O139 mlst scheme selection bugfix
#333
kapsakcj
closed
4 months ago
5
Set phred to 33 on trimmomatic task
#332
cimendes
closed
3 months ago
1
[Kraken2_Standalone] Make task compatible with uncompressed FASTQ files
#331
cimendes
closed
4 months ago
1
[Augur_PHB] Update ncov repo commit and remove reference input to augur clades task
#330
sage-wright
closed
4 months ago
4
[Freyja_Plot] -- Fail gracefully with low coverage samples
#329
kevinlibuit
opened
5 months ago
3
[New workflow] Add GAMBIT core task and standalone workflow for testing
#328
michellescribner
closed
2 months ago
0
pangolin TMPDIR add and CI updates & improvements
#327
kapsakcj
closed
5 months ago
3
[feature request] automatically convert spaces to dashes in workflows that accept strings
#326
kapsakcj
closed
1 month ago
6
[Gene Coverage] Modularize the gene coverage
#325
sage-wright
closed
3 months ago
0
Fix CI in main branch
#324
sage-wright
closed
5 months ago
0
[TheiaMeta] Binning with SemiBin2
#323
cimendes
closed
4 months ago
6
Check Organism Abundance From The Kraken report for TheiaCoV Workflows
#322
jrotieno
closed
4 months ago
1
[Feature Request] Binning for TheiaMeta if reference is not provided
#321
cimendes
closed
4 months ago
0
[feature request] remove 2 required inputs from theiacov_fasta_batch_phb workflow
#320
kapsakcj
closed
4 months ago
0
theiacov_fasta_batch_PHB wf improvements
#319
kapsakcj
closed
4 months ago
2
Revert "Adding `assembly_mean_coverage` metrics for flu in TheiaCoV_Illumina_PE_PHB"
#318
sage-wright
closed
5 months ago
0
Added Freyja coverage output to Terra table
#317
emmadoughty
closed
4 months ago
0
expose optional input parameter disk_size for kraken2 standalone wfs
#316
kapsakcj
closed
5 months ago
12
[feature request] expose disk_size optional input for kraken workflows
#315
kapsakcj
closed
5 months ago
0
Adding `assembly_mean_coverage` metrics for flu in TheiaCoV_Illumina_PE_PHB
#314
jrotieno
closed
5 months ago
0
missing `assembly_mean_coverage` value for flu
#313
jrotieno
closed
5 months ago
0
Percent reference coverage for Mpox genes
#312
emily-smith1
closed
3 months ago
0
Additional Updates to Flu antiviral Calls in TheiaCoV Workflows
#311
jrotieno
closed
4 months ago
1
TheiaCoV and TheiaProk workflows standardization & organism default subworkflow
#310
jrotieno
closed
4 months ago
7
[Mercury] potential issue with mercury_prep_n_batch with clearlabs data
#309
kapsakcj
closed
2 weeks ago
1
[TheiaMeta] Populate midas outputs to data table
#308
cimendes
opened
5 months ago
0
restore vadr_num_alerts string output to theiacov_fasta workflow
#307
kapsakcj
closed
5 months ago
0
vadr_num_alerts not output in TheiaCoV_FASTA
#306
sage-wright
closed
5 months ago
0
theiacov_fasta wf logic change for flu
#305
kapsakcj
closed
5 months ago
6
TheiaCoV_Fasta_PHB failing when flu_subtype input is blank
#304
jrotieno
closed
5 months ago
0
Samples_To_Ref_Tree_PHB: changed "organism" input to "nextclade_dataset_name"
#303
jrotieno
closed
5 months ago
3
Changing the "Samples_To_Ref_Tree_PHB" `organism` input to `nextclade_dataset_name`
#302
jrotieno
closed
5 months ago
0
Maximum estimated genome size
#301
andrewjpage
closed
1 month 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
3 months ago
11
Use the organism parameter workflow in all TheiaCoV workflows
#290
sage-wright
closed
4 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
6 months ago
0
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