The Clarity LIMS Product Analytics Integration v1.3.0 allows you to aggregate and analyze lab data from the workflow in a single location. Data is uploaded to the Illumina Connected Analytics (ICA) service.
Refer to individual integration package requirement on enabling UPA. Note that ICA subscription is only required to view data on ICA UI.
Clarity LIMS Product Analytics Integration v1.3.0 includes the following changes:
The step_completed.groovy script no longer fails when there are zero outputs for a step, such as no output step and file placeholder.
The nextseq1k2k_analysisrun_completed.groovy script removes the # of > = Q30 Bases (PF) and Mean Quality Score (PF) fields. These fields are no longer supported in the NextSeq 1000/2000 Sequencing v2.4 workflows.
The configure_upa.sh script provides the default value during setup.
Configurable properties are now in the database and can be updated with the omxProps-ConfigTool utility.
This integration also supports the following workflows:
NovaSeq 6000 v3
NextSeq 1000/2000
NovaSeq X Series
Library Prep Validation
Other workflows can be customized to add Clarity LIMS Product Analytics integration capabilities. For more information, refer to Automation and Workflow Customization.
Clarity LIMS Product Analytics Integration v1.3.0 supports the applicable workflows identified in Supported Workflows. The NextSeq 1000/2000 Sequencing v2.4 workflow and later requires this integration due to updates to the nextseq1k2k_analysisrun_completed.groovy script.
Components
Clarity LIMS Product Analytics Integration v1.3.0 includes the following required components:
BaseSpaceLIMS-unified-products-analytics — The core service of the Clarity LIMS Product Analytics Integration. This service installs the daemon service that publishes messages to the product analytics through the ICA service.
BaseSpaceLIMS-unified-products-analytics-scripts — The automation scripts of the Clarity LIMS Product Analytics Integration. If new workflows or new product analytics scripts are introduced, this component can be upgraded.
Automation Scripts
The Clarity LIMS Product Analytics Integration v1.3.0 automation scripts are installed through the BaseSpaceLIMS-unified-products-analytics-scripts RPM. These scripts process Clarity LIMS data and prepare data for upload to the ICA service. There are two types of CLPA scripts: common and workflow-specific.
Common Clarity LIMS Product Analytics Scripts
Common CLPA scripts can be used with any compatible workflows. The following lists and describes the common CLPA scripts.
Register Step Started Automation
Script Name: common/step_started.groovy
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Sends the step start time information to CLPA.
Can be used on any step.
Register Step Completed Automation
Script Name: common/step_completed.groovy
Trigger Location: Step
Trigger Style: Automatic upon exit
Purpose/Notes:
Sends the step completed time information to CLPA.
Can be used on any step.
Register Sample Automation
Script Name: common/register_sample.groovy
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Sends sample information used by the lab workflow to CLPA.
Can be used on any step, but it is recommended that this script is enabled at the first step of the workflow.
Only one Register Sample automation is required per workflow.
Register Pool Automation
Script Name: common/pooling.groovy
Trigger Location: Step
Trigger Style: Automatic upon exit
Purpose/Notes:
Sends pool and library information used by the lab workflow to CLPA.
Can be used on any pooling step.
It is expected that libraries in the pool have been through the Add Labels step. Control samples do not need a label.
Workflow-specific scripts work with Illumina workflows. These scripts require a specific set of custom fields and a specific protocol order in the workflow. The following table shows the workflow-specific scripts.
As many of the scripts in this table share trigger location and style, they are combined into a single automation.
Records the NextSeq1k2k analysis status and result.
This script requires the Cloud Analysis Workflow Versions and Local Analysis Workflow Versions custom fields from the Load to Reagent Cartridge (NextSeq 1000/2000 Sequencing) step.
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)
Workflow Version:
v1.0 and later
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Records the sequencing run configuration.
This script requires all custom fields related to the run configuration from the Load to Library Tube Strip (NovaSeq X Series Sequencing) step.
These scripts require custom fields to be available at their corresponding steps (listed under Clarity LIMS Product Analytics Automation Name and Remarks). Adding or enabling workflow-specific CLPA scripts on non-Illumina workflows is not supported. Data loss can occur.