Qc accreditation

[sylvinite]

Description

WIP. The features of this PR primarily concerns bioinformaticians

Summary of the changes made:

• QC thresholds are now defined in config and auto-colors the QC report based on thresholds (NTC samples are excluded)
• Reports are now saved in an additional 'reports' folder for easier access
• Reports are now given distinct versions (as opposed to implied by date)
• Command 'analyse collection' was added to easily run Clinical Genomics samples from multiple projects
• microSALT now falls back to external sample name, if said sample doesn't resolve to a Clinical Genomics name
• Bug that gave the database user-write permission is now fixed
• Span criteria is now percentage instead of decimal based
• microSALT now warns if fastq file exceeds 1GB

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

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

Test routine:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh qc-accreditation
• us
• source activate S_microSALT
• export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json
• Remove existing database (path for it found in /home/proj/dropbox/microSALT.json)
• microSALT analyse project MIC3109
• microSALT analyse project MIC4107
• microSALT analyse collection MIC4109

1. Verify that the reports for the 3 projects are in line with doc 1797 section 3.3.4.
2. Change the thresholds section of /home/proj/dropbox/microSALT.json to make all the different warn and fail scenarios trigger. Re-generate a report with microSALT utils report.
3. Re-run analysis for MIC4107. Check that the report version section of the report updates.
4. Do an ls -l on the database found in/home/proj/dropbox/microSALT.json`. Make sure it has group-write access
5. Possibly more to come.. (External names, multiprep)

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