Additional typing definitions

[sylvinite]

Description

The features of this PR primarily concerns end-users.

• Added Virulence typing definitions
• Added Plasmid identification definitions
• Added FimH typing definitions
• References in config file is now a single parent path

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

This is a description of the tests necessary to verify the stability of the PR.

Basic test routine:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh BRANCHNAME
• _Select installer options "release", "SmicroSALT" and "BRANCHNAME"
• us
• _source activate S_microSALT_
• _export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json_
• microSALT analyse project MIC3109
• microSALT analyse project MIC3552
• microSALT analyse project MIC3557
• microSALT analyse project MIC4107
• microSALT analyse project MIC4109

_Verify that the results for projects MIC3109, MIC3552, MIC3557, MIC4107 & MIC4109 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

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