merge from devel to master #18
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prep release 92.8.1
pull from devel to master to create release 92.8.1
Update test data as well.
Add a new instrument format record for NovaSeqX.
This instrument type is no longer classified as a sequencing instrument. It is recognised as a cBot. This instrument type is added as a new type to the graphical listing of instruments.
Correct handling of the 'cBot 2' type instrument
Parse RunParameters.xml and RunInfo.xml to retrieve necessary information. Added a new method - platform_NovaSeqX. Added tests for this new method and some existing methods.
Ability to retrieve info about a NovaSeqX run.
Reimplemented the 'Instrument Types' list on the tracking runs web page so that new NovaSeq models apear there automatically. Excluded very old instrument models.
Tracking server - Novaseqx UI representation
Removed provisions for cif files.
No wash pending status for NovaSeqX
Identification of run completion for NovaSeqX
Updated cycle and tile counting
Record all recent changes
Previous values were causing issues in Jammy. New values use more resources but service is more stable. Originally found at: https://dev.to/joetancy/php-fpm-with-apache2-2mk0 https://thecustomizewindows.com/2023/04/how-to-install-apache-mpm-worker-and-php-fpm-on-ubuntu-server/
Single change event cfg so we can bugfix release
Update devel with bugfix release from master
Limit DRAGEN analysis to human samples only.
pin dbd::mysql to 4.050
Moved tests for aggregation across lanes to a new test scripts. Tests for a new merge by library method will be added to this new test script.
Also refactored the method itself.
We use the name of the Application in RunParameters.xml to detect that the instrument belongs to the NovaSeq type. Newer NovaSeqX instrument we have has the following definition for the application: <Application>NovaSeqXSeries Control Software</Application> This pull request fixes the reg exp we use to ensure that the above definition does not result in the instrument being classified as NovaSeq.
Distinguish between NovaSeq and NovaSeqX RunParams.
Ensure insert size is returned for compositions.
Added a method for aggregation by library
Added records for undocumented changed.
Fixed incorrect string comparison
Name variables consistently. Source dependencies from the branch that is the target.
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