Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
Loading...
The documents in this section support the integration of the Clarity LIMS Product Analytics service. This integration supports on premise and Illumina cloud hosted deployments of Clarity LIMS v6.0 and later. Illumina Preset Protocols v2.3 or later is required for automation.
Release Date: July 2024
Document Version: 2
Clarity LIMS Product Analytics (CLPA) integration supports on-premise or hosted installations. Refer to Compatibility under Instruments & Integrations for the instrument integrations that is supported by CLPA.
if any of the samples in the pools has been assigned QC flag in prior steps before entering these steps for UPA Scripts v1.2.0, v1.2.1 and v1.3.0.
The Clarity LIMS Product Analytics Integration v1.5.0 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.
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 .
Refer to under Instruments & Integrations for workflows applicable to Clarity LIMS Product Analytics Integration v1.5.0.
Clarity LIMS Product Analytics Integration v1.5.0 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.
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.
The installed scripts are the same as that of .
Release Date: December 2024
These release notes describe the key changes to software components for the Clarity LIMS Product Analytics Integration v1.4.0.
Refer to Compatibility under Instruments & Integrations.
Support of MiSeq i100 Series sequencing protocol.
Updates of scripts to track NovaSeq X sequencing run:
novaseqxseries/register_novaseqxseries_run.groovy
novaseqxseries/novaseqxseries_seqrun_completed.groovy
Fixed payload generation issue for NextSeq 1000/2000 Sequencing workflow due to automation triggered before step fields are populated.
Release Date: July 2024
Document Version: 2
Clarity LIMS Product Analytics (CLPA) Integration is provided to integrate and make available Clarity data to Illumina Connected Analytics (ICA). CLPA allows user to aggregate and analyze lab data from end-to-end workflow in a single location.
These data are uploaded through ICA. Note that ICA subscription is only required to view data on ICA UI.
CLPA integration supports the workflows:
Updates of CLPA Integration installation script prompts
NextSeq 1000/2000
NovaSeq 6000 v3
NovaSeq X Series
Library Prep Validation
Other workflows (e.g. User's own custom workflow and other Illumina library preparation workflow) can be customized to add CLPA integration capabilities. This guide provides instructions to configure workflow with CLPA integration.
Contact Illumina Support for help to enable UPA on these older workflows:
NovaSeq Workflow v3.3, v3.5 and v3.7
NextSeq 1000/2000 Sequencing v2.1 Workflow
BaseSpaceLIMS-unified-product-analytics and BaseSpaceLIMS-unified-product-analytics-scripts are installed and configured
IPP v2.3 and above is installed and at least 1 supported workflow installed.
Submitted Sample UDF "Illumina Universal Sample Identifier" is required by all UPA automation scripts.
The Universal Sample Identifier is a Submitted Sample custom field used by the Register Sample automation. The field assigns a unique identifier to a sample across Illumina workflows. This identifier is used by CLPA to associate the sample with the workflows and analysis that result from a sequencing run and analysis (eg, sample lineage and traceability). Enter the Universal Sample Identifier value during sample accessioning. If the identifier is not provided during sample accessioning, the Register Sample automation does not have access to this value at run time. The CLPA association between the samples and other analytics data is also restricted.
When you install any of the CLPA enabled workflows, the Illumina Universal Sample Identifier custom field is automatically created. If the CLPA enabled workflows are not installed, the custom field must be created manually. When using the Illumina Universal Sample Identifier, the recommended data format is
For more information on installing CLPA enabled workflows, contact Illumina Support.
Add the Illumina Universal Sample Identifier Submitted Sample custom field:
On the main menu, select Configuration, and then select the Custom Fields tab.
On the Global Fields tab, in the Submitted Sample list, select the plus icon to create a custom field.
Enter Illumina Universal Sample Identifier as the field name.
Set the following properties:
For Field Type, select Text.
For Required Field, select No.
For Read Only, select No.
Select Save.
Common CLPA automation scripts are used for workflow customization. Each of these automation scripts logs a message into a log file that is defined with the parameter -l. Because steps can have different log placeholder positions, you must update the -l parameter to reference the correct log file placeholder (E.g., {compoundOutputFileLuid1}).
The following automations can be used on any step.
Step Started:
Step Completed:
The Register Sample automation can be used on the Library Prep step. If there are multiple steps in the Library Prep workflow, only add the Register Sample automation to the first step of the protocol. The script is as follows.
The Register Pool automation is available for the Pooling workflow. The script is as follows.
Customize the workflow with CLPA automation as follows.
Identify the type of CLPA automation to be added along with the trigger location and style. For more information on CLPA automation types and trigger location and styles, refer to Automation Scripts in Configuration for the UPA version of interest.
Identify the protocol step to be customized.
Check for any existing automations on the triggers (eg, Step/Automatic upon entry or Step/Automatic upon exit). If there is an existing automation, modify the script as follows.
Append the automation after the existing script with &&. Refer to the following examples.
ℹ When modifying an existing script, make sure to append the automation using the correct quotation marks ("). If you are appending an existing script on the next line, make sure that a backslash (\) is added on the last line of the script.
Before append:
After append:
Update the -l parameter to identify the correct Log File placeholder location.
{compoundOutputFileLuid0} in the example refers to the first file placeholder.
If necessary, update the automation name to describe the new behavior.
In the Automation Use section, enable the step.
Save the automation.
If there is not an existing automation on the protocol step, check for an existing automation that has been configured as follows.
Identify the automation that is being used (e.g., Register Step Started).
Make sure that the log file setting for the existing script has the
Go to Configuration and select Lab Work.
Select the step and configure the Trigger Location/Style. Refer to Automation Scripts in Configuration for the UPA version of interest.
After the automation is enabled, the automation configuration option becomes available on the Step configuration page.
Save the step.
CLPA v1.5.0 introduced a new feature that allows you to send additional Custom Field information in the step_completed.groovy script. By default, the script does not include any Custom Fields until you configure the following properties on the System Settings page.
Property
Description
Example
integration.upa.v1.includeStepFields
Configures which Step Custom Fields to include when sending data to ICA.
Supports multiple values separated by commas or use * for all fields.
* to include all populated Step Custom Fields in the step.
Molarity, Progress, "Run name", "Phix %" to send only the 4 specified Step Custom Fields.
integration.upa.v1.excludeStepFields
Configures which Step Custom Fields should not be included in the sent data.
This only takes effect when includeStepFields is configured as *. Supports multiple values separated by commas.
Name, "Invoice number"
integration.upa.v1.includeArtifactFields
Configures which Derived Sample Custom Fields to include when sending data to ICA.
Supports multiple values separated by commas or use * for all fields.
* to include all populated Derived Sample Custom Fields in the step.
Status, "Loading concentration", "pass, failed or completed" to send only the 3 specified Derived Sample Custom Fields.
integration.upa.v1.excludeArtifactFields
Configures which Derived Sample Custom Fields should not be included in the sent data.
This only takes effect when includeArtifactFields is configured as *. Supports multiple values separated by commas.
Sex, "Case number"
Note: Values are case-sensitive, use double quotes around Custom Field names that contain spaces or special characters. Text type Custom Fields will not be included in the data sent.
Release Date: November 2025
These release notes describe the key changes to software components for the Clarity LIMS Product Analytics Integration v1.5.0.
Refer to Compatibility under Instruments & Integrations.
step_start.groovy now includes the name of technician that started the step.
step_completed.groovy now sends these additional information:
Name of technician completing the step
Improved handling of empty UDF values.
Updated configure_upa.sh script.
Fixed payload generation issue for NextSeq 1000/2000 Sequencing workflow due to automation triggered before step fields are populated.
Fixed configuration issue when switching CLPA from workgroup to personal account.
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"usi.<clarity_hostname>.<sampleId>bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/register_sample.groovy'bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/pooling.groovy'Reagent lot associated with the step (if any)
Instrument associated with the step (if any)
Step custom field (if configured)
Input artifact custom field (if configured)
Output artifact custom field (if configured)
Added new optional properties to support the sending of custom field data:
integration.upa.v1.includeStepFields
integration.upa.v1.excludeStepFields
integration.upa.v1.includeArtifactFields
integration.upa.v1.excludeArtifactFields
If the Log File location is the same, enable the step in the Automation Use section.
If the Log File location is not the same, create a separate automation and enable the step in the Automation Use section of the new automation.
Save the automation.
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar \
script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} \
-l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"The novaseqxseries_associate_seqrun.groovy and nextseq1k2k_associate_seqrun.groovy scripts can now associate libraries to sequencing run when any sample in the pool(s) has been assigned QC flags prior to entering the AUTOMATED - Sequencing Run step in the workflow.
The pooling.groovy script no longer fails when any samples in the pool(s) has been assigned QC flags prior to entering pooling steps in the workflow.
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.
Refer to individual integration package requirement on enabling UPA. Note that ICA subscription is only required to view data on ICA UI.
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 .
Refer to under Instruments & Integrations for workflows applicable to Clarity LIMS Product Analytics Integration v1.4.0.
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.
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.
The installed scripts are the same as that of with additional updates provided in this section.
Workflow-specific scripts work with Illumina workflows. These scripts require a specific set of custom fields and a specific protocol order in the workflow.
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.
Scripts that share the same trigger location and style are combined into a single automation.
Script Name: miseqi100series/register_miseqi100series_run.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing)
Workflow Version:
Script Name: miseqi100series/miseqi100series_associate_seqrun.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing)
Workflow Version
Script Name: miseqi100series/miseqi100series_seqrun_started.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing)
Workflow Version
Script Name: miseqi100series/miseqi100series_seqrun_completed.groovy
Used In:
AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing)
Workflow Version
The Clarity LIMS Product Analytics Integration v1.3.1 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.
This integration supports the following workflows:
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.
Clarity LIMS Product Analytics Integration v1.3.1 supports the applicable workflows identified in Supported Workflows. These workflows require this integration due to fixes that supports CLPA generation of payload (for pooling step) and association of library to sequencing run when samples go through QC step in workflow:
NextSeq 1000/2000 Sequencing v2.4 workflow and later
NovaSeq X Series Sequencing v1.1 workflow and later
Clarity LIMS Product Analytics Integration v1.3.1 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.
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. The installed scripts are the same as that of Clarity LIMS Product Analytics Integration v1.3.0
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.
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.
v1.0 and later
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Records the started time of the sequencing run
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.
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.
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.
Release Date: June 2024
These release notes describe the key changes to software components for the Clarity LIMS Product Analytics Integration v1.3.0.
Refer to Compatibility under Instruments & Integrations.
Configurable properties can now be configured via System Settings.
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.
The step_completed.groovy script no longer fails when there are zero outputs for a step, such as no output step and file placeholder.
if any of the samples in the pools has been assigned QC flag in prior steps before entering these steps.
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.
Clarity LIMS Product Analytics Integration v1.2.0 supports the applicable workflows identified in .
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.
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 CLPA scripts can be used with any compatible workflows. The following lists and describes the common CLPA scripts.
Script Name: common/step_started.groovy
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Script Name: common/step_completed.groovy
Trigger Location: Step
Trigger Style: Automatic upon exit
Purpose/Notes:
Script Name: common/register_sample.groovy
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Script Name: common/pooling.groovy
Trigger Location: Step
Trigger Style: Automatic upon exit
Purpose/Notes:
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.
Script Name: nextseq1k2k/nextseq1k2k_associate_seqrun.groovy
Used In:
AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)
Trigger Location: Step
Script Name: nextseq1k2k/nextseq1k2k_seqrun_started.groovy
Used In:
AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)
Trigger Location: Step
Script Name: nextseq1k2k/nextseq1k2k_seqrun_completed.groovy
Used In:
AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)
Trigger Location: Step
Script Name: nextseq1k2k/register_nextseq1k2k_run.groovy
Used In:
AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)
Trigger Location: Step
Script Name: nextseq1k2k/nextseq1k2k_analysisrun_completed.groovy
Used In:
Demultiplexing (NextSeq 1000/2000 Sequencing)
Trigger Location: Step
Script Name: novaseq6000/novaseq_associate_seqrun.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Trigger Location: Step
Script Name: novaseq6000/novaseq_seqrun_started.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Trigger Location: Step
Script Name: novaseq6000/novaseq_seqrun_completed.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Trigger Location: Step
Script Name: novaseq6000/register_novaseq_run.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Trigger Location: Step
Script Name: novaseqxseries/novaseqxseries_associate_seqrun.groovy
Used In:
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)
Trigger Location: Step
Script Name: novaseqxseries/novaseqxseries_seqrun_started.groovy
Used In:
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)
Trigger Location: Step
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.
Refer to individual integration package requirement on enabling UPA. Note that ICA subscription is only required to view data on ICA UI.
This integration supports the following workflows:
Can be used on any step.
Can be used on any step.
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.
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.
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.
Purpose/Notes:
Records the started time of the sequencing run
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.
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.
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.
Purpose/Notes:
Associates the sequencing run with the samples.
This association links the Instrument Run ID with the sample IDs.
Purpose/Notes:
Records the started time of the sequencing run.
Purpose/Notes:
Records the following information:
Run completion time
Run status
Run metrics
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)
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.
Purpose/Notes:
Records the started time of the sequencing run.
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.
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.
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.
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.
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.
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 CLPA scripts can be used with any compatible workflows. The following lists and describes the common CLPA scripts.
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.
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 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.
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.
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
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
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.
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.
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.
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
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)
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.
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.
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
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.
This script requires the Cloud Run ID custom field from the Load to Reagent Cartridge (NextSeq 1000/2000 Sequencing) step.
This script also requires the Cloud Run ID custom field from the Load to Library Tube Strip (NovaSeq X Series Sequencing) step.
Release Date: June 2023
These release notes describe the key changes to software components for the Clarity LIMS Product Analytics Integration v1.2.0.
Refer to Compatibility under Instruments & Integrations.
Updated Java libraries and thrid party dependency libraries
Updated Groovy version.
Fixed security vulnerabilities.
if any of the samples in the pools has been assigned QC flag in prior steps before entering these steps.