> For the complete documentation index, see [llms.txt](https://help.claritylims.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.claritylims.illumina.com/instruments-and-integrations/novaseq-x-series/novaseq-x-series-workflow-and-configuration/novaseq-x-series-workflow-and-configuration-v2.0/novaseq-x-series-sequencing-v2.0.md). # NovaSeq X Series Sequencing v2.0 ## Protocol 1: NovaSeq X Series Sequencing v2.0 Protocol Type = Sequencing **Next Steps Configuration** * Step(s): * 1: Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0) * Start Next Step = Manual * Assign Next Step = Automatic * 2: Make Bulk Pool (NovaSeq X Series Sequencing v2.0) * Start Next Step = Manual * Assign Next Step = Automatic * 3: Dilute and Denature (NovaSeq X Series Sequencing v2.0) * Start Next Step = Manual * Assign Next Step = Automatic * 4: Load to Library Tube Strip (NovaSeq X Series Sequencing v2.0) * Start Next Step = Manual * Assign Next Step = Automatic * 5: AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v2.0) * Start Next Step = Manual * Assign Next Step = Automatic * 6: AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v2.0) * Assign Next Step = Manual | **Step** | **To Step 1** | **To Step 2** | **To Step 3** | **To Step 4** | **To Step 5** | **To Step 6** | | -------- | ------------- | ------------- | ------------- | ------------- | ------------- | ------------- | | 1 | | ✓ | ✓ | ❌ | ❌ | ❌ | | 2 | | | ✓ | ❌ | ❌ | ❌ | | 3 | | | | ✓ | ❌ | ❌ | | 4 | | | | | ✓ | ❌ | | 5 | | | | | | ✓ | | 6 | | | | | | | ### Step 1: Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0) * Master Step Name = Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0) * Step Type = No Outputs * Instrument Types * NovaSeq X Series * Vendor = Illumina {% hint style="info" %} The version of Assign Analysis Configuration Template (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Validate Sample Names and Register Step Started * Trigger Location = Step * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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 'submittedSamples.each { sample -> if ( !sample.name.matches( ::[A-Za-z0-9_-]+:: ) ) { fail ( ::Submitted sample :: + sample.name + :: should only have alphanumeric, dash, and underscore characters. Please rename and try again.:: ) } }' -log {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} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
1. Retrieve ACT List * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/novaseqxseries/automation/novaseqxseries-automation.jar script:retrieve_act_list -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -n 'INSTRUMENT_USED' -t true" ``` {% endcode %}
2. Retrieve ACT Information * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/novaseqxseries/automation/novaseqxseries-automation.jar script:retrieve_act_info -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -a '{udf:Analysis Configuration Template}' -n 'INSTRUMENT_USED'" ``` {% endcode %}
Apply Selected ACT to Samples and Set Next Step * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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 -t false -h false -exp 'if (!input.hasValue(::Molarity (nM)::)) { fail(::The Molarity cannot be empty.::); } else if (input.::Molarity (nM):: <= 0) { fail(::The Molarity cannot be negative or zero.::); }' -log {compoundOutputFileLuid1} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/novaseqxseries/automation/novaseqxseries-automation.jar -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -a '{udf:Analysis Configuration Template}' -n 'INSTRUMENT_USED' --derivedSampleInstrumentIdUdf 'Instrument ID' script:validate_indexes script:assign_act && /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 -t false -h false -exp 'if (step.::Skip Pooling::) { nextStep = ::Dilute and Denature (NovaSeq X Series Sequencing v2.0):: } else { nextStep = ::Make Bulk Pool (NovaSeq X Series Sequencing v2.0):: }' -log {compoundOutputFileLuid1}" ``` {% endcode %} > ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
Register Step Completed * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------- | -------------- | -------------- | ----------------------------------------- | | Analysis Configuration Template | Text | | Default = No Analysis | | Application | Text | Read Only | | | Application Version | Text | Read Only | | | Index Adapter Kit | Text | Read Only | | | Library Prep Kit | Text | Read Only | | | Reference Genome | Text | Read Only | | | Secondary Analysis Mode | Text | Read Only | | | Skip Pooling | Toggle Switch | Required Field | Default = False | * Sample Table * Sample Display Default = Collapse * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | ACT Name | Text | Read Only | | | Derived Sample | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | ### Step 2: Make Bulk Pool (NovaSeq X Series Sequencing v2.0) * Master Step Name = Make Bulk Pool (NovaSeq X Series Sequencing v2.0) * Step Type = Pooling * Aliquot Generation = Fixed, 1 * Naming Convention = {PoolName} * Reagent Kits * Resuspension Buffer (RSB) {% hint style="info" %} The version of Make Bulk Pool (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Register Step Started * Trigger Location = Step * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Validate Analysis Configurations * Trigger Location = Pooling * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:validate_same_udf_value_for_analytes -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -f 'Instrument ID' -f 'Analysis Location' -v 'perPool' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/novaseqxseries/automation/novaseqxseries-automation.jar -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -m PerPool -n 'INPUT.Instrument ID' script:validate_analysis_config script:validate_physical_logical_configurations" ``` {% endcode %}
Calculate Volumes * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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} -log {compoundOutputFileLuid1} \ script:evaluateDynamicExpression \ -exp 'if (!input.hasValue(::Molarity (nM)::)) { return; }; if (output.hasValue(::Number of Samples in Pool::)) { output.::Number of Samples in Pool:: = output.::Number of Samples in Pool:: + 1; } else { output.::Number of Samples in Pool:: = 1; }' -t true \ script:evaluateDynamicExpression \ -exp 'output.::Bulk Pool Volume (ul):: = 100 * step.::Number of Lanes to Sequence::; output.::NovaSeq X Flowcell Type:: = step.::Flowcell Type::; output.::Final Loading Concentration (pM):: = step.::Final Loading Concentration (pM)::; input.::Per Sample Volume (ul):: = 2 * output.::Bulk Pool Volume (ul):: / input.::Molarity (nM):: / output.::Number of Samples in Pool::; output.::Total Sample Volume (ul):: = 0;' -t true \ script:calculate_multipool_adjusted_per_sample_volume -t \ script:evaluateDynamicExpression \ -exp 'if (output.hasValue(::Total Sample Volume (ul)::)) { output.::Total Sample Volume (ul):: = output.::Total Sample Volume (ul):: + input.::Adjusted Per Sample Volume (ul)::; } else { output.::Total Sample Volume (ul):: = input.::Adjusted Per Sample Volume (ul)::; }' -t true \ script:evaluateDynamicExpression \ -exp 'if (output.::Total Sample Volume (ul):: > output.::Bulk Pool Volume (ul)::) { output.::RSB Volume (ul):: = 0 } else { output.::RSB Volume (ul):: = output.::Bulk Pool Volume (ul):: - output.::Total Sample Volume (ul):: }' -t true \ && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} script:driver_file_generator \ -t /opt/gls/clarity/extensions/conf/driverfiletemplates/NovaSeqXSeries_Bulk_Pool1.csv -o 1.csv \ script:driver_file_generator \ -t /opt/gls/clarity/extensions/conf/driverfiletemplates/NovaSeqXSeries_Bulk_Pool2.csv -o 2.csv \ && cat 1.csv 2.csv > {compoundOutputFileLuid0}.csv \ && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -log {compoundOutputFileLuid1} \ script:evaluateDynamicExpression \ -exp 'output.::Number of Samples in Pool:: = ::::; output.::Total Sample Volume (ul):: = ::::; output.::Bulk Pool Volume (ul):: = ::::;' -t true \ && echo 'Calculate Volume completed successfully'" ``` {% endcode %}
Set Next Step * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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} -log {compoundOutputFileLuid1} \ script:evaluateDynamicExpression -exp 'if (!input.hasValue(::Molarity (nM)::)){ return; }; if (input.hasValue(::Instrument ID::)) {output.::Instrument ID:: = input.::Instrument ID::}; if (input.hasValue(::Analysis Location::)) {output.::Analysis Location:: = input.::Analysis Location::}; nextStep = ::ADVANCE::;'" ``` {% endcode %}
Register Pools and Register Step Completed * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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} -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} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Pooling * Label Uniqueness = On * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------------------------- | -------------- | -------------- | ----------------------------------------------------------------------------------------------------------------------------------------- | | Final Loading Concentration (pM) | Numeric | Required Field | | | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Minimum Per Sample Volume (ul) | Numeric | Required Field | | | Number of Lanes to Sequence | Numeric | Required Field | Decimal Places Displayed = 0 | * Sample Table * Sample Display Default = Collapse * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------------------- | -------------- | -------------- | ------------------------------------------------------------------------------------------------------ | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Derived Sample | Final Loading Concentration (pM) | Numeric | Required Field | | | Derived Sample | NovaSeq X Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | RSB Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 3: Dilute and Denature (NovaSeq X Series Sequencing v2.0) * Master Step Name = Dilute and Denature (NovaSeq X Series Sequencing v2.0) * Step Type = Standard * Derived Sample Generation = Variable, 2 * Naming Convention = {InputItemName}\_WP{OutputItemNumber} * Reagent Kits * NaOH * Resuspension Buffer (RSB) * TT2 {% hint style="info" %} The version of Dilute and Denature (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Copy Custom Fields and Register Step Started * Trigger Location = Step * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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 -h false -log {compoundOutputFileLuid1} -exp ' if (input.hasValue(::NovaSeq X Flowcell Type::)) { output.::NovaSeq X Flowcell Type:: = input.::NovaSeq X Flowcell Type:: }; if (input.hasValue(::Final Loading Concentration (pM)::)) { output.::Final Loading Concentration (pM):: = input.::Final Loading Concentration (pM):: };' \ && /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} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Calculate Volumes * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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} -log {compoundOutputFileLuid1} \ script:evaluateDynamicExpression -t true \ -exp ' if (!output.hasValue(::NovaSeq X Flowcell Type::) || !output.hasValue(::Final Loading Concentration (pM)::)) { fail(::Please ensure all samples have a value assigned for NovaSeq X Flowcell Type and Final Loading Concentration (pM) custom field.::) }; \ if (output.::NovaSeq X Flowcell Type:: == ::1.5B:: || output.::NovaSeq X Flowcell Type:: == ::5B:: || output.::NovaSeq X Flowcell Type:: == ::10B::) { output.::NaOH Volume (ul):: = 8.5; output.::TT2 Volume (ul):: = 127.5; output.::BP Aliquot Volume (ul):: = output.::Final Loading Concentration (pM):: * 170 / (2 * 1000); output.::RSB Volume (ul):: = 34 - output.::BP Aliquot Volume (ul)::; if (step.::1-2% PhiX Spike-In::) { output.::PhiX Volume (ul):: = 1; output.::PhiX Concentration (pM):: = 300; } else { output.::PhiX Volume (ul):: = ::::; output.::PhiX Concentration (pM):: = ::::; }; } else { output.::NaOH Volume (ul):: = 14; output.::TT2 Volume (ul):: = 210; output.::BP Aliquot Volume (ul):: = output.::Final Loading Concentration (pM):: * 280 / (2 * 1000); output.::RSB Volume (ul):: = 56 - output.::BP Aliquot Volume (ul)::; if (step.::1-2% PhiX Spike-In::) { output.::PhiX Volume (ul):: = 1.6; output.::PhiX Concentration (pM):: = 300; } else { output.::PhiX Volume (ul):: = ::::; output.::PhiX Concentration (pM):: = ::::; }; }' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {stepURI:v2} -u {username} -p {password} \ script:driver_file_generator \ -t /opt/gls/clarity/extensions/conf/driverfiletemplates/NovaSeqXSeries_Dilute_Denature_Calculate_Volumes.csv -o {compoundOutputFileLuid0}.csv -q true -destLIMSID {compoundOutputFileLuid0} -l {compoundOutputFileLuid1} \ && echo 'Calculate Volumes completed successfully.'" ``` {% endcode %}
Set Next Step * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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 -t false -h false -exp 'if (input.hasValue(::Instrument ID::)) {output.::Instrument ID:: = input.::Instrument ID::}; if (input.hasValue(::Analysis Location::)) {output.::Analysis Location:: = input.::Analysis Location::}; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}" ``` {% endcode %}
Register Step Completed * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------ | -------------- | -------------- | ----------------------------------------- | | 1-2% PhiX Spike-In | Toggle Switch | Required Field | Default = False | * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------------------- | -------------- | -------------- | ------------------------------------------------------------------------------------------------------ | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Derived Sample | BP Aliquot Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 1 | | Derived Sample | Final Loading Concentration (pM) | Numeric | Required Field | | | Derived Sample | NaOH Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | NovaSeq X Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | RSB Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | TT2 Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 4: Load to Library Tube Strip (NovaSeq X Series Sequencing v2.0) * Master Step Name = Load to Library Tube Strip (NovaSeq X Series Sequencing v2.0) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} {% hint style="info" %} The version of Load to Library Tube Strip (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Validate Flowcell Inputs, Analysis Configurations and Register Step Started * Trigger Location = Step * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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} -l {compoundOutputFileLuid1} \ script:validate_same_udf_value_for_analytes -f 'Analysis Location' -f 'NovaSeq X Flowcell Type' \ script:validate_selected_container \ -fn 'NovaSeq X Flowcell Type' -fv '1.5B' -ct 'Library 2-tube Strip' \ -fn 'NovaSeq X Flowcell Type' -fv '5B' -ct 'Library 8-tube Strip' \ -fn 'NovaSeq X Flowcell Type' -fv '10B' -ct 'Library 8-tube Strip' \ -fn 'NovaSeq X Flowcell Type' -fv '25B' -ct 'Library 8-tube Strip' && \ /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/novaseqxseries/automation/novaseqxseries-automation.jar -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -m PerRun -n 'INPUT.Instrument ID' script:validate_analysis_config script:validate_physical_logical_configurations && \ /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} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Validate Library Tube Strip Barcode * Trigger Location = Placement * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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:validate_output_containers -l {compoundOutputFileLuid1} -r 'Library 8-tube Strip:LC[0-9]{7}-L[A-Z]1' -r 'Library 2-tube Strip:LC[0-9]{7}-L[A-Z]2' -max 1" ``` {% endcode %}
Validate Run Setup and Create Sample Sheet * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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 (!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::); }; \ if (!step.::BCL Convert Version::.matches(::[a-zA-Z0-9.]+::)) { fail(::BCL Convert Version contains prohibited characters. Please check to make sure BCL Convert Version only contains alphanumeric characters and periods.::); };' \ -log {compoundOutputFileLuid1} \ -t true \ && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/novaseqxseries/automation/novaseqxseries-automation.jar script:generate_sample_sheet -i {stepURI:v2} -u {username} -p {password} -c {compoundOutputFileLuid0} -l {compoundOutputFileLuid1} -n 'INPUT.Instrument ID'" ``` {% endcode %}
Set Next Step * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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 -t false -h false -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}" ``` {% endcode %}
Register Step Completed * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------------------------------------------------------------------------------------ | -------------- | -------------- | ----------------------------------------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample |

Instrument ID

ℹ Only applicable for on-premise integration

| Text | Read Only | | | Derived Sample | NovaSeq X Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ----------------------- | -------------- | -------------- | ----------------------------------------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | NovaSeq X Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Row * Destination Containers * Library 2-tube Strip * Rows * Number: 1 * Naming: Numeric * Start at: 1 * Columns * Number: 1 * Naming: Numeric * Start at: 1 * Library 8-tube Strip * Rows * Number: 1 * Naming: Numeric * Start at: 1 * Columns * Number: 1 * Naming: Numeric * Start at: 1 #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------------------------------------------------------------------------------- | -------------- | -------------- | ---------------------------------------------------------------------- | | BCL Convert Version | Text | | | | Create Planned Run | Toggle Switch | Required Field | Default = True | | Index 1 Cycles | Numeric | Required Field |

Presets

| | Index 2 Cycles | Numeric | Required Field |

Presets

| |

Instrument

ℹ Only applicable for on-premise integration.

| Text | Read Only | | | Read 1 Cycles | Numeric | Required Field |

Presets

| | Read 2 Cycles | Numeric | Required Field |

Presets

| | Run Name | Text | Required Field | | * Sample Table * Sample Display Default = Collapse * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 5: AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v2.0) * Master Step Name = AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v2.0) * Step Type = Analysis * Measurement Generation = Fixed, 1 * Naming Convention = Lane {InputWellLocation:0,1} * Reagent Kits * Buffer Cartridge * Supplier = Illumina * Lyophilization Cartridge * Supplier = Illumina * Reagent Cartridge * Supplier = Illumina {% hint style="info" %} The version of AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Register NovaSeq X Series Sequencing Run Started * Trigger Location = Step * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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} -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} -s 'com/illumina/upa/scripts/novaseqxseries/register_novaseqxseries_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} -s 'com/illumina/upa/scripts/novaseqxseries/novaseqxseries_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} -s 'com/illumina/upa/scripts/novaseqxseries/novaseqxseries_seqrun_started.groovy'" ``` {% endcode %}
Register NovaSeq X Series Sequencing Run Completed * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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} -s 'com/illumina/upa/scripts/novaseqxseries/novaseqxseries_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} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ----------------------------------- | -------------- | ----------- | ----------------------------------------- | | Current Cycle | Text | Read Only | | | Current Read | Text | Read Only | | | Flow Cell Expiration Date | Text | Read Only | | | Flow Cell ID | Text | Read Only | | | Flow Cell Lot Number | Text | Read Only | | | Flow Cell Part Number | Text | Read Only | | | Flow Cell Side | Text | Read Only | | | Flow Cell Type | Text | Read Only | | | Instrument Control Software Version | Text | Read Only | | | Instrument ID | Text | Read Only | | | Instrument Type | Text | Read Only | | | Library Tube Strip Barcode | Text | Read Only | | | Output Folder | Text | Read Only | | | Run Name | Text | Read Only | | | Run Status | Text | Read Only | | | Sequencing Log | Multiline Text | Read Only | | * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------- | -------------- | ----------- | ----------------------------------------- | | Container | % Aligned R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % Aligned R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % Bases >=Q30 R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % Bases >=Q30 R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % Error Rate R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % Error Rate R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % Occupied | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % PF | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | % Phasing R1 | Numeric | Read Only | Decimal Places Displayed = 3 | | Container | % Phasing R2 | Numeric | Read Only | Decimal Places Displayed = 3 | | Container | % Prephasing R1 | Numeric | Read Only | Decimal Places Displayed = 3 | | Container | % Prephasing R2 | Numeric | Read Only | Decimal Places Displayed = 3 | | Container | Container Name | Built-in | | | | Container | Intensity Cycle 1 R1 | Numeric | Read Only | | | Container | Intensity Cycle 1 R2 | Numeric | Read Only | | | Container | LIMS ID (Container) | Built-in | | | | Container | Reads PF | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | Well | Built-in | | | | Container | Yield (Gb) R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | Yield (Gb) R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Measurement | % Aligned R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | % Aligned R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | % Bases >=Q30 R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | % Bases >=Q30 R2 | Numeric | Read Only | | | Measurement | % Error Rate R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | % Error Rate R2 | Numeric | Read Only | | | Measurement | % Occupied | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | % PF | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | % Phasing R1 | Numeric | Read Only | Decimal Places Displayed = 3 | | Measurement | % Phasing R2 | Numeric | Read Only | Decimal Places Displayed = 3 | | Measurement | % Prephasing R1 | Numeric | Read Only | Decimal Places Displayed = 3 | | Measurement | % Prephasing R2 | Numeric | Read Only | Decimal Places Displayed = 3 | | Measurement | Intensity Cycle 1 R1 | Numeric | Read Only | | | Measurement | Intensity Cycle 1 R2 | Numeric | Read Only | | | Measurement | Reads PF | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | Yield (Gb) R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Measurement | Yield (Gb) R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 6: AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v2.0) * Master Step Name = AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v2.0) * Step Type = Demultiplexing * Measurement Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} {AppliedReagentLabels} {% hint style="info" %} The version of AUTOMATED - Analysis Run (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed. {% endhint %} #### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------ | -------------- | ----------- | ----------------------------------------- | | Analysis Result Location | Text | Read Only | | | Analysis Status | Text | Read Only | | | Log | Multiline Text | Read Only | | * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | --- # Agent Instructions This documentation is published with GitBook. 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