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Configuration

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.

Known Issues

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.

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 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.

⚠️ 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.

Register NextSeq1k2k Run Association

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.

Register NextSeq1k2k RunStarted

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

Register NextSeq1k2k RunCompleted

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.

Register NextSeq1k2k Run

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.

Register Analysis Completed

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.

Register NovaSeq Run Association

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.

Register NovaSeq RunStarted

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.

Register NovaSeq RunCompleted

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

Register NovaSeq Run

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)

Register NovaSeq X Run Association

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.

Register NovaSeq X RunStarted

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.

Register NovaSeq X RunCompleted

Script Name: novaseqxseries/novaseqxseries_seqrun_completed.groovy

Used In:

  • AUTOMATED - Sequencing Run (NovaSeq X 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 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)

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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