Refactor SMRT Cell pooling calculator to comply with the changes in SMRT Link 25.1

[Karl-Svard]

Added

• New flag --sequencing-container-udf
• New flag --control-volume-udf

Changed

• Updated the calculations to be based on the amount of SMRT cells to be loaded
• The amount of control added to the pool is now calculated and set

Steps to consider while deploying

• Configuration changes:
• Documentation updates:
• Inform users by email:

Review:

• Code approved by
• Tests executed on stage by: (Document the test done with screen shots and description.)
• "Merge and deploy" approved by

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[Karl-Svard]

Tested on stage

New config for automation Calculate Revio Pooling Volumes:

bash -c -l "conda activate cg_lims &&  lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate revio-pooling --concentration-udf 'Concentration (ng/ul)' -v 'Volume of sample (ul)' -b 'Volume Buffer (ul)' --total-volume-udf 'Total Volume (ul)' --size-udf 'Size (bp)' --target-volume-udf 'Total Volume per SMRT Cell (ul)' --target-concentration-udf 'Target Loading Concentration (pM)' --sequencing-container-udf 'SMRT Cells to Load' --control-volume-udf 'Volume Sequencing Control (ul)'"

Success message:

Fail message: