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Illumina Connected Software

Configuration

Release Date: July 2024

Document Version: 2

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.

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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

  • 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.

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Supported Workflows

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.

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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.

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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.

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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.

chevron-rightRegister Step Started Automationhashtag

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.

chevron-rightRegister Step Completed Automationhashtag

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.

chevron-rightRegister Sample Automationhashtag

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.

chevron-rightRegister Pool Automationhashtag

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.

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Workflow-Specific Clarity LIMS Product Analytics Scripts

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.

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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.

As many of the scripts in this table share trigger location and style, they are combined into a single automation.

chevron-rightRegister NextSeq1k2k Run Associationhashtag

Script Name: nextseq1k2k/nextseq1k2k_associate_seqrun.groovy

Used In:

  • AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)

Workflow Version:

  • v2.2

  • v2.3 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.

chevron-rightRegister NextSeq1k2k RunStartedhashtag

Script Name: nextseq1k2k/nextseq1k2k_seqrun_started.groovy

Used In:

  • AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)

Workflow Version:

  • v2.2

  • v2.3 and later

Trigger Location: Step

Trigger Style: Automatic upon entry

Purpose/Notes:

  • Records the started time of the sequencing run

chevron-rightRegister NextSeq1k2k RunCompletedhashtag

Script Name: nextseq1k2k/nextseq1k2k_seqrun_completed.groovy

Used In:

  • AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)

Workflow Version:

  • v2.2

  • v2.3 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 Cloud Run ID custom field from the Load to Reagent Cartridge (NextSeq 1000/2000 Sequencing) step.

chevron-rightRegister NextSeq1k2k Runhashtag

Script Name: nextseq1k2k/register_nextseq1k2k_run.groovy

Used In:

  • AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)

Workflow Version:

  • v2.2

  • v2.3 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 in the Load to Reagent Cartridge (NextSeq 1000/2000 Sequencing) step.

chevron-rightRegister Analysis Completedhashtag

Script Name: nextseq1k2k/nextseq1k2k_analysisrun_completed.groovy

Used In:

  • Demultiplexing (NextSeq 1000/2000 Sequencing)

Workflow Version:

  • v2.2

  • v2.3 and later

Trigger Location: Step

Trigger Style: Automatic upon exit

Purpose/Notes:

  • 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.

chevron-rightRegister NovaSeq Run Associationhashtag

Script Name: novaseq6000/novaseq_associate_seqrun.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

Workflow Version:

  • v3.4

  • v3.6

  • v3.8 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.

chevron-rightRegister NovaSeq RunStartedhashtag

Script Name: novaseq6000/novaseq_seqrun_started.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

Workflow Version:

  • v3.4

  • v3.6

  • v3.8 and later

Trigger Location: Step

Trigger Style: Automatic upon entry

Purpose/Notes:

  • Records the started time of the sequencing run.

chevron-rightRegister NovaSeq RunCompletedhashtag

Script Name: novaseq6000/novaseq_seqrun_completed.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

Workflow Version:

  • v3.4

  • v3.6

  • v3.8 and later

Trigger Location: Step

Trigger Style: Automatic upon exit

Purpose/Notes:

  • Records the following information:

    • Run completion time

    • Run status

    • Run metrics

chevron-rightRegister NovaSeq Runhashtag

Script Name: novaseq6000/register_novaseq_run.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

Workflow Version:

  • v3.4

  • v3.6

  • v3.8 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.

    • For Standard workflow: Dilute and Denature (NovaSeq 6000)

    • For XP workflow: Load to Flow Cell (NovaSeq 6000)

chevron-rightRegister NovaSeq X Run Associationhashtag

Script Name: novaseqxseries/novaseqxseries_associate_seqrun.groovy

Used In:

  • AUTOMATED - Sequencing Run (NovaSeq X 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.

chevron-rightRegister NovaSeq X RunStartedhashtag

Script Name: novaseqxseries/novaseqxseries_seqrun_started.groovy

Used In:

  • 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 started time of the sequencing run.

chevron-rightRegister NovaSeq X RunCompletedhashtag

Script Name: novaseqxseries/novaseqxseries_seqrun_completed.groovy

Used In:

  • AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)

Workflow Version:

  • v1.0 and v1.1

Trigger Location: Step

Trigger Style: Automatic upon exit

Purpose/Notes:

  • Records the following information:

    • Run completion time

    • Run status

    • Run metrics

  • This script also requires the Cloud Run ID custom field from the Load to Library Tube Strip (NovaSeq X Series Sequencing) step.

chevron-rightRegister NovaSeq X Runhashtag

Script Name: novaseqxseries/register_novaseqxseries_run.groovy

Used In:

  • 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.

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