Manual Upgrade

NovaSeq X Series Integration Package v1.3.0 includes modifications to the existing NovaSeq X Series Workflows to support these changes:

Update existing containers (Library 2-tube Strip and Library 8-tube Strip)
Update global field (BP Aliquot Volume (ul))
Update existing automations
Update Load to Library Tube Strip master step global fields
Update AUTOMATED - Sequencing Run master step and step, including run metrics displayed
Update AUTOMATED - Analysis Run master step
Upgrade Clarity LIMS Product Analytics Integration (if enabled)

If you do not want to use the latest workflow (NovaSeq X Series Sequencing v1.2) available in IPP v2.10.0, then update your existing workflow configuration manually using the following information as required.

1. Update Existing Containers

Library 2-tube Strip container

On the Configuration tab, select Consumables
Select Containers.
Select the existing Library 2-tube Strip container.
Update Naming of Rows to Numeric.
Update Start at of Rows to 1.

Library 8-tube Strip container

Repeat the update instructions of Library 2-tube Strip container above for the existing Library 8-tube Strip container.

2. Update Global Field (BP Aliquot Volume (ul))

The derived sample global field BP Aliquot Volume (ul) is used in Calculate Volumes automation in Dilute and Denature step.

On the configuration tab, select Custom Fields.
Select Global Fields.
Expand Derived Sample.
Select BP Aliquot Volume (ul).
Update Decimal Places Displayed from 0 to 1.

3. Update Automations

There is a minor update of Command Line for Validate Run Setup and Create Planned Run automation, as well as, renaming of several automations to improve readability and provide more clarity of the automation function.

Update Validate Run Setup and Create Planned Run Automation

Updates to the Command Line is to improve the error message.

On the configuration tab, select Automation.
Select Validate Run Setup and Create Planned Run automation.
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} \ 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:evaluateDynamicExpression \ script:evaluateDynamicExpression \ -exp 'if (!step.::Run Name::.matches(::[a-zA-Z0-9-_]+[a-zA-Z0-9-_. ]*::)) { fail(::Run Name contains prohibited characters. Please check to make sure Run Name only contains alphanumeric characters, spaces, dashes, periods and underscores. Run Name must start with alphanumeric, a dash or an underscore::); }; if (step.::Run Name::.length() > 255) { fail(::Run Name shall not exceed 255 characters.::); }; if (step.::Index 2 Cycles:: > 0 && step.::Index 1 Cycles:: == 0) { fail(::Index 1 Cycles cannot be zero if Index 2 Cycles is non-zero::); };' \ -exp 'if (!step.::Run Name::.matches(::[a-zA-Z0-9-_]+[a-zA-Z0-9-_. ]*::)) { fail(::Run Name contains prohibited characters. Please check to make sure Run Name only contains alphanumeric characters, spaces, dashes, periods and underscores. Run Name must start with alphanumeric, a dash or an underscore::); }; if (step.::Run Name::.length() > 255) { fail(::Run Name shall not exceed 255 characters.::); }; if (step.::Index 2 Cycles:: > 0 && step.::Index 1 Cycles:: == 0) { fail(::Index 1 Cycles cannot be zero if Index 2 Cycles is non-zero::); };' \ -log {compoundOutputFileLuid1} \ -log {compoundOutputFileLuid1} \ -t true \ -t true \ && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/SIS/SISServices/extensions/automation/novaseqxseries-automation.jar script:generate_sample_sheet -i {stepURI:v2} -u {username} -p {password} -c {compoundOutputFileLuid0} -l {compoundOutputFileLuid1}"

[Optional] Rename Automations

On the configuration tab, select Automation.
Rename the automations as specified in the table below.

Old Automation Name

New Automation Name

Used in Step

AUTOMATED - Sequencing Run

Register Step Started and Register NovaSeq X Run and Register NovaSeq X Run Association and Register NovaSeq X RunStarted

AUTOMATED - Sequencing Run

Validate Reagent Labels and Apply Selected ACT to Samples and Set Next Step

Apply Selected ACT to Samples and Set Next Step

Assign Analysis Configuration Template

Validate Flowcell Inputs and Validate Analysis Configurations and Register Step Started

Validate Flowcell Inputs, Analysis Configurations and Register Step Started

Load to Library Tube Strip

Validate Sample Names and Retrieve Analysis Configuration Template List and Register Step Started

Validate Sample Names, Retrieve ACT List and Register Step Started

Assign Analysis Configuration Template

4. Update Load to Library Tube Strip Step

Rename Cloud Run ID to Planned Run ID

On the configuration tab, select Custom Fields.
Select Master Step Fields
Expand Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1).
Rename Cloud Run Id to Planned Run ID.

Add Instrument Type

New instrument type NovaSeq X is now supported.

On the configuration tab, select Custom Fields.
Select Master Step Fields.
Expand Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1).
Add Instrument Type field as specified in the image.

On the configuration tab, select Lab Work.
Select Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1) step.
Under Record Details, add Instrument Type to Master Step Fields.

5. Update AUTOMATED - Sequencing Run Step

There are configuration updates on the AUTOMATED - Sequencing Run master step and step, as well as updates to the run metrics displayed.

Update Master Step Configuration

On the configuration tab, select Lab Work.
Select AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) master step.
Under Step Type, update Derived Sample Generation to Fixed with 1 Derived Sample generated.
Under Step Type, update Naming Convention to Lane {InputWellLocation:0,1}

Remove Unused RTA Version Master Step Field

On the configuration tab, select Custom Fields.
Select Master Step Fields.
Expand AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1).
Delete RTA Version.

[Optional] Expand Sample Table By Default

On the configuration tab, select Lab Work.
Select AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1) step.
Select Record Details milestone.
Under Sample Table, update Sample Display Default to Expand.

Update Run Metrics

Reflect Reads PF Metrics at Run Level

On the configuration tab, select Custom Fields.
Select Global Fields.
Add Reads PF field as specified in the image.
Select Save.
On the configuration tab, select Lab Work.
Select AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step.
Under Record Details, remove Reads PF R1 and Reads PF R2 from Table Columns.
Add Reads PF to Table Columns.

Reflect % PF Metrics at Run Level

On the configuration tab, select Custom Fields.
Select Global Fields.
Add % PF field as specified in the image.
Select Save.
On the configuration tab, select Lab Work.
Select AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step.
Under Record Details, remove %PF R1 and %PF R2 from Table Columns.
Add % PF to Table Columns.

Add % Occupied

On the configuration tab, select Custom Fields.
Select Global Fields.
Expand Container.
Add % Occupied field as specified in the image.

On the configuration tab, select Lab Work.
Select AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step.
Under Record Details, add % Occupied to Table Columns.

Remove Cluster Density R1 and Cluster Density R2

On the configuration tab, select Lab Work.
Select AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step.
Under Record Details, remove Cluster Density R1 and Cluster Density R2 from Table Columns.

On the configuration tab, select Custom Fields.
Select Global Fields.
Expand Container.
Delete Cluster Density R1 and Cluster Density R2.

6. Update AUTOMATED - Analysis Run Master Step

Update Master Step Configuration

On the configuration tab, select Lab Work.
Select AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1) master step.
Under Step Type, update Naming Convention to {SubmittedSampleName} {AppliedReagentLabels}