# Manual Upgrade
NovaSeq X Series Integration Package v1.3.0 includes modifications to the existing NovaSeq X Series Workflows to support these [changes](https://help.claritylims.illumina.com/instruments-and-integrations/novaseq-x-series/novaseqx/novaseqx-v1.3.0/novaseqx-v1.3.0-release-notes):
1. Update existing containers (Library 2-tube Strip and Library 8-tube Strip)
2. Update global field (BP Aliquot Volume (ul))
3. Update existing automations
4. Update Load to Library Tube Strip master step global fields
5. Update AUTOMATED - Sequencing Run master step and step, including run metrics displayed
6. Update AUTOMATED - Analysis Run master step
7. 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**
1. On the Configuration tab, select **Consumables**
2. Select **Containers**.
3. Select the existing **Library 2-tube Strip** container.
4. Update **Naming** of Rows to Numeric.
5. 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))
{% hint style="info" %}
The derived sample global field BP Aliquot Volume (ul) is used in Calculate Volumes automation in Dilute and Denature step.
{% endhint %}
1. On the configuration tab, select **Custom Fields**.
2. Select **Global Fields**.
3. Expand **Derived Sample**.
4. Select **BP Aliquot Volume (ul)**.
5. 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.
1. On the configuration tab, select **Automation**.
2. Select **Validate Run Setup and Create Planned Run** automation.
3. 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**
1. On the configuration tab, select **Automation**.
2. Rename the automations as specified in the table below.
| **Old Automation Name** | **New Automation Name** | **Used in Step** |
| ------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------- | -------------------------------------- |
| Register NovaSeq X RunCompleted and Register Step Completed | Register NovaSeq X Series Sequencing Run Completed | AUTOMATED - Sequencing Run |
| Register Step Started and Register NovaSeq X Run and Register NovaSeq X Run Association and Register NovaSeq X RunStarted | Register NovaSeq X Series Sequencing Run Started | 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**
1. On the configuration tab, select **Custom Fields**.
2. Select **Master Step Fields**
3. Expand **Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1)**.
4. Rename **Cloud Run Id** to **Planned Run ID**.
**Add Instrument Type**
{% hint style="info" %}
New instrument type NovaSeq X is now supported.
{% endhint %}
1. On the configuration tab, select **Custom Fields**.
2. Select **Master Step Fields**.
3. Expand **Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1)**.
4. Add **Instrument Type** field as specified in the image.
5. On the configuration tab, select **Lab Work**.
6. Select **Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1)** step.
7. 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**
1. On the configuration tab, select **Lab Work**.
2. Select **AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)** master step.
3. Under Step Type, update Derived Sample Generation to **Fixed with 1 Derived Sample generated**.
4. Under Step Type, update Naming Convention to **Lane {InputWellLocation:0,1}**
**Remove Unused RTA Version Master Step Field**
1. On the configuration tab, select **Custom Fields**.
2. Select **Master Step Fields**.
3. Expand **AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)**.
4. Delete **RTA Version**.
**\[Optional] Expand Sample Table By Default**
1. On the configuration tab, select **Lab Work**.
2. Select **AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1)** step.
3. Select Record Details milestone.
4. Under Sample Table, update **Sample Display Default** to **Expand**.
**Update Run Metrics**
*Reflect Reads PF Metrics at Run Level*
1. On the configuration tab, select **Custom Fields**.
2. Select **Global Fields**.
3. Add **Reads PF** field as specified in the image.
4. Select **Save**.
5. On the configuration tab, select **Lab Work**.
6. Select **AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)** step.
7. Under Record Details, remove **Reads PF R1** and **Reads PF R2** from Table Columns.
8. Add **Reads PF** to Table Columns.
*Reflect % PF Metrics at Run Level*
1. On the configuration tab, select **Custom Fields**.
2. Select **Global Fields**.
3. Add **% PF** field as specified in the image.
4. Select **Save**.
5. On the configuration tab, select **Lab Work**.
6. Select **AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)** step.
7. Under **Record Details**, remove **%PF R1** and **%PF R2** from Table Columns.
8. Add **% PF** to Table Columns.
*Add % Occupied*
1. On the configuration tab, select **Custom Fields**.
2. Select **Global Fields**.
3. Expand **Container**.
4. Add **% Occupied** field as specified in the image.
5. On the configuration tab, select **Lab Work**.
6. Select **AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)** step.
7. Under Record Details, add **% Occupied** to Table Columns.
*Remove Cluster Density R1 and Cluster Density R2*
1. On the configuration tab, select **Lab Work**.
2. Select **AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)** step.
3. Under Record Details, remove **Cluster Density R1** and **Cluster Density R2** from Table Columns.
4. On the configuration tab, select **Custom Fields**.
5. Select **Global Fields**.
6. Expand **Container**.
7. Delete **Cluster Density R1** and **Cluster Density R2**.
## 6. Update AUTOMATED - Analysis Run Master Step
**Update Master Step Configuration**
1. On the configuration tab, select **Lab Work**.
2. Select **AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1)** master step.
3. Under Step Type, update Naming Convention to **{SubmittedSampleName} {AppliedReagentLabels}**
**Rename Library Tube Strip Barcode to App Session ID**
1. On the configuration tab, select **Custom Fields**.
2. Select **Master Step Fields**.
3. Expand **AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1)**.
4. Rename **Library Tube Strip Barcode** to **App Session ID**.
## 7. Upgrade Clarity LIMS Product Analytics Integration (if enabled)
{% hint style="info" %}
The changes are due to updates on container configuration.
{% endhint %}
1. Upgrade to Clarity LIMS Product Analytics Integration v1.4.0
2. Restart the CLPA integration service
