SMRT Link EPPs

[Karl-Svard]

Added

• New EPP for creating Sample Setup CSVs
• New EPP for creating pooling calculation CSVs
• New EPP for calculating Revio pooling volumes
• New EPP for automatically setting Revio sequencing options
• New models and classes for SMRT Link CSV creation

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

[Karl-Svard]

Automations set up on stage

Generate SMRT Link Sample Setup CSV

Step: Preparing ABC Complex (Revio)
Activation type: Manual

bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} files create-smrtlink-sample-setup -f {compoundOutputFileLuid1}"

Calculate Revio Pooling Volumes

Step: Pooling Samples for Sequencing (Revio)
Activation type: Manual

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 'Pool Volume (ul)' --target-concentration-udf 'Target Pool Concentration (pM)'"

Generate SMRT Link Pooling Calculation CSV

NOTE: This automation will probably be removed in the future. It is solely being used for testing purposes

Step: Pooling Samples for Sequencing (Revio)
Activation type: Manual

bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} files create-smrtlink-pooling-calculation -f {compoundOutputFileLuid1}"

Generate SMRT Link Run Design CSV

Step: Set Up Sequencing Run (Revio)
Activation type: Manual

bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} files create-smrtlink-run-design -f {compoundOutputFileLuid1}"

Set Revio Sequencing Options

Step: Set Up Sequencing Run (Revio)
Activation type: Manual (On entry to record details in the future)

bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set set-revio-sequencing-settings"

[idalindegaard]

Vilket otroligt jobb du har gjort! Det har varit mycket nytt för dig att sätta dig in i och sen skapa fungerande skript. Tycker det ser riktigt snyggt och prydligt ut! Har bara några småkommentarer, och frågor om vad några saker innebär mest för att jag är nyfiken