# 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.

{% 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 %}

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](https://help.claritylims.illumina.com/instruments-and-integrations/upa/upa-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.

## **Supported Workflows**

Clarity LIMS Product Analytics Integration v1.2.0 supports the applicable workflows identified in [Supported Workflows](https://help.claritylims.illumina.com/instruments-and-integrations/upa/upa-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.

<details>

<summary>Register Step Started Automation</summary>

**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.

</details>

<details>

<summary>Register Step Completed Automation</summary>

**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.

</details>

<details>

<summary>Register Pool Automation</summary>

**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.

</details>

<details>

<summary>Register Sample Automation</summary>

**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.

</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 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 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.

<details>

<summary>Register NextSeq1k2k Run Association</summary>

**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.

</details>

<details>

<summary>Register NextSeq1k2k RunStarted</summary>

**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

</details>

<details>

<summary>Register NextSeq1k2k RunCompleted</summary>

**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.

</details>

<details>

<summary>Register NextSeq1k2k Run</summary>

**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.

</details>

<details>

<summary>Register Analysis Completed</summary>

**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.

</details>

<details>

<summary>Register NovaSeq Run Association</summary>

**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.

</details>

<details>

<summary>Register NovaSeq RunStarted</summary>

**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.

</details>

<details>

<summary>Register NovaSeq RunCompleted</summary>

**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

</details>

<details>

<summary>Register NovaSeq Run</summary>

**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)

</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)

**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)

**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)

**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)

**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>