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:
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 .
Clarity LIMS Product Analytics Integration v1.3.0 supports the applicable workflows identified in . 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/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 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:
Script Name: nextseq1k2k/nextseq1k2k_seqrun_started.groovy
Used In:
AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)
Workflow Version:
Script Name: nextseq1k2k/nextseq1k2k_seqrun_completed.groovy
Used In:
AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)
Workflow Version:
Script Name: nextseq1k2k/register_nextseq1k2k_run.groovy
Used In:
AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing)
Workflow Version:
Script Name: nextseq1k2k/nextseq1k2k_analysisrun_completed.groovy
Used In:
Demultiplexing (NextSeq 1000/2000 Sequencing)
Workflow Version:
Script Name: novaseq6000/novaseq_associate_seqrun.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Workflow Version:
Script Name: novaseq6000/novaseq_seqrun_started.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Workflow Version:
Script Name: novaseq6000/novaseq_seqrun_completed.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Workflow Version:
Script Name: novaseq6000/register_novaseq_run.groovy
Used In:
AUTOMATED - NovaSeq Run (NovaSeq 6000)
Workflow Version:
Script Name: novaseqxseries/novaseqxseries_associate_seqrun.groovy
Used In:
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)
Workflow Version:
Script Name: novaseqxseries/novaseqxseries_seqrun_started.groovy
Used In:
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing)
Workflow Version:
Can be used on any step.
Can be used on any step.
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.
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.
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.
v2.2
v2.3 and later
Trigger Location: Step
Trigger Style: Automatic upon entry
Purpose/Notes:
Records the started time of the sequencing run
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.
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.
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.
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.
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.
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
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)
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 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.
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.
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.