issues
search
Clinical-Genomics
/
microSALT
Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
2
stars
3
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Should we report the number of non-trimmed reads?
#131
henningonsbring
closed
2 years 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
Save job_ids.yaml file for trailblazer tracking
#126
Mropat
closed
3 years ago
0
Added support to run ANY resistance DB
#125
sylvinite
closed
7 months ago
1
Emails with reports from slurm not received
#124
talnor
closed
3 years ago
7
Updated and fixed bugs in pubmlst and ncbi downloads
#123
talnor
closed
3 years ago
3
Automatic reference downloader doesnt kick in
#122
sylvinite
closed
3 years ago
1
Attempt to make resistance searches more compatible
#121
sylvinite
closed
3 years ago
0
Adding self tests
#120
henningonsbring
closed
3 years ago
0
Improve citability of microSALT
#119
sylvinite
closed
3 years ago
1
Completely mock the database for self-tests
#118
sylvinite
closed
1 year ago
1
Add static report storage
#117
sylvinite
closed
3 years ago
1
Improved report storage architecture
#116
sylvinite
closed
3 years ago
0
Fix reportfolder
#115
sylvinite
closed
3 years ago
0
Better support reruns
#114
sylvinite
closed
1 year ago
1
Add output prefix
#113
talnor
closed
3 years ago
1
Add prefix to all output files
#112
sylvinite
closed
3 years ago
1
Deliverables file fix
#111
sylvinite
closed
3 years ago
0
Deliverables file generation on old runs
#110
sylvinite
closed
3 years ago
0
Identify microSALT's measurement uncertainty
#109
sylvinite
closed
3 years ago
0
Revise deliverables file
#108
sylvinite
closed
3 years ago
0
HOTFIX: Fetch reference version number for external references
#107
talnor
closed
4 years ago
0
ERROR - Reference update function failed prematurely. Review immediately
#106
patrikgrenfeldt
closed
3 years ago
1
"Total reads" header
#105
henningonsbring
closed
3 years ago
0
Chronic: microSALT attempts to write to a read only database
#104
barrystokman
closed
3 years ago
6
Patching struct
#103
sylvinite
closed
4 years ago
1
Proper display of non pubMLST-compatible organisms
#102
sylvinite
closed
4 years ago
0
Samtools hotfix
#101
sylvinite
closed
4 years ago
0
Duplicate loci hits are now obfuscated
#100
sylvinite
closed
4 years ago
0
resistance regex supports references version
#99
b4ckm4n
closed
4 years ago
0
Add contamination and duplication checks
#98
sylvinite
closed
1 year ago
1
Replace microSALT LIMS dependency
#97
sylvinite
closed
4 years ago
0
Add additional typing databases
#96
sylvinite
closed
1 year ago
0
Add core genome analysis
#95
sylvinite
closed
1 year ago
1
Improve code coverage to 85%
#94
sylvinite
closed
1 year ago
1
Parameter file support
#93
sylvinite
closed
4 years ago
0
Low-quality resistance calls into code_examples
#92
sylvinite
closed
4 years ago
0
Contamination
#91
sylvinite
closed
7 months ago
0
Autobatch utility
#90
sylvinite
closed
4 years ago
0
Coverage improvement
#89
sylvinite
closed
4 years ago
0
Stability bundle
#88
sylvinite
closed
4 years ago
0
Collections (dev) now work better
#87
sylvinite
closed
4 years ago
0
Added a few more test assertions
#86
sylvinite
closed
4 years ago
0
Code coverage improvements
#85
sylvinite
closed
4 years ago
0
fix: select default branch
#84
ingkebil
closed
4 years ago
2
Install script travis compatible
#83
sylvinite
closed
4 years ago
0
Expanded testing. init now initializes logger, auto-creates directories
#82
sylvinite
closed
4 years ago
0
Previous
Next