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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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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
[TheiaMeta] Remove subworkflow for assembly with metaspades and pilon; remove exposed krakendb input from QC subworkflow
#380
cimendes
closed
3 months ago
4
upgrade pasty to v1.0.3
#379
kapsakcj
closed
3 months ago
3
[FastP & FastQC] output FastP and FastQC reports & output name changes
#378
sage-wright
closed
3 months ago
5
[Style Guide] Semantic adjustments throughout the PHB universe
#377
cimendes
closed
3 months ago
7
[TheiaProk] expose sistr optional inputs to TheiaProk wfs
#376
kapsakcj
opened
4 months ago
1
Upgrade to nextclade v3 & update default dataset tags
#375
kapsakcj
closed
3 months ago
8
[TheiaProk] Enable plasmidfinder to be skipped
#374
sage-wright
closed
3 months ago
7
[TheiaProk] Update MLST database
#373
cimendes
closed
3 months ago
1
Fix Empty Mean Coverage for Flu HA and NA Assemblies
#372
jrotieno
closed
3 months ago
7
adding optional arguments to freyja boot and demix calls
#371
jrotieno
closed
3 months ago
1
[BaseSpace_Fetch] hide preemptible input parameter
#370
cimendes
closed
3 months ago
0
[VADR_Update] cpu, docker and disk_size not exposed for the VADR task
#369
cimendes
closed
3 months ago
0
[VADR] maxlen -> maxlength and minlen -> minlength as per style-guide
#368
cimendes
closed
3 months ago
0
[QUAST] min_contig_len -> min_contig_length as per style guide
#367
cimendes
closed
3 months ago
0
[read_QC_trim] trim_quality_trim_score -> trim_quality_min_score
#366
cimendes
closed
3 months ago
0
[read_QC_trim] trim_minlen -> trim_minlength to respect new style-guide
#365
cimendes
closed
3 months ago
0
[TheiaMeta] cpu, docker, memory and disk_size not exposed to Terra for metaspades
#364
cimendes
closed
3 months ago
0
bug fix on fastq-dl task/SRA_fetch workflow for cpu variable
#363
kapsakcj
closed
4 months ago
1
`cpu` is no longer a variable in the SRA_Fetch task
#362
watronfire
closed
4 months ago
4
[TheiaCoV_Illumina_PE] assembly_mean_coverage always being reported as empty for flu samples
#361
cimendes
closed
3 months ago
0
tiny bug in theiavalidate export_two_tsvs task
#360
kapsakcj
closed
4 months ago
0
disable call caching for rasusa standalone workflow
#359
kapsakcj
closed
3 months ago
0
Add a warning column to SRA_Fetch if SRALite file format is detected
#358
cimendes
closed
3 months ago
1
[TheiaProk] Add Kraken to TheiaProk_ONT
#357
cimendes
closed
1 month ago
1
Add additional antivirals to flu
#356
sage-wright
closed
3 months ago
0
[TheiaProk] Add additional read QC to TheiaProk_ONT
#355
michellescribner
closed
1 month ago
0
[BaseSpace_Fetch] NextSeq PulseNet workflow incompatible with BaseSpace Fetch
#354
michellescribner
opened
4 months ago
0
[Snippy_Streamline] Add Snippy_variants QC outputs
#353
emmadoughty
opened
4 months ago
0
[Snippy_Streamline] Use gbff downloaded by Assembly_Fetch as the reference, if `include_gbff` = true
#352
emmadoughty
opened
4 months ago
0
Output whole genome SNP matrix for Snippy_Streamline and Snippy_Tree workflows even when core_genome used
#351
jrotieno
closed
4 months ago
1
Freyja_FASTQ_PHB doesn't allow additional arguments
#350
michellescribner
closed
3 months ago
0
upgrade TheiaCov workflows to use nextclade v3.x
#349
kapsakcj
closed
3 months ago
0
[Snippy_Streamline] Add fastBAPS
#348
emmadoughty
opened
4 months ago
0
fix dockstore: add empty.json file and update .dockstore.yml with absolute paths to it
#347
kapsakcj
closed
4 months ago
2
Change relative paths to absolute paths in .dockstore.yml
#346
kathy-t
closed
4 months ago
2
[BUSCO] Update to latest release - v5.6.1
#345
cimendes
closed
2 months ago
2
[TheiaMeta] Version in main broken on dockstore
#344
cimendes
closed
4 months ago
0
[Terra_2_NCBI] Add OneHealthEnteric BioSample package
#343
sage-wright
closed
3 months ago
0
[Terra_2_NCBI] Add OneHealthEnteric BioSample package
#342
sage-wright
opened
4 months ago
0
Percent Gene Coverage Task Modularization
#341
sage-wright
closed
3 months ago
7
[TheiaMeta] Add more QC to TheiaMeta
#340
emmadoughty
opened
4 months ago
0
Output whole genome SNP matrix for Snippy_Streamline and Snippy_Tree workflows even when core_genome used
#339
emmadoughty
closed
4 months ago
0
[Freyja_FASTQ] output usher_barcodes file to table
#338
sage-wright
closed
4 months ago
2
[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
4 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
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