# 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.

{% hint style="danger" %}
Refer to individual integration package requirement on enabling UPA. Note that ICA subscription is only required to view data on ICA UI.
{% endhint %}

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](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/upa-workflow-customization).

## Supported Workflows

Clarity LIMS Product Analytics Integration v1.3.0 supports the applicable workflows identified in [Supported Workflows](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/upa/upa-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.

<details>

<summary>Register Step Started Automation</summary>

**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.

</details>

<details>

<summary>Register Step Completed Automation</summary>

**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.

</details>

<details>

<summary>Register Sample Automation</summary>

**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.

</details>

<details>

<summary>Register Pool Automation</summary>

**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.

</details>

### 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.

{% hint style="danger" %}
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.
{% endhint %}

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

<details>

<summary>Register NextSeq1k2k Run Association</summary>

**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.

</details>

<details>

<summary>Register NextSeq1k2k RunStarted</summary>

**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

</details>

<details>

<summary>Register NextSeq1k2k RunCompleted</summary>

**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.

</details>

<details>

<summary>Register NextSeq1k2k Run</summary>

**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.

</details>

<details>

<summary>Register Analysis Completed</summary>

**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.

</details>

<details>

<summary>Register NovaSeq Run Association</summary>

**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.

</details>

<details>

<summary>Register NovaSeq RunStarted</summary>

**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.

</details>

<details>

<summary>Register NovaSeq RunCompleted</summary>

**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

</details>

<details>

<summary>Register NovaSeq Run</summary>

**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)

</details>

<details>

<summary>Register NovaSeq X Run Association</summary>

**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.

</details>

<details>

<summary>Register NovaSeq X RunStarted</summary>

**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.

</details>

<details>

<summary>Register NovaSeq X RunCompleted</summary>

**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.

</details>

<details>

<summary>Register NovaSeq X Run</summary>

**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.

</details>


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