Clarity LIMS Software
Illumina Connected Software

Manual Upgrade

⚠️ NovaSeq Integration Package v3.6.0 contains modifications to the existing automations from NovaSeq Integration Package v3.5.1. The NovaSeq Sequencing v3.8 workflow and Illumina Preset Protocols (IPP) v2.6 are required for the integration package to work.

  • If you do not want to upgrade the existing NovaSeq Sequencing workflow to the latest version through IPP, you can update the workflow configuration manually from NovaSeq Integration package v3.5.1 to v3.6.0 by completing the following steps.

  • For manual upgrades from versions prior to v3.5.1, please refer to manual upgrade guides for those versions.

The key change between NovaSeq 6000 v3.7 workflow and NovaSeq 6000 v3.8 workflow that comes with NovaSeq 6000 Integration v3.6.0 is the addition of Clarity LIMS Product Analytics (CLPA) enabled automation scripts. If CLPA is not required, it is not necessary to perform this manual upgrade.

Add New Automations

  1. From Configuration, select the Automation tab.

  2. Add the automations in the following table:

Automation Name

Command Line

Master Steps

Register NovaSeq RunCompleted & Register Step Completed

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/novaseq6000/novaseq_seqrun_completed.groovy' && /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'"

  • AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.7)

Register Pools & Register Step Completed

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' && /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'"

  • Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v3.7)

  • Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v3.7)

Register Step Completed

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'"

  • Dilute, Denature & ExAmp (NovaSeq 6000 v3.7)

  • Load to Flowcell (NovaSeq 6000 v3.7)

Register Step Started¹

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'"

  • Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v3.7)

  • Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v3.7)

Register Step Started²

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/step_started.groovy'"

  • Define Run Format (NovaSeq 6000 v3.7)

Register Step Started & Register NovaSeq Run & Register NovaSeq Run Association & Register NovaSeq RunStarted

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/step_started.groovy' && /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/novaseq6000/register_novaseq_run.groovy' && /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/novaseq6000/novaseq_associate_seqrun.groovy' && /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/novaseq6000/novaseq_seqrun_started.groovy'"

  • AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.7)

¹ This automation has -l {compoundOutputFileLuid0} in the log file output index.

² This automation has -l {compoundOutputFileLuid1} in the log file output index.

Modify Routing Script Automation on Define Run Format (NovaSeq 6000 v3.7) Step

  1. From Configuration, select the Automation tab.

  2. Under the Step Automation tab, select the Routing Script automation that is enabled on the Define Run Format (NovaSeq 6000 v3.7) master step.

  3. In the automation name field, change the name to Routing Script & Register Step Completed.

  4. Update the existing command line as follows. Changes are in red.

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Loading Workflow Type' \ --FIELD_VALUE 'NovaSeq Standard' \ --WORKFLOW 'NovaSeq 6000 v3.7' \ --STEP 'Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v3.7)' \ --INPUTS_OR_OUTPUTS 'INPUTS' \ \ --FIELD_NAME 'Loading Workflow Type' \ --FIELD_VALUE 'NovaSeq Xp' \ --WORKFLOW 'NovaSeq 6000 v3.7' \ --STEP 'Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v3.7)' \ --INPUTS_OR_OUTPUTS 'INPUTS' \ && /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'"

  5. Select Save.

Modify Routing Script Automation on Dilute and Denature (NovaSeq 6000 v3.7) Step

  1. From Configuration, select the Automation tab.

  2. Under the Step Automation tab, select the Routing Script automation that is enabled on the Dilute and Denature (NovaSeq 6000 v3.7) master step.

  3. In the automation name field, change the name to Routing Script & Register Step Completed.

  4. Update the existing command line as follows. Changes are in red.

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Loading Workflow Type' \ --FIELD_VALUE 'NovaSeq Standard' \ --WORKFLOW 'NovaSeq 6000 v3.7' \ --STEP 'Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v3.7)' \ --INPUTS_OR_OUTPUTS 'INPUTS' \ \ --FIELD_NAME 'Loading Workflow Type' \ --FIELD_VALUE 'NovaSeq Xp' \ --WORKFLOW 'NovaSeq 6000 v3.7' \ --STEP 'Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v3.7)' \ --INPUTS_OR_OUTPUTS 'INPUTS' \ && /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'"

  5. Select Save.

Modify Validate Inputs and Selected Container Automation on Load to Flowcell (NovaSeq 6000 v3.7) Step

  1. From Configuration, select the Automation tab.

  2. Under the Step Automation tab, select the Validate Inputs and Selected Container automation that is enabled on the Load to Flowcell (NovaSeq 6000 v3.7) master step.

  3. In the automation name field, change the name to Validate Inputs and Selected Container & Register Step Started.

  4. Update the existing command line as follows. Changes are in red.

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:validate_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -validateSelectedContainer true && /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'"

  5. Select Save.

Modify Validate Inputs Flowcell Type Automation on Dilute, Denature & ExAmp (NovaSeq 6000 v3.7) Step

  1. From Configuration, select the Automation tab.

  2. Under the Step Automation tab, select the Validate Inputs Flowcell Type automation that is enabled on the Dilute, Denature & ExAmp (NovaSeq 6000 v3.7) master step.

  3. In the automation name field, change the name to Validate Inputs Flowcell Type & Register Step Started.

  4. Update the existing command line as follows. Changes are in red.

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:validate_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} && /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'"

  5. Select Save.

Modify Validate Single Input Automation on Dilute and Denature (NovaSeq 6000 v3.7) Step

  1. From Configuration, select the Automation tab.

  2. Under the Step Automation tab, select the Validate Single Input automation that is enabled on the Dilute and Denature (NovaSeq 6000 v3.7) master step.

  3. In the automation name field, change the name to Validate Single Input & Register Step Started.

  4. Update the existing command line as follows. Changes are in red.

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:validateSampleCount -min 1 -max 1 && /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'"

  5. Select Save.

Set Trigger Location and Style for New Automations

  1. From Configuration, select the Lab Work tab.

  2. Change the trigger locations and styles for the automations in the following table:

Step Name

Automation Configuration

Define Run Format (NovaSeq 6000 v3.7)

Register Step Started

  • Trigger Location: Step

  • Trigger Style: Automatic upon entry

Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v3.7)

Register Step Started

  • Trigger Location: Step

  • Trigger Style: Automatic upon entry

Register Pools & Register Step Completed

  • Trigger Location: Step

  • Trigger Style: Automatic upon exit

Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v3.7)

Register Step Started

  • Trigger Location: Step

  • Trigger Style: Automatic upon entry

Register Pools & Register Step Completed

  • Trigger Location: Step

  • Trigger Style: Automatic upon exit

Dilute, Denature & ExAmp (NovaSeq 6000 v3.7)

Register Step Completed

  • Trigger Location: Step

  • Trigger Style: Automatic upon exit

Load to Flowcell (NovaSeq 6000 v3.7)

Register Step Completed

  • Trigger Location: Step

  • Trigger Styler: Automatic upon exit

AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.7)

Register Step Started & Register NovaSeq Run & Register NovaSeq Run Association & Register NovaSeq RunStarted

  • Trigger Location: Step

  • Trigger Style: Automatic upon entry

Register NovaSeq RunCompleted & Register Step Completed

  • Trigger Location: Step

  • Trigger Style: Automatic upon exit

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