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theiagen
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public_health_bacterial_genomics
GNU Affero General Public License v3.0
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Add qc_check task to TheiaProk
#182
michellescribner
closed
1 year ago
0
update pasty_docker default; add `pasty_comment` string output for PE and SE wfs
#181
kapsakcj
closed
1 year ago
1
Eld docs dev
#180
emmadoughty
closed
1 year ago
5
adds p. aeruginosa subworkflow and pasty for serogrouping
#179
jrotieno
closed
1 year ago
2
Add Core_Gene_SNP workflow
#178
michellescribner
closed
1 year ago
1
Fixed printf to convert sci notation to integers
#177
frankambrosio3
closed
1 year ago
0
Handle scientific notation with mash sketch outputs
#176
frankambrosio3
closed
1 year ago
0
Fja nullarbor2 dev
#175
frankambrosio3
closed
1 year ago
2
Fja tbprofiler update
#174
frankambrosio3
closed
1 year ago
3
Fja expose bam and vcf dev
#173
frankambrosio3
closed
1 year ago
1
Modify midas parsing
#172
michellescribner
closed
1 year ago
0
rare SeqSero2 failure
#171
kapsakcj
closed
1 year ago
3
Adds bakta task
#170
michellescribner
closed
1 year ago
0
Add fastp task, modify read trimming parameters, and modify estimated coverage calculations
#169
michellescribner
closed
1 year ago
4
Add option for user to specify organism
#168
emmadoughty
closed
1 year ago
2
ensure WDL compatibility with Azure
#167
kapsakcj
closed
1 year ago
1
Add option to kSNP3 to create maximum likelihood and neighbor joining trees
#166
michellescribner
closed
1 year ago
1
Update cg_pipeline input to clean reads
#165
michellescribner
closed
1 year ago
0
Estimated coverage calculated with raw reads rather than clean reads
#164
michellescribner
closed
1 year ago
0
update default mlst docker image to staphb/mlst:2.23.0 & fix CI env
#163
kapsakcj
closed
1 year ago
1
Adds shigella subworkflow
#162
kapsakcj
closed
1 year ago
1
Fix gambit parsing for next_taxon_rank is None
#161
michellescribner
closed
1 year ago
1
add task for Abaum plasmid typing to TheiaProk_Illumina_PE and SE
#160
kapsakcj
closed
1 year ago
0
Add midas as optional TheiaProk task
#159
michellescribner
closed
1 year ago
0
Add option to hide point mutations from AMRFinderPlus output & update default amrfinderplus docker image
#158
michellescribner
closed
1 year ago
1
FKS1 detection (C.auris)
#157
kevinlibuit
opened
1 year ago
1
Swap Prokka for Bakta
#156
kevinlibuit
closed
1 year ago
3
Request for Snippy workflow
#155
kevinlibuit
closed
1 year ago
2
add workflow for bakta
#154
rpetit3
closed
1 year ago
0
Average read length after trimming
#153
kevinlibuit
opened
1 year ago
0
Secondary-species abundance QC
#152
kevinlibuit
closed
1 year ago
2
update gambit task to v0.5.0 docker image
#151
michellescribner
closed
1 year ago
0
AMR genes csv output file
#150
frankambrosio3
opened
1 year ago
0
Spneumo subworkflow enhancements: docker & GPS db version outputs and upgrade default pbptyper docker
#149
kapsakcj
closed
1 year ago
0
Kleborate updates
#148
kapsakcj
closed
1 year ago
6
add fastq-scan additional outputs - read lengths
#147
kapsakcj
opened
1 year ago
0
kSNP3 task edit: changed file suffix from .tree to .nwk
#146
kapsakcj
closed
1 year ago
2
Adds drug class output to TheiaProk
#145
michellescribner
closed
1 year ago
0
add kraken to theiaprok
#144
sage-wright
opened
2 years ago
1
add MIDAS for contamination detection
#143
kapsakcj
closed
1 year ago
0
float Kleborate/K pnemoniae K & O locus calls to Terra table
#142
kapsakcj
closed
1 year ago
4
Add Streptococcus pneumoniae subworkflow
#141
kapsakcj
closed
2 years ago
10
cgMLST
#140
emmadoughty
opened
2 years ago
0
Vibrio spp sub-workflow for TheiaProk
#139
emmadoughty
opened
2 years ago
2
Adds subworkflow for A. baumannii, includes Kaptive task (K & O typing)
#138
erikwolfsohn
closed
1 year ago
26
amrfinderplus task updates
#137
kapsakcj
closed
2 years ago
5
amrfinderplus mincov minid inputs should be floats not integers
#136
kapsakcj
closed
2 years ago
1
nmen, ngon, h influ serotyping
#135
sage-wright
closed
1 year ago
1
remove compression from alignment files
#134
michellescribner
closed
2 years ago
0
snp-dists output matrix not ordered correctly
#133
sage-wright
closed
1 year ago
0
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