Illumina Connected Software

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 also 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.

New Features and Updates

Clarity LIMS Product Analytics Integration v1.4.0 includes the following changes:

  • Support of MiSeq i100 Series instrument

  • Updates of scripts to track NovaSeq X sequencing run:

    • novaseqxseries/register_novaseqxseries_run.groovy

    • novaseqxseries/novaseqxseries_seqrun_completed.groovy

  • Updates of CLPA Integration installation script prompts

  • Fix payload generation issue for NextSeq 1000/2000 Sequencing workflow due to automation triggered before step fields are populated.

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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