New library normalization script for Revio

[idalindegaard]

Added

• new script file in EPPs>udfs>calculate named library_normalization_revio.py
• updated base.py with the new script
• added+moved out some functions that are used in both the new script and in library_normalization.py

Changed

Fixed

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

[idalindegaard]

Testing of new and updated scripts

Step: Normalization of Revio (WGS) samples for sequencing v1

New EPP "Calculate Volume Normalization (Revio)"

bash -c -l "conda activate cg_lims &&  lims -c  /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid}  udf calculate library-normalization-revio -sudf 'Volume (ul)' -b 'Volume Buffer (ul)' --concentration-udf 'Concentration' --final-concentration-udf 'Final Concentration (ng/ul)' --total-volume-udf 'Total Volume (ul)'"

Before running the EPP:

Successful calculation of volumes:

Error messages when the sample concentration is lower than the target concentration:

Error messages with missing value for the Volume (ul) udf

Error messages with missing value for the Concentration udf

Step: Normalization of WGS samples for sequencing v1

No EPP change.

Successful calculation of volumes:

Error message when the sample concentration is lower than the target concentration:

Error message with missing value for the Concentration (nM) udf

Error log:

Conclusion: The tests were successful! The new script+EPP works and nothing broke in the updated library normalization script

[Karl-Svard]

Nice work 🔥

I did some very minor commits that you could take a look at if you're interested