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Clinical-Genomics
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microSALT
Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
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Metrics file not output for case
#176
seallard
opened
1 week ago
2
Move CI to GitHub Actions
#175
samuell
opened
3 weeks ago
1
Switch CI from TravisCI to GitHub Actions
#174
samuell
opened
3 weeks ago
0
Fix #149: Missing or mis-reported resistances
#173
samuell
opened
3 weeks ago
0
MicroSALT cannot start single sample case
#172
beatrizsavinhas
opened
5 months ago
0
Add deployment
#171
talnor
closed
5 months ago
0
Slurm id file naming
#170
seallard
opened
5 months ago
0
Fix missing duplication rate in json report
#169
seallard
closed
6 months ago
1
Duplication rate missing in json output
#168
seallard
opened
6 months ago
0
Jobs cannot be tracked for microsalt
#167
seallard
opened
6 months ago
0
Fixed conda installation
#166
talnor
closed
5 months ago
0
Use of --isolate flag, and update of SPAdes assembler
#165
talnor
opened
6 months ago
1
assembly issues in arcC loci for Staphylococcus Aureus
#164
talnor
opened
6 months ago
0
HTML reports unnecessarily pulls content from the web - with potential privacy and security concerns
#163
samuell
opened
11 months ago
0
Update CODEOWNERS
#162
pbiology
closed
11 months ago
0
Improve description of analytical limitations in reports
#161
talnor
opened
11 months ago
4
Bump flask from 1.1.2 to 2.3.2
#160
dependabot[bot]
opened
1 year ago
0
fix(SWEDAC) SWEDAC logo only on MW samples
#159
Vince-janv
closed
1 year ago
3
Remove swedac logo if analyses that are not accredited are run
#158
moahaegglund
closed
1 year ago
3
Replace travis with github actions
#157
talnor
closed
1 year ago
1
What should we trend in vogue for microsalt?
#156
henningonsbring
closed
1 year ago
7
Update housekeeper deliverables
#155
talnor
opened
2 years ago
1
Set slurm QoS based on priority of case for microSALT
#154
moahaegglund
closed
1 year ago
1
specify openjdk version
#153
henningonsbring
closed
2 years ago
1
Trimmomatic randomly fails
#152
talnor
closed
2 years ago
1
Testing cleaning up microsalt install script
#151
henningonsbring
closed
2 years ago
1
microSALT cannot be installed on hasta
#150
talnor
closed
2 years ago
1
Issue with reporting resistance OXA-48
#149
talnor
opened
2 years ago
10
Add automatic blacking
#148
talnor
closed
1 year ago
3
Add all samples to report
#147
talnor
opened
2 years ago
1
Changing Allel information in typing report for Novel allels
#146
Vince-janv
closed
1 year ago
1
Update pr template
#145
talnor
closed
5 months ago
3
Make validation samples available
#144
talnor
closed
1 year ago
1
Fix dependencies
#143
talnor
closed
2 years ago
1
Add reference genome size to typing report
#142
henningonsbring
closed
2 years ago
8
Add fields in the report for important resistances
#141
talnor
closed
1 year ago
1
microSALT report - text for MLST thresholds above table is not correct
#140
emmser
opened
2 years ago
1
Bug in external pubMLST reference updates
#139
talnor
closed
2 years ago
2
Blast db creation bug
#138
talnor
closed
2 years ago
2
CG doesnt find mandatory files
#137
sylvinite
opened
3 years ago
1
Typing of Mycobacterium abscessus fail
#136
henningonsbring
closed
1 year ago
1
Bump pyyaml from 5.3.1 to 5.4
#135
dependabot[bot]
closed
2 years ago
1
slurmid hotfix
#134
sylvinite
closed
3 years ago
0
Put if case around swedac logotype based on RUNID
#133
sylvinite
closed
1 year ago
2
Updated pubMLST download links
#132
talnor
closed
3 years ago
2
Should we report the number of non-trimmed reads?
#131
henningonsbring
closed
1 year ago
1
Fixed bug in mlst download for some organisms
#130
talnor
closed
3 years ago
1
Issues with downloading from PubMLST
#129
talnor
closed
3 years ago
1
Add catch for samples mixed with same species
#128
talnor
closed
1 year ago
1
Fixed a bug when running bad sample.
#127
sylvinite
closed
3 years ago
0
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