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.
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.
From Configuration, select the Custom Fields tab.
In Global Fields, create a new Measurement field with the following properties:
From Configuration, select the Custom Fields tab.
Select the Master Step Fields tab.
From Configuration, select the Lab Work tab.
Navigate to the Steps pane and select Demultiplexing (NextSeq 1000/2000 Sequencing v2.3).
From Configuration, select the Lab Work tab.
Navigate to the Steps pane and select Demultiplexing (NextSeq 1000/2000 Sequencing v2.3).
From Configuration, select the Automation tab, and then select the Step Automation tab.
Select Validate Reagent Cartridge Barcode.
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:
Field Name — Index Sequencing
Field Type — Text
Required Field — No
Read Only — Yes
Select Save.
Select Demultiplexing (NextSeq 1000/2000 Sequencing v2.3) to display the applicable fields.
Select Criteria 1 - Source Data Field.
In the Additional Options pane, remove # of > = Q30 Bases (PF) from the Dropdown Items list.
Select Criteria 2 - Source Data Field.
In the Additional Options pane, remove # of > = Q30 Bases (PF) from the Dropdown Items list.
Select Save.
Select the Master Step tab, and then select Record Details.
In the Step File Placeholders pane, rename Demultiplex Stats to Run Metrics.
Select Save.
Select the Step tab, and then select Record Details.
Add the Analysis Status field as follows.
In the Step Data pane, select + to open the Master Step Fields pane.
Select Analysis Status, and then select the check mark to add the field to the Master Step Fields list.
Update the Sample Table as follows.
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)
Select + to open the Fields pane.
Select Measurement to open the field drop-down list.
Select Index Sequence.
Reorder the table columns as follows.
[Derived Sample] Sample Name
[Measurement] Index Sequence
Select Save.
In Automation Details, replace the content of the Command Line field with the following command:
Select Save.
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
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}"[Measurement] # Reads
[Measurement] # Perfect Index Reads
[Measurement] # One Mismatch Index Reads
[Container] Container Name
[Project] Project Name