Workflow Customization
Release Date: July 2024
Document Version: 2
Clarity LIMS Product Analytics (CLPA) Integration is provided to integrate and make available Clarity data to Illumina Connected Analytics (ICA). CLPA allows user to aggregate and analyze lab data from end-to-end workflow in a single location.
These data are uploaded through ICA. Note that ICA subscription is only required to view data on ICA UI.
CLPA integration supports the workflows:
Other workflows (e.g. User's own custom workflow and other Illumina library preparation workflow) can be customized to add CLPA integration capabilities. This guide provides instructions to configure workflow with CLPA integration.
BaseSpaceLIMS-unified-product-analytics and BaseSpaceLIMS-unified-product-analytics-scripts are installed and configured
IPP v2.3 and above is installed and at least 1 supported workflow installed.
Submitted Sample UDF "Illumina Universal Sample Identifier" is required by all UPA automation scripts.
Universal Sample Identifier
The Universal Sample Identifier is a Submitted Sample custom field used by the Register Sample automation. The field assigns a unique identifier to a sample across Illumina workflows. This identifier is used by CLPA to associate the sample with the workflows and analysis that result from a sequencing run and analysis (eg, sample lineage and traceability). Enter the Universal Sample Identifier value during sample accessioning. If the identifier is not provided during sample accessioning, the Register Sample automation does not have access to this value at run time. The CLPA association between the samples and other analytics data is also restricted.
When you install any of the CLPA enabled workflows, the Illumina Universal Sample Identifier custom field is automatically created. If the CLPA enabled workflows are not installed, the custom field must be created manually. When using the Illumina Universal Sample Identifier, the recommended data format is
For more information on installing CLPA enabled workflows, contact Illumina Support.
Add the Illumina Universal Sample Identifier Submitted Sample custom field:
On the main menu, select Configuration, and then select the Custom Fields tab.
On the Global Fields tab, in the Submitted Sample list, select the plus icon to create a custom field.
Enter Illumina Universal Sample Identifier as the field name.
Use Common CLPA Automation
Common CLPA automation scripts are used for workflow customization. Each of these automation scripts logs a message into a log file that is defined with the parameter -l. Because steps can have different log placeholder positions, you must update the -l parameter to reference the correct log file placeholder (E.g., {compoundOutputFileLuid1}).
The following automations can be used on any step.
The Register Sample automation can be used on the Library Prep step. If there are multiple steps in the Library Prep workflow, only add the Register Sample automation to the first step of the protocol. The script is as follows.
The Register Pool automation is available for the Pooling workflow. The script is as follows.
Workflow Customization
Customize the workflow with CLPA automation as follows.
Identify the type of CLPA automation to be added along with the trigger location and style. For more information on CLPA automation types and trigger location and styles, refer to Automation Scripts in Configuration for the UPA version of interest.
Identify the protocol step to be customized.
Check for any existing automations on the triggers (eg, Step/Automatic upon entry or Step/Automatic upon exit). If there is an existing automation, modify the script as follows.
CLPA Additional Configuration (v1.5.0 and onwards)
CLPA v1.5.0 introduced a new feature that allows you to send additional Custom Field information in the step_completed.groovy script. By default, the script does not include any Custom Fields until you configure the following properties on the System Settings page.
Note: Values are case-sensitive, use double quotes around Custom Field names that contain spaces or special characters. Text type Custom Fields will not be included in the data sent.
