Clarity LIMS Software
Illumina Connected Software

Configuration

The Clarity LIMS Product Analytics Integration v1.2.0 allows you to aggregate and analyze lab data from the workflow in a single location. The integration also integrates Clarity LIMS data into the Clarity LIMS Product Analytics (CLPA) service. Data are 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.

CLPA integration supports the workflows: NovaSeq 6000 v3, NextSeq 1000/2000, NovaSeq X Series and 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 v1.2.0 is used with Clarity LIMS v6.2 and later. The integration supports on-site and hosted installations of Clarity LIMS. Illumina Preset Protocols (IPP) v2.6 or later is required for automation.

Known Issues

Supported Workflows

Clarity LIMS Product Analytics Integration v1.2.0 supports the applicable workflows identified in Supported Workflows.

Components

Clarity LIMS Product Analytics Integration v1.2.0 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 Illumina Connected Analytics.

  • 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 v1.2.0 automation scripts are installed through the BaseSpaceLIMS-unified-products-analytics-scripts RPM. These scripts process Clarity LIMS data and prepare data for upload to Illumina Connected Analytics. 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:

  • Saves information on the step start time.

  • 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:

  • Saves information on the step-completed time.

  • Can be used on any step.

Register Pool Automation

Script Name: common/register_sample.groovy

Trigger Location: Step

Trigger Style: Automatic upon entry

Purpose/Notes:

  • Saves sample information used by the lab workflow.

  • Can be used on any step.

  • It is recommended that this script is enabled at the first step of the workflow.

  • Only one is required per workflow.

  • This script requires the Submitted Sample field named Illumina Universal Sample Identifier.

Register Sample Automation

Script Name: common/pooling.groovy

Trigger Location: Step

Trigger Style: Automatic upon exit

Purpose/Notes:

  • Saves pool and library information used by the Clarity LIMS workflow.

  • 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 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 shows the workflow-specific scripts.

⚠️ 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 share trigger location and style, they are combined into a single automation. Unless specified otherwise, the automations are applicable to all CLPA-enabled versions of the relevant workflow steps.

Register NextSeq1k2k Run Association

Script Name: nextseq1k2k/nextseq1k2k_associate_seqrun.groovy

Used In:

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

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 NextSeq1k2k RunStarted

Script Name: nextseq1k2k/nextseq1k2k_seqrun_started.groovy

Used In:

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

Trigger Location: Step

Trigger Style: Automatic upon entry

Purpose/Notes:

  • Records the started time of the sequencing run

Register NextSeq1k2k RunCompleted

Script Name: nextseq1k2k/nextseq1k2k_seqrun_completed.groovy

Used In:

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

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.

Register NextSeq1k2k Run

Script Name: nextseq1k2k/register_nextseq1k2k_run.groovy

Used In:

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

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.

Register Analysis Completed

Script Name: nextseq1k2k/nextseq1k2k_analysisrun_completed.groovy

Used In:

  • Demultiplexing (NextSeq 1000/2000 Sequencing)

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.

Register NovaSeq Run Association

Script Name: novaseq6000/novaseq_associate_seqrun.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

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 NovaSeq RunStarted

Script Name: novaseq6000/novaseq_seqrun_started.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

Trigger Location: Step

Trigger Style: Automatic upon entry

Purpose/Notes:

  • Records the started time of the sequencing run.

Register NovaSeq RunCompleted

Script Name: novaseq6000/novaseq_seqrun_completed.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

Trigger Location: Step

Trigger Style: Automatic upon exit

Purpose/Notes:

  • Records the following information:

    • Run completion time

    • Run status

    • Run metrics

Register NovaSeq Run

Script Name: novaseq6000/register_novaseq_run.groovy

Used In:

  • AUTOMATED - NovaSeq Run (NovaSeq 6000)

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)

Register NovaSeq X Run Association

Script Name: novaseqxseries/novaseqxseries_associate_seqrun.groovy

Used In:

  • AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)

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 NovaSeq X RunStarted

Script Name: novaseqxseries/novaseqxseries_seqrun_started.groovy

Used In:

  • AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)

Trigger Location: Step

Trigger Style: Automatic upon entry

Purpose/Notes:

  • Records the started time of the sequencing run.

Register NovaSeq X RunCompleted

Script Name: novaseqxseries/novaseqxseries_seqrun_completed.groovy

Used In:

  • AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)

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.

Register NovaSeq X Run

Script Name: novaseqxseries/register_novaseqxseries_run.groovy

Used In:

  • AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)

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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