Clinical-Genomics/microSALT issues and pull requests

#187 - Fix #185: Add back more greedy elimination of similar results

Pull Request - State: closed - Opened by samuell 12 days ago

#186 - Accomodate pubMLST authentication change

Issue - State: open - Opened by Vince-janv 16 days ago - 1 comment

#185 - Duplication of resistance genes in typing report

Issue - State: closed - Opened by samuell 19 days ago - 5 comments
Labels: bug

#184 - Fix #183: Remove potentially consufing "Kmer täckning" columns

Pull Request - State: closed - Opened by samuell about 1 month ago - 1 comment

#183 - Remove the "kmer täckning" column in typing report

Issue - State: closed - Opened by samuell about 1 month ago

#182 - Fix missing vim genes

Pull Request - State: closed - Opened by samuell 2 months ago - 2 comments

#181 - Update pull_request_template.md

Pull Request - State: closed - Opened by AnnaLeinfelt 3 months ago

#180 - Issue with reporting VIM resistance genes

Issue - State: open - Opened by samuell 3 months ago - 4 comments
Labels: KS requests, bug

#179 - 149 fix missing resistances

Pull Request - State: closed - Opened by samuell 3 months ago - 2 comments

#178 - Release candidate 4.0.0

Pull Request - State: closed - Opened by samuell 4 months ago
Labels: dependencies

#177 - Release Candidate 4.0.0

Pull Request - State: closed - Opened by samuell 4 months ago

#176 - Metrics file not output for case

Issue - State: open - Opened by seallard 5 months ago - 2 comments
Labels: bug

#175 - Move CI to GitHub Actions

Pull Request - State: closed - Opened by samuell 5 months ago - 1 comment

#174 - Switch CI from TravisCI to GitHub Actions

Issue - State: open - Opened by samuell 5 months ago - 1 comment
Labels: Effort L, Gain M

#173 - Fix #149: Missing or mis-reported resistances

Pull Request - State: closed - Opened by samuell 5 months ago

#172 - MicroSALT cannot start single sample case

Issue - State: open - Opened by beatrizsavinhas 9 months ago
Labels: bug

#171 - Add deployment

Pull Request - State: closed - Opened by talnor 10 months ago

#170 - Slurm id file naming

Issue - State: open - Opened by seallard 10 months ago

#169 - Fix missing duplication rate in json report

Pull Request - State: closed - Opened by seallard 10 months ago - 1 comment

#168 - Duplication rate missing in json output

Issue - State: open - Opened by seallard 10 months ago
Labels: bug

#167 - Jobs cannot be tracked for microsalt

Issue - State: open - Opened by seallard 10 months ago
Labels: bug

#166 - Fixed conda installation

Pull Request - State: closed - Opened by talnor 11 months ago

#165 - Use of --isolate flag, and update of SPAdes assembler

Pull Request - State: closed - Opened by talnor 11 months ago - 2 comments

#164 - assembly issues in arcC loci for Staphylococcus Aureus

Issue - State: open - Opened by talnor 11 months ago
Labels: bug

#163 - HTML reports unnecessarily pulls content from the web - with potential privacy and security concerns

Issue - State: open - Opened by samuell over 1 year ago
Labels: bug

#162 - Update CODEOWNERS

Pull Request - State: closed - Opened by pbiology over 1 year ago

#161 - Improve description of analytical limitations in reports

Issue - State: open - Opened by talnor over 1 year ago - 4 comments

#160 - Bump flask from 1.1.2 to 2.3.2

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#159 - fix(SWEDAC) SWEDAC logo only on MW samples

Pull Request - State: closed - Opened by Vince-janv almost 2 years ago - 3 comments

#158 - Remove swedac logo if analyses that are not accredited are run

Issue - State: closed - Opened by moahaegglund almost 2 years ago - 3 comments
Labels: Urgency L

#157 - Replace travis with github actions

Issue - State: closed - Opened by talnor over 2 years ago - 1 comment

#156 - What should we trend in vogue for microsalt?

Issue - State: closed - Opened by henningonsbring over 2 years ago - 7 comments

#155 - Update housekeeper deliverables

Issue - State: open - Opened by talnor almost 3 years ago - 1 comment

#154 - Set slurm QoS based on priority of case for microSALT

Issue - State: closed - Opened by moahaegglund almost 3 years ago - 1 comment

#153 - specify openjdk version

Pull Request - State: closed - Opened by henningonsbring almost 3 years ago - 1 comment

#152 - Trimmomatic randomly fails

Issue - State: closed - Opened by talnor almost 3 years ago - 1 comment
Labels: bug

#151 - Testing cleaning up microsalt install script

Pull Request - State: closed - Opened by henningonsbring almost 3 years ago - 1 comment

#150 - microSALT cannot be installed on hasta

Issue - State: closed - Opened by talnor almost 3 years ago - 1 comment
Labels: bug

#149 - Issue with reporting resistance OXA-48

Issue - State: closed - Opened by talnor almost 3 years ago - 11 comments
Labels: KS requests, bug

#148 - Add automatic blacking

Issue - State: closed - Opened by talnor about 3 years ago - 3 comments

#147 - Add all samples to report

Issue - State: open - Opened by talnor about 3 years ago - 1 comment
Labels: KS requests

#146 - Changing Allel information in typing report for Novel allels

Issue - State: closed - Opened by Vince-janv about 3 years ago - 1 comment
Labels: KS requests

#145 - Update pr template

Pull Request - State: closed - Opened by talnor about 3 years ago - 3 comments

#144 - Make validation samples available

Issue - State: closed - Opened by talnor about 3 years ago - 1 comment

#143 - Fix dependencies

Pull Request - State: closed - Opened by talnor about 3 years ago - 1 comment

#142 - Add reference genome size to typing report

Pull Request - State: closed - Opened by henningonsbring about 3 years ago - 8 comments

#141 - Add fields in the report for important resistances

Issue - State: closed - Opened by talnor about 3 years ago - 1 comment
Labels: KS requests

#140 - microSALT report - text for MLST thresholds above table is not correct

Issue - State: open - Opened by emmser over 3 years ago - 1 comment

#139 - Bug in external pubMLST reference updates

Issue - State: closed - Opened by talnor over 3 years ago - 2 comments

#138 - Blast db creation bug

Issue - State: closed - Opened by talnor over 3 years ago - 2 comments

#137 - CG doesnt find mandatory files

Issue - State: open - Opened by sylvinite over 3 years ago - 1 comment
Labels: Gain M, uSALT

#136 - Typing of Mycobacterium abscessus fail

Issue - State: closed - Opened by henningonsbring over 3 years ago - 1 comment

#135 - Bump pyyaml from 5.3.1 to 5.4

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#134 - slurmid hotfix

Pull Request - State: closed - Opened by sylvinite over 3 years ago

#133 - Put if case around swedac logotype based on RUNID

Issue - State: closed - Opened by sylvinite over 3 years ago - 2 comments

#132 - Updated pubMLST download links

Pull Request - State: closed - Opened by talnor over 3 years ago - 2 comments

#131 - Should we report the number of non-trimmed reads?

Issue - State: closed - Opened by henningonsbring almost 4 years ago - 1 comment
Labels: CG requests

#130 - Fixed bug in mlst download for some organisms

Pull Request - State: closed - Opened by talnor almost 4 years ago - 1 comment

#129 - Issues with downloading from PubMLST

Issue - State: closed - Opened by talnor almost 4 years ago - 1 comment

#128 - Add catch for samples mixed with same species

Issue - State: closed - Opened by talnor almost 4 years ago - 1 comment

#127 - Fixed a bug when running bad sample.

Pull Request - State: closed - Opened by sylvinite almost 4 years ago

#126 - Save job_ids.yaml file for trailblazer tracking

Pull Request - State: closed - Opened by Mropat almost 4 years ago

#125 - Added support to run ANY resistance DB

Pull Request - State: closed - Opened by sylvinite almost 4 years ago - 1 comment

#124 - Emails with reports from slurm not received

Issue - State: closed - Opened by talnor almost 4 years ago - 7 comments

#123 - Updated and fixed bugs in pubmlst and ncbi downloads

Pull Request - State: closed - Opened by talnor about 4 years ago - 3 comments

#122 - Automatic reference downloader doesnt kick in

Issue - State: closed - Opened by sylvinite about 4 years ago - 1 comment

#121 - Attempt to make resistance searches more compatible

Pull Request - State: closed - Opened by sylvinite about 4 years ago

#120 - Adding self tests

Pull Request - State: closed - Opened by henningonsbring about 4 years ago

#119 - Improve citability of microSALT

Issue - State: closed - Opened by sylvinite about 4 years ago - 1 comment
Labels: Effort L, Gain L, uSALT

#118 - Completely mock the database for self-tests

Issue - State: closed - Opened by sylvinite about 4 years ago - 1 comment
Labels: Effort M, Gain L, uSALT

#117 - Add static report storage

Issue - State: closed - Opened by sylvinite about 4 years ago - 1 comment
Labels: Effort L, Gain L, uSALT

#116 - Improved report storage architecture

Pull Request - State: closed - Opened by sylvinite about 4 years ago

#115 - Fix reportfolder

Pull Request - State: closed - Opened by sylvinite about 4 years ago

#114 - Better support reruns

Issue - State: closed - Opened by sylvinite about 4 years ago - 1 comment

#113 - Add output prefix

Pull Request - State: closed - Opened by talnor about 4 years ago - 1 comment

#112 - Add prefix to all output files

Issue - State: closed - Opened by sylvinite about 4 years ago - 1 comment

#111 - Deliverables file fix

Pull Request - State: closed - Opened by sylvinite about 4 years ago

#110 - Deliverables file generation on old runs

Issue - State: closed - Opened by sylvinite about 4 years ago
Labels: Effort M, Gain M, uSALT

#109 - Identify microSALT's measurement uncertainty

Issue - State: closed - Opened by sylvinite about 4 years ago
Labels: Effort H, Gain H

#108 - Revise deliverables file

Issue - State: closed - Opened by sylvinite about 4 years ago
Labels: Effort L, Gain L

#107 - HOTFIX: Fetch reference version number for external references

Pull Request - State: closed - Opened by talnor about 4 years ago

#106 - ERROR - Reference update function failed prematurely. Review immediately

Issue - State: closed - Opened by patrikgrenfeldt about 4 years ago - 1 comment
Labels: Effort L, Gain L

#105 - "Total reads" header

Issue - State: closed - Opened by henningonsbring over 4 years ago

#104 - Chronic: microSALT attempts to write to a read only database

Issue - State: closed - Opened by barrystokman over 4 years ago - 6 comments
Labels: Effort L, Gain L

#103 - Patching struct

Pull Request - State: closed - Opened by sylvinite over 4 years ago - 1 comment

#102 - Proper display of non pubMLST-compatible organisms

Pull Request - State: closed - Opened by sylvinite over 4 years ago

#101 - Samtools hotfix

Pull Request - State: closed - Opened by sylvinite over 4 years ago

#100 - Duplicate loci hits are now obfuscated

Pull Request - State: closed - Opened by sylvinite over 4 years ago

#99 - resistance regex supports references version

Pull Request - State: closed - Opened by b4ckm4n over 4 years ago

#98 - Add contamination and duplication checks

Issue - State: closed - Opened by sylvinite almost 5 years ago - 1 comment
Labels: Major

#97 - Replace microSALT LIMS dependency

Issue - State: closed - Opened by sylvinite almost 5 years ago
Labels: Major, Effort M, Gain M, uSALT

#96 - Add additional typing databases

Issue - State: closed - Opened by sylvinite almost 5 years ago
Labels: Major

#95 - Add core genome analysis

Issue - State: closed - Opened by sylvinite almost 5 years ago - 1 comment
Labels: Major

#94 - Improve code coverage to 85%

Issue - State: closed - Opened by sylvinite almost 5 years ago - 1 comment
Labels: Major, Effort M, Gain L, uSALT