Configuration
The Clarity LIMS Product Analytics Integration v1.4.0 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.
This integration supports the following workflows:
NovaSeq 6000 v3
NextSeq 1000/2000
NovaSeq X Series
MiSeq i100 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.
Supported Workflows
Refer to Compatibility under Instruments & Integrations for workflows applicable to Clarity LIMS Product Analytics Integration v1.4.0.
Components
Clarity LIMS Product Analytics Integration v1.4.0 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 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.
New and Updated Workflow-Specific Clarity LIMS Product Analytics Scripts
The installed scripts are the same as that of Clarity LIMS Product Analytics Integration v1.3.0 with additional updates provided in this section.
Workflow-specific scripts work with Illumina workflows. These scripts require a specific set of custom fields and a specific protocol order in the workflow.
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.
Scripts that share the same trigger location and style are combined into a single automation.
New Scripts
Register MiSeq i100 Series Run
Script Name: miseqi100series/register_miseqi100series_run.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 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 Dry Cartridge (MiSeq i100 Series Sequencing) step.
Register MiSeq i100 Series Run Association
Script Name: miseqi100series/miseqi100series_associate_seqrun.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing)
Workflow Version:
v1.0 and later
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Associates the sequencing run with the samples.
This association links the Instrument Run ID with the sample IDs.
Register MiSeq i100 Series RunStarted
Script Name: miseqi100series/miseqi100series_seqrun_started.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing)
Workflow Version:
v1.0 and later
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Records the started time of the sequencing run
Register MiSeq i100 Series RunCompleted
Script Name: miseqi100series/miseqi100series_seqrun_completed.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing)
Workflow Version:
v1.0 and later
Trigger Location: Step
Trigger Style: Automatic upon exit
Purpose/Notes:
Records the following information:
Run completion time
Run status
Run metrics
This script requires the Planned Run ID custom field from the Load to Dry Cartridge (MiSeq i100 Series Sequencing) step.
Updated Scripts
Register NovaSeq X Run
Script Name: novaseqxseries/register_novaseqxseries_run.groovy
Used In:
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)
Workflow Version:
v1.2 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.
This script has been updated to remove the unused RTA Version custom field from the Load to Library Tube Strip (NovaSeq X Series Sequencing) step.
Register NovaSeq X RunCompleted
Script Name: novaseqxseries/novaseqxseries_seqrun_completed.groovy
Used In:
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)
Workflow Version:
v1.2 and later
Trigger Location: Step
Trigger Style: Automatic upon exit
Purpose/Notes:
Records the following information:
Run completion time
Run status
Run metrics
This script has been updated to require the Planned Run ID custom field from the Load to Library Tube Strip (NovaSeq X Series Sequencing) step.
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