issues
search
theiagen
/
public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
https://public-health-viral-genomics-theiagen.readthedocs.io/
GNU Affero General Public License v3.0
41
stars
17
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Update Mercury Prep and Mercury Batch workflows to generate output compatible with GISAID's v4 command line uploader
#226
erikwolfsohn
opened
8 months ago
0
Update readme
#225
sage-wright
closed
1 year ago
0
update readme
#224
sage-wright
closed
1 year ago
0
update checksums
#223
sage-wright
closed
1 year ago
0
Add "consortium" to Mercury_Prep
#222
sage-wright
closed
1 year ago
1
wf_ivar_consensus obscures min_freq option
#221
michellescribner
closed
1 year ago
0
Add intermediate frequency mutations screen TheiaCoV
#220
michellescribner
closed
1 year ago
1
Mercury Fix when collection_date is missing
#219
sage-wright
closed
1 year ago
0
Update README.md
#218
kevinlibuit
closed
1 year ago
0
update default pangolin docker to staphb/pangolin:4.2-pdata-1.18.1.1 and nextclade_dataset_tag for SC2
#217
kapsakcj
closed
1 year ago
2
Fix Bug RE Type-B subtyping (TheiaCoV_Illumina PE flu track)
#216
kevinlibuit
closed
1 year ago
0
update github actions workflow
#215
kapsakcj
closed
1 year ago
6
Add detection for aa substitutions associated with tamiflu-resistance
#214
cimendes
closed
1 year ago
0
update nextclade TSV parsing for SC2: `clade_legacy`. Also update Flu & nextclade
#213
kapsakcj
closed
1 year ago
6
nextclade parsing changes into stable dev branch
#212
kapsakcj
closed
1 year ago
2
Expose minimum coverage option in Freyja_Plot
#211
sage-wright
closed
1 year ago
0
Enable alternative read and assembly files
#210
sage-wright
closed
1 year ago
2
Mercury_Prep_N_Batch: make state input variable optional
#209
sage-wright
closed
1 year ago
0
Add mincov to Freyja_Plot
#208
sage-wright
closed
1 year ago
0
Enable alternative read and assembly files
#207
sage-wright
closed
1 year ago
1
Mercury_Prep_N_Batch: fixes
#206
sage-wright
closed
1 year ago
1
Smw excluded mercury dev
#205
sage-wright
closed
1 year ago
0
quality exclusion write out
#204
sage-wright
closed
1 year ago
0
Update version and SC2 references
#203
kevinlibuit
closed
1 year ago
1
Ensure bbduk outputs are ordered
#202
kevinlibuit
closed
1 year ago
0
Fix lowercase things
#201
sage-wright
closed
1 year ago
0
IRMA fails with too many reads
#200
frankambrosio3
opened
1 year ago
2
Fix conditional logic in Mercury Prep N Batch
#199
sage-wright
closed
1 year ago
0
Fja hiv merge dev
#198
frankambrosio3
closed
1 year ago
1
Pangolin_Update redundant output variable
#197
sage-wright
closed
1 year ago
0
the Mercury_Prep_N_Batch workflow
#196
sage-wright
closed
1 year ago
1
TheiaCov output - Nextclade_lineage empty
#195
kapsakcj
closed
1 year ago
0
Adding flu organism track
#194
kevinlibuit
closed
1 year ago
1
Azure compatibility
#193
sage-wright
closed
1 year ago
0
Implement workflow logic to use "mpox" as the target organism for TheiaCoV MPXV analysis
#192
frankambrosio3
opened
1 year ago
0
Add organism track for flu characterization
#191
kevinlibuit
closed
1 year ago
1
adds support for running VADR on WNV samples
#190
kapsakcj
closed
1 year ago
0
Make pipelines azure comaptible.
#189
vsmalladi
closed
1 year ago
4
link to the notion page in 2.2.0
#188
neranjan007
opened
2 years ago
1
ensure WDL compatibility with Azure
#187
vsmalladi
closed
1 year ago
2
Rp3 add support for adapter files in bbduk, update ci test
#186
kapsakcj
closed
2 years ago
0
add support for adapter files in bbduk, update ci test
#185
rpetit3
closed
2 years ago
2
allow user to specify adapters FASTA for trimming with bbduk
#184
kapsakcj
closed
2 years ago
0
fastq-scan fails on large FASTQs
#183
kapsakcj
opened
2 years ago
2
Add optional arguments input to trimmomatic task and add fastp task
#182
michellescribner
closed
2 years ago
0
Fja merc dev
#181
frankambrosio3
closed
2 years ago
0
VADR for WNV
#180
kevinlibuit
closed
1 year ago
2
VADR for MPXV
#179
kevinlibuit
closed
2 years ago
1
Aviti compatibility
#178
kevinlibuit
closed
2 years ago
1
Add fastp option to TheiaCoV_Illumina_* workflows
#177
michellescribner
closed
1 year ago
1
Next