# Configuration

The Clarity LIMS Product Analytics Integration v1.4.0 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
* MiSeq i100 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

Refer to [Compatibility](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/compatibility) under Instruments & Integrations for workflows applicable to Clarity LIMS Product Analytics Integration v1.4.0.

* [Library Prep Validation (available from Illumina Preset Protocols)](https://help.connected.illumina.com/clarity-lims/compatibility#illumina-preset-protocol)
* [MiSeq i100 Series (Hosted)](https://help.connected.illumina.com/clarity-lims/compatibility#miseq-i100-series)
* [NextSeq 1000/2000 (Hosted)](https://help.connected.illumina.com/clarity-lims/compatibility#nextseq-10002000)
* [NovaSeq X Series (Hosted)](https://help.connected.illumina.com/clarity-lims/compatibility#novaseq-x-series)
* [NovaSeq 6000 (API-based)](https://help.connected.illumina.com/clarity-lims/compatibility#novaseq-6000)

## Components

Clarity LIMS Product Analytics Integration v1.4.0 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 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.

### New and Updated Workflow-Specific Clarity LIMS Product Analytics Scripts

{% hint style="danger" %}
The installed scripts are the same as that of [Clarity LIMS Product Analytics Integration v1.3.0](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/clarity-lims-product-analytics-v1.3.0/upa-v1.3.0-configuration#automation-scripts) with additional updates provided in this section.
{% endhint %}

Workflow-specific scripts work with Illumina workflows. These scripts require a specific set of custom fields and a specific protocol order in the workflow.

{% 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 %}

Scripts that share the same trigger location and style are combined into a single automation.

#### New Scripts

<details>

<summary>Register MiSeq i100 Series Run</summary>

**Script Name**: miseqi100series/register\_miseqi100series\_run.groovy

**Used In**:

* AUTOMATED - Sequencing Run (MiSeq i100 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 Dry Cartridge (MiSeq i100 Series Sequencing) step.

</details>

<details>

<summary>Register MiSeq i100 Series Run Association</summary>

**Script Name**: miseqi100series/miseqi100series\_associate\_seqrun.groovy

**Used In**:

* AUTOMATED - Sequencing Run (MiSeq i100 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 MiSeq i100 Series RunStarted</summary>

**Script Name**: miseqi100series/miseqi100series\_seqrun\_started.groovy

**Used In**:

* AUTOMATED - Sequencing Run (MiSeq i100 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 MiSeq i100 Series RunCompleted</summary>

**Script Name**: miseqi100series/miseqi100series\_seqrun\_completed.groovy

**Used In**:

* AUTOMATED - Sequencing Run (MiSeq i100 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 requires the Planned Run ID custom field from the Load to Dry Cartridge (MiSeq i100 Series Sequencing) step.

</details>

#### Updated Scripts

<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**:

* v1.2 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.
  * This script has been updated to remove the unused RTA Version custom field from the Load to Library Tube Strip (NovaSeq X Series Sequencing) step.

</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**:

* v1.2 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 has been updated to require the Planned Run ID custom field from the Load to Library Tube Strip (NovaSeq X Series Sequencing) step.

</details>