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 now logs multiple libprep, sequencing and analysis of the same sample- 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 automatically tries if a sample folder is an external name if it doesn't resolve as a Clinical Genomics name
Bug that gave the database user-write permission is now fixed
Span criteria is now percentage instead of decimal based
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
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
Verify that the reports for the 3 projects are in line with doc 1797 section 3.3.4.
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.
Re-run analysis for MIC4107. Check that the report version section of the report updates.
Do an ls -l on the database found in/home/proj/dropbox/microSALT.json`. Make sure it has group-write access
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
Description
WIP. The features of this PR primarily concerns bioinformaticians
Summary of the changes made:
If not self-evident, also mention what prompted the change.
Primary function of PR
Testing
Test routine:
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh qc-thresholdsussource activate S_microSALTexport MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json/home/proj/dropbox/microSALT.json)microSALT analyse project MIC3109microSALT analyse project MIC4107microSALT analyse collection MIC4109/home/proj/dropbox/microSALT.jsonto make all the different warn and fail scenarios trigger. Re-generate a report withmicroSALT utils report.MIC4107. Check that the report version section of the report updates.ls -l on the database found in/home/proj/dropbox/microSALT.json`. Make sure it has group-write accessTest results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR.
Sign-offs