Added support to run ANY resistance DB

[sylvinite]

Description

The features of this PR primarily concerns end-users

Summary of the changes made:

• [x] Removed explicit ExPEC integration
• [x] Added cli line to add custom virulence calls
• [x] Added VFDB parsing support
• [x] Put if case around swedac logotype based on RUNID
• [x] Add MultiQC run to microSALT
• [x] Finish up microSALT webserver support
• [x] Fixed a bug where a new allele was reported as a known ST
• [x] Added CLI command to update databases
• [x] Add custom_target to former ExPEC entries.

Primary function of PR

• [ ] Hotfix
• [ ] Patch
• [x] Minor functionality improvement
• [ ] 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

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Test routine to verify the stability of the PR:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh BRANCHNAME

• us

• _source activate S_microSALT_

• Start analysis of ACC7470 normally

• Start analysis of ACC5551 with --custom_target flag pointing to https://github.com/Clinical-Genomics/microSALT/tree/master/unique_references/ExPEC.fsa

• Verify that the results for projects ACC5551 are consistent with the results attached to AMSystem doc 1490, Microbial_WGS.xlsx

  • Check that ACC7470 doesn't have the SWEDAC logo
  • Check that ACC7470 has a New allele for it's length-deprived sample
  • Look for MultiQC results in e-mailed results, make sure the report isnt broken

• Run microSALT utils refer update. Make sure it works / doesn't error and crash.

• Run microSALT utils view. Make sure the started webpage / webserver looks ok.

Test results

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

Sign-offs

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

[talnor]

Closing stale PR. Further development will be done in JASEN.