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

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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

The version of Assign Analysis Configuration Template (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Validate Sample Names and Register Step Started

Trigger Location = Step
Trigger Style = Automatic upon entry

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'"

1. Retrieve ACT List

Trigger Location = Record Details
Trigger Style = Manual button

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"

2. Retrieve ACT Information

Trigger Location = Record Details
Trigger Style = Manual button

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'"

Apply Selected ACT to Samples and Set Next Step

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

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.

Trigger Location = Step
Trigger Style = Automatic upon exit

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'"

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)

The version of Make Bulk Pool (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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'"

Validate Analysis Configurations

Trigger Location = Pooling
Trigger Style = Automatic upon exit

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"

Calculate Volumes

Trigger Location = Record Details
Trigger Style = Manual button

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'"

Set Next Step

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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::;'"

Trigger Location = Step
Trigger Style = Automatic upon exit

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'"

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
Presets
90
140
150
160
180
Decimal Places Displayed = 0
Flowcell Type
Text Dropdown
Required Field
Presets
1.5B
5B
10B
25B
Minimum Per Sample Volume (ul)
Numeric
Required Field
Default = 2
Decimal Places Displayed = 2
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
  Presets
  225
  400
  Decimal Places Displayed = 0
  Derived Sample
  NovaSeq X Flowcell Type
  Text Dropdown
  Required Field
  Presets
  1.5B
  5B
  10B
  25B
  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

The version of Dilute and Denature (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Copy Custom Fields and Register Step Started

Trigger Location = Step
Trigger Style = Automatic upon entry

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'"

Calculate Volumes

Trigger Location = Record Details
Trigger Style = Manual button

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.'"

Set Next Step

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Trigger Location = Step
Trigger Style = Automatic upon exit

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'"

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
  Presets
  225
  400
  Decimal Places Displayed = 0
  Derived Sample
  NaOH Volume (ul)
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Derived Sample
  NovaSeq X Flowcell Type
  Text Dropdown
  Required Field
  Presets
  1.5B
  5B
  10B
  25B
  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}

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.

Automations

Validate Flowcell Inputs, Analysis Configurations and Register Step Started

Trigger Location = Step
Trigger Style = Automatic upon entry

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'"

Validate Library Tube Strip Barcode

Trigger Location = Placement
Trigger Style = Automatic upon exit

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"

Validate Run Setup and Create Sample Sheet

Trigger Location = Record Details
Trigger Style = Manual button

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'"

Set Next Step

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Trigger Location = Step
Trigger Style = Automatic upon exit

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'"

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
1.5B
5B
10B
25B
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
1.5B
5B
10B
25B
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
0
6
8
Index 2 Cycles
Numeric
Required Field
Presets
0
6
8
Instrument
ℹ Only applicable for on-premise integration.
Text
Read Only
Read 1 Cycles
Numeric
Required Field
Presets
51
101
151
301
Read 2 Cycles
Numeric
Required Field
Presets
51
101
151
301
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

The version of AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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'"

Trigger Location = Step
Trigger Style = Automatic upon exit

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'"

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}

The version of AUTOMATED - Analysis Run (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

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

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Last updated 4 months ago

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