Manual Upgrade

NextSeq 1000/2000 Integration v2.5.0 supports future ICA services and includes new custom fields and modifications to existing automations. The integration package requires the NextSeq 1000/2000 Sequencing v2.4 workflow. You can install this workflow through the Illumina Preset Protocols (IPP). If you do not want to upgrade through the IPP, you can manually upgrade the workflow configuration.

Modify the Existing NextSeq 1000/2000 Workflow

To modify the existing NextSeq 1000/2000 Sequencing v2.3 workflow, you must make the following changes:

• Add the Measurement global field.

• Modify the Master Step field.

• Modify the Demultiplexing (NextSeq 1000/2000 Sequencing v2.3) master and protocol steps.

• Update the Validate Reagent Cartridge Barcode step automation.

Add Index Sequence Global Field

1. From Configuration, select the Custom Fields tab.

2. In Global Fields, create a new Measurement field with the following properties:

   • Field Name — Index Sequencing

   • Field Type — Text

   • Required Field — No

   • Read Only — Yes

3. Select Save.

Modify Master Step Field

1. From Configuration, select the Custom Fields tab.

2. Select the Master Step Fields tab.

3. Select Demultiplexing (NextSeq 1000/2000 Sequencing v2.3) to display the applicable fields.

4. Select Criteria 1 - Source Data Field.

5. In the Additional Options pane, remove # of > = Q30 Bases (PF) from the Dropdown Items list.

6. Select Criteria 2 - Source Data Field.

7. In the Additional Options pane, remove # of > = Q30 Bases (PF) from the Dropdown Items list.

8. Select Save.

Modify Demultiplexing (NextSeq 1000/2000 Sequencing v2.3) Master Step

1. From Configuration, select the Lab Work tab.

2. Navigate to the Steps pane and select Demultiplexing (NextSeq 1000/2000 Sequencing v2.3).

3. Select the Master Step tab, and then select Record Details.

4. In the Step File Placeholders pane, rename Demultiplex Stats to Run Metrics.

5. Select Save.

Modify Demultiplexing (NextSeq 1000/2000 Sequencing v2.3) Protocol Step

1. From Configuration, select the Lab Work tab.

2. Navigate to the Steps pane and select Demultiplexing (NextSeq 1000/2000 Sequencing v2.3).

3. Select the Step tab, and then select Record Details.

4. Add the Analysis Status field as follows.

   1. In the Step Data pane, select + to open the Master Step Fields pane.

   2. Select Analysis Status, and then select the check mark to add the field to the Master Step Fields list.

5. Update the Sample Table as follows.

   1. In the Sample Table pane, navigate to the Table Columns pane and remove the following fields:

      • [Measurement] # of > = Q30 Bases (PF)

      • [Measurement] Mean Quality Score (PF)

   2. Select + to open the Fields pane.

   3. Select Measurement to open the field drop-down list.

   4. Select Index Sequence.

   5. Reorder the table columns as follows.

      • [Derived Sample] Sample Name

      • [Measurement] Index Sequence

      • [Container] Well

      • [Measurement] # Reads

      • [Measurement] # Perfect Index Reads

      • [Measurement] # One Mismatch Index Reads

      • [Container] Container Name

      • [Project] Project Name

   6. Select Save.

Update Validate Reagent Cartridge Barcode Step Automation

1. From Configuration, select the Automation tab, and then select the Step Automation tab.

2. Select Validate Reagent Cartridge Barcode.

3. In Automation Details, replace the content of the Command Line field with the following command:

   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 -exp 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-[A-Z0-9]{4}:: ) ) {fail ( ::Invalid Reagent Cartridge Barcode. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1}"

4. Select Save.

Modify NextSeq 1000/2000 Sequencing v2.5.0 Integration Package Configuration

When the /opt/gls/clarity/config/configure_nextseq1k2k.sh script is running as part of the installation and configuration process, do not use the default names for the automated sequencing and demultiplexing steps. Instead, use the names in the modified workflow.

This integration moves the integration service and integration-related properties from the configuration files to the database.

To make modifications after configuration, use the omxProps-ConfigTool utility to update the following properties:

Property	Description
integration.nextseq1k2k.v2.automatedStepNames	Comma-separated step names for the automated sequencing step
integration.nextseq1k2k.v2.analysisStepNames	Comma-separated step names for the demultiplexing step