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

Basic cgMLST implementation #73

Closed sylvinite closed 10 months ago

sylvinite commented 5 years ago

Description

End-users:

New core-genome distance analysis (based on cgmlst.org)

Primary function of PR

[ ] Hotfix
[ ] Patch
[ ] Minor functionality improvement
[x] New type of analysis
[ ] Backward-breaking functionality improvement
[ ] This change requires internal documents to be updated
[ ] This change requires another repository to be updated

Testing:

bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh new_definitions
Select options: yes, yes, new_definitions
us
source activate S_microSALT
export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json
microSALT analyse project ACC5551 (CG matrix comparison)
microSALT analyse project MIC4109
microSALT analyse project MIC3109

Make sure results converge in accordance with 1797:10 section 3.3.4
Check that the runfile.sh of a single sample has the --careful flag present
Use the command microSALT utils report MIC3109 --output . twice; and make sure both reports are present
Evaluate the report for a "Responsible bioinformatician field" and confirm that it suggests it's you.

Test results

Sign-offs

[ ] Code reviewed by @sylvinite
[ ] Code tested by @octocat
[ ] Approved to run at Clinical-Genomics by @ingkebil