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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 and TheiaMeta] Add CheckM for assembly QC (completeness and contamination)
#476
cimendes
opened
1 month ago
0
[Terra_2_NCBI] remove metadata requirements with skip_biosample == true
#475
sage-wright
closed
1 month ago
2
[Gambitcore - Internal] Downgrade gambit database to stable v1.3.0
#474
cimendes
closed
1 week ago
0
[Internal - Gambitcore] Downgrade database to stable 1.3.0 version
#473
cimendes
closed
1 week ago
6
[New workflow - Internal] Gambit fastq for internal testing and evaluation
#472
cimendes
opened
1 month ago
1
[feature request] output fastq-scan JSONs in all workflows that include it
#471
kapsakcj
opened
1 month ago
0
[TheiaProk_ONT] Read QC Trim runtime parameters not exposed on Terra
#470
cimendes
opened
1 month ago
0
[Flu] Assembly mean coverage & read screen clean-up
#469
sage-wright
closed
1 month ago
1
IRMA bug fixes & improvements; theiacov_illumina_pe wf updates for Flu
#468
kapsakcj
closed
1 week ago
6
[TheiaProk_ONT] Tun Tiptofts on downsampled samples instead of raw reads
#467
cimendes
opened
1 month ago
0
[New workflow - internal] Gambitcore for assembly quality assessment with GAMBIT
#466
cimendes
closed
1 month ago
2
[Reorder Matrix - Phylogenetics] Set phandango colouring to false by default
#465
cimendes
closed
3 weeks ago
0
output VADR annotations (esp. for Flu) & upgrade to VADR docker w/ new Flu model files
#464
kapsakcj
opened
1 month ago
0
[TheiaProk] salmonella tool
#463
sage-wright
closed
1 month ago
0
[TBProfiler] update TBProfiler to v6.2.0 and tbp-parser to v1.5.0
#462
sage-wright
opened
1 month ago
0
[RASUSA] Upgrade to latest stable version 2.0.0
#461
cimendes
opened
1 month ago
0
[TheiaProk] Add detection of prophages via phastaf
#460
cimendes
opened
1 month ago
0
[TheiaProk_ONT] add patch fix to kmc estimated genome size to not go over 10Mbp
#459
cimendes
closed
1 month ago
2
[Augur] Set sample_metadata_tsvs input in Augur_PHB to optional
#458
emily-smith1
closed
1 week ago
2
upgrade IRMA default to v1.1.5; copy docker image to GAR
#457
kapsakcj
closed
1 week ago
0
Improved documentation of BaseSpace authentication
#456
michellescribner
opened
1 month ago
0
Exposing r1 and r2 mean_q_clean and mean_readlength_clean
#455
jrotieno
closed
1 month ago
1
[theiacov] update default pangolin docker image to pdata 1.27 & other default docker images when applicable
#454
kapsakcj
closed
1 week ago
2
[SRA_Fetch] When re-running workflow, any warnings are not overwritten
#453
emmadoughty
closed
2 months ago
1
[TheiaProk_ONT and TheiaCoV_ONT] Expose additional QC metrics from nanoplot for both raw and clean reads
#452
cimendes
closed
1 month ago
2
[SRA-Fetch] Output what version of the workflow was run, similar to TheiaCoV, TheiaProk, TheiaEuk
#451
cimendes
opened
2 months ago
0
Prokka-Like Genome Annotation for Virus Genomes in the TheiaCoV Workflows
#450
jrotieno
opened
2 months ago
0
[PHB] Error on requestor pays files
#449
andrewjpage
opened
2 months ago
0
Update version to v2.0.1
#448
sage-wright
closed
2 months ago
1
[maintenance] change default location for midas_db to requester pays bucket
#447
kapsakcj
closed
2 months ago
0
update default midas_db location to requester pays bucket
#446
kapsakcj
closed
2 months ago
2
update bakta to latest version; host the "full" db as well as "light" db on requester pays bucket
#445
kapsakcj
opened
2 months ago
0
[taxon table] update the taxon tables to match workflow outputs
#444
sage-wright
opened
2 months ago
0
[experimental] Add StxTyper for Shiga toxin subtyping
#443
kapsakcj
opened
2 months ago
0
[theiacov_ont] update to use organism_parameters.genome_length in read screen task
#442
kapsakcj
closed
2 months ago
0
[TheiaCoV] set default kraken_target_organism for RSV-A and RSV-B
#441
kapsakcj
closed
2 months ago
0
[TheiaCoV wfs] run nextclade by default for RSV-A & RSV-B in all TheiaCov workflows
#440
kapsakcj
closed
2 months ago
0
[TheiaProk] output r1_mean_q_clean and r2_mean_q_clean
#439
sage-wright
closed
1 month ago
0
[TheiaProk_ONT] Add Kraken2 as part of read_qc
#438
cimendes
closed
1 month ago
2
[IRMA] bug in output FASTA file for HA segment of Flu B samples is empty
#437
kapsakcj
closed
1 week ago
0
TheiaCoV wf support for RSV - run nextclade by default and small optimizations (kraken_target_organism, genome_length)
#436
kapsakcj
closed
2 months ago
3
[Terra_2_NCBI] skip-biosample should prevent biosample value checks
#435
sage-wright
closed
1 month ago
0
[TheiaCoV_ONT] add WNV
#434
sage-wright
opened
2 months ago
0
[TheiaMeta] add ONT!
#433
sage-wright
opened
2 months ago
0
[Mercury] add flu
#432
sage-wright
opened
2 months ago
1
Add abricate as optional module
#431
jrotieno
closed
1 month ago
3
[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
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