Release candidate 4.0.0

[samuell]

Description

##Remove elements in cursive as needed.##

The features of this PR primarily concerns end-users/bioinformaticians/internals

Summary of the changes made:

If not self-evident, mention what prompted the change.

Primary function of PR

• [ ] Hotfix
• [ ] Patch
• [ ] Minor functionality improvement
• [ ] New type of analysis
• [x] 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_
• _(SITUATIONAL) export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json_
• Select a relevant subset of the following:
• microSALT analyse project MIC3109
• microSALT analyse project MIC4107
• microSALT analyse project MIC4109
• microSALT analyse project ACC5551

_Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 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

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