# IGA NovaSeq Sequencing v2.1 ## Overview IGA NovaSeq Sequencing v2.1 contains preset protocols that support the setup of previously prepared libraries used with the NovaSeq instrument. These protocols can be used with the IGA Library Prep Automated v2.1 workflow. They also provide the following functions: * File-based integration with the Hamilton robots that are used for liquid handling steps. * Automated calculation of sample and buffer volumes. * Automated calculation or display of reagents. * When required, automatic step transition. ## Protocol 1: Run Format (IGA) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Define Run Format (IGA) * Master Step Name = Define Run Format (IGA v2.1) * Step Type = No Outputs #### Automations
Register Sample & Register Step Started (IGA v2.1) * 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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/register_sample.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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Define Run Format - Assign Workflow and Flowcell Type to Samples & Set Next Steps to Remove from Workflow (IGA v2.1) * 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 = ::REMOVE:: ; input.::Minimum Molarity (nM):: = (5 * input.::Final Loading Concentration (pM)::)/1000 ; if (!input.hasValue(::Normalized Molarity (nM)::)) { fail(::The Normalized Molarity cannot be empty.::) ; } else if (input.::Normalized Molarity (nM):: < input.::Minimum Molarity (nM)::) { input.::Warning:: = ::The Normalized Molarity is too low.:: ; input.::Loading Workflow Type:: = ::[Remove from workflow]:: ; } else { input.::Warning:: = ::n/a:: }' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Define Run Format - Routing Script (IGA v2.1) * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Loading Workflow Type' \ --FIELD_VALUE 'NovaSeq Standard' \ --WORKFLOW 'Illumina Genomics Architecture - NovaSeq Sequencing v2.1' \ --STEP 'Make Bulk Pool for NovaSeq Standard (IGA v2.1)' \ --INPUTS_OR_OUTPUTS 'INPUTS' \ \ --FIELD_NAME 'Loading Workflow Type' \ --FIELD_VALUE 'NovaSeq Xp' \ --WORKFLOW 'Illumina Genomics Architecture - NovaSeq Sequencing v2.1' \ --STEP 'Make Bulk Pool for NovaSeq Xp (IGA v2.1)' \ --INPUTS_OR_OUTPUTS 'INPUTS'" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Reagent Name | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Reagent Name | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | --------------------------------------------- | -------------- | ----------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | IGA WF Build Version | Text | Read Only | Default = 2.1.0.1 | | Quick reference checklist: Define Run Format. | Multiline Text | Read Only |

Defaults =
User tasks for this page:
- Below, assign 'Loading Workflow Type', 'Flowcell Type', and the NovaSeq 'Final Loading Concentration (pM)'.
- Click 'Next Steps'.

| * Step File Placeholders * Log file - Automatically attached * Sample Table (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 | Adjusted Per Sample Volume (ul) | Numeric | | | | Derived Sample | Final Loading Concentration (pM) | Numeric Dropdown | | | | Derived Sample | Flowcell Type | Text Dropdown | | | | Derived Sample | Loading Workflow Type | Text Dropdown | | | | Derived Sample | Minimum Molarity (nM) | Numeric | | | | Derived Sample | Normalized Molarity (nM) | Numeric | | | | Derived Sample | Per Sample Volume (ul) | Numeric | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Warning | Text | | | | Project | Project Name | Built-in | | | ## Protocol 2: NovaSeq Standard Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Make Bulk Pool for NovaSeq Standard * Master Step Name = Make Bulk Pool for NovaSeq Standard (IGA v2.1) * Step Type = Pooling * Aliquot Generation = Fixed, 1 * Naming Convention = {PoolName} * Control Types * PhiX v3 #### Automations
Register Sample & Register Step Started (IGA v2.1) * 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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/register_sample.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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Pooling NovaSeq Standard - Show Warning Message (IGA v2.1) * Trigger Location = Pooling * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 \ /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/NovaSeq_pooling_warning.py \ -s {stepURI:v2} \ -u {username} \ -p {password} \ -l {compoundOutputFileLuid0}" ``` {% endcode %}
Validate Inputs Flowcell Type and Number of Pools (IGA v2.1) * 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_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -validateSingleOutput false -poolType bulk \ && PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/validate_flowcell_pools.py -s {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0}" ``` {% endcode %}
NovaSeq Make Bulk Pool - Output Plate BPP Barcode Check (Duplicates Allowed) (IGA v2.1) * 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:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-BPP:: ) ) {fail ( ::Invalid BPP Plate Barcode. This plate ID must be in the format LPxxxxxxx-BPP, where 'x' is a digit 0-9, e.g. LP1234567-BPP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} \ && PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/validate_multiple_destination_plates.py -s {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0}" ``` {% endcode %}
Make Bulk Pool NovaSeq Standard - Calculate Volumes and Generate Hamilton Input File (IGA v2.1) * 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} -t true -log {compoundOutputFileLuid0} \ script:evaluateDynamicExpression \ -h false \ -exp 'step.::Number of Samples in Pool:: = step.::Number of Samples in Pool:: + 1' \ script:evaluateDynamicExpression \ -h false \ -exp 'if ( input.::Flowcell Type:: == ::SP:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Flowcells to Sequence:: * 100 + 30 } ; if ( input.::Flowcell Type:: == ::S1:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Flowcells to Sequence:: * 100 + 30 } ; if ( input.::Flowcell Type:: == ::S2:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Flowcells to Sequence:: * 150 + 30 } ; if ( input.::Flowcell Type:: == ::S4:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Flowcells to Sequence:: * 310 + 30 } ; input.::Per Sample Volume (ul):: = 0' \ && PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 \ /opt/gls/clarity/extensions/IGA_2.1/make_bpp/calculate_sample_volume.py \ -s {stepURI:v2} \ -u {username} \ -p {password} \ && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -t true -log {compoundOutputFileLuid0} \ script:calculate_adjusted_per_sample_volume \ script:evaluateDynamicExpression \ -h false \ -exp 'step.::Total Sample Volume (ul):: = step.::Total Sample Volume (ul):: + input.::Adjusted Per Sample Volume (ul)::' \ script:evaluateDynamicExpression \ -h false \ -exp 'if (step.::Total Sample Volume (ul):: >= step.::Bulk Pool Volume (ul)::) {output.::RSB Volume (ul):: = 0} else {output.::RSB Volume (ul):: = step.::Bulk Pool Volume (ul):: - step.::Total Sample Volume (ul)::} ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type:: ; if ( input.::Flowcell Type:: == ::SP:: ) { output.::Volume of Pool to Denature (ul):: = 100 ; output.::NaOH Volume (ul):: = 25 ; output.::Tris-HCl Volume (ul):: = 25 } ; if ( input.::Flowcell Type:: == ::S1:: ) { output.::Volume of Pool to Denature (ul):: = 100 ; output.::NaOH Volume (ul):: = 25 ; output.::Tris-HCl Volume (ul):: = 25 } ; if ( input.::Flowcell Type:: == ::S2:: ) {output.::Volume of Pool to Denature (ul):: = 150 ; output.::NaOH Volume (ul):: = 37.50 ; output.::Tris-HCl Volume (ul):: = 37.50 } ; ; if ( input.::Flowcell Type:: == ::S4:: ) { output.::Volume of Pool to Denature (ul):: = 310 ; output.::NaOH Volume (ul):: = 77.50 ; output.::Tris-HCl Volume (ul):: = 77.50 }' \ && \ /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \ -i {stepURI:v2} -u {username} -p {password} -t true -log {compoundOutputFileLuid0} \ script:evaluateDynamicExpression \ -h false \ -exp 'step.::Number of Samples in Pool:: = step.::Number of Samples in Pool:: - 1; step.::Total Sample Volume (ul):: = step.::Total Sample Volume (ul):: - input.::Adjusted Per Sample Volume (ul)::' \ && \ /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \ script:driver_file_generator \ -i {stepURI:v2} \ -u {username} \ -p {password} \ -q true \ -destLIMSID {compoundOutputFileLuid1} \ -t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/MakeBPFile_NovaSeq_template.csv \ -o Output_plate_name.csv \ -l {compoundOutputFileLuid2} && \ PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 \ /opt/gls/clarity/extensions/IGA_2.1/make_bpp/apply_multiple_bulk_pools.py \ -s {stepURI:v2} \ -u {username} \ -p {password} \ --min-volume {udf:Minimum Per Sample Volume (ul)} \ --selected-cf {udf:Apply Correction Factors} \ --hamilton-limsid {compoundOutputFileLuid1} \ --custom-cf-limsid {compoundOutputFileLuid4} \ -l {compoundOutputFileLuid5} " ``` {% endcode %}
Make Bulk Pool NovaSeq Standard - Validate Hamilton Output File Name if Present, Parse Instrument ID, Set Next Steps to Advance (IGA v2.1) * 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 'step.::Liquid Handling Instrument ID:: = ::::' -log {compoundOutputFileLuid0} \ && \ /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/01_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid3} -i 'Liquid Handling Instrument ID' \ && \ /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.hasValue(::Liquid Handling Instrument ID::)) {step.::Liquid Handling Instrument ID:: = ::NO HAMILTON OUTPUT FILE UPLOADED:: } ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Register Step Completed (IGA v2.1) * 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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/pooling.groovy'" ``` {% endcode %}
Validate Unique Indexes (IGA v2.1) * Trigger Location = Not Used {% 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:validateUniqueIndexes" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------------ | -------------- | -------------- | ------------------------------------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------------ | -------------- | -------------- | ------------------------------------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Pooling * Label Uniqueness = On * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column #### Placement = Enabled * Defaults * Well Sort Order = Column * Placement Pattern = Column * Destination Containers * 96 well plate #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | --------------------------------------------------------------------------------------- | -------------- | -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Number of Flowcells to Sequence | Numeric | Required Field | | | Minimum Per Sample Volume (ul) | Numeric | Required Field | | | Liquid Handling Instrument ID | Text | Read Only | | | Apply Correction Factors | Text Dropdown | Required Field | | | Quick reference checklist: Make Bulk Pool for NovaSeq Standard. i) pre Liquid Handler | Multiline Text | Read Only | | | Quick reference checklist: Make Bulk Pool for NovaSeq Standard. ii) post Liquid Handler | Multiline Text | Read Only | | * Step File Placeholders * Calculation Log - Automatically attached * Hamilton Make Bulk Pool Input File - Automatically attached * Hamilton file log - Automatically attached * Hamilton Output File - Manually uploaded * Custom Correction Factors - Manually uploaded * Index Correction Log - Automatically attached * Sample Table (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 | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | NaOH Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | RSB Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Tris-HCl Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | Volume of Pool to Denature (ul) | Numeric | Read Only | Decimal Places Displayed = 0 | | Project | Project Name | Built-in | | | ### Step 2: Dilute and Denature * Master Step Name = Dilute and Denature (IGA v2.1) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * NaOH * Supplier = Illumina * Resuspension Buffer (RSB) * Supplier = Illumina * Tris-HCl * Supplier = Illumina #### Automations
Validate Single Input (IGA v2.1) * 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:validateSampleCount -min 1 -max 1 && \ /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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Validate Library Tube Barcode (IGA v2.1) * 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:evaluateDynamicExpression -exp 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-[A-Z]{3}:: ) ) {fail ( ::Invalid Library Tube Barcode. This must be in the format CCxxxxxxx-CCC, where 'x' is a digit 0-9 and 'C' is an uppercase letter, e.g. LP1234567-ABC. Please verify and try again.:: ) } ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' -log {compoundOutputFileLuid1}" ``` {% endcode %}
Dilute and Denature NovaSeq Standard - Generate Hamilton Library Tube Input File, Validate Run Setup, and Generate SampleSheet (IGA v2.1) * 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/DriverFileGenerator.jar \ script:driver_file_generator \ -i {stepURI:v2} \ -u {username} \ -p {password} \ -q true \ -destLIMSID {compoundOutputFileLuid2} \ -t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/LoadToLibTubeFile_NovaSeqStd_template.csv \ -o Output_plate_name.csv \ -l {compoundOutputFileLuid3} && \ /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 'step.::Run Mode:: = input.::Flowcell Type:: ; if (!step.::Experiment Name::.matches(::[a-zA-Z0-9-_]+::)) { fail(::Experiment Name contains prohibited characters. Allowed characters are: a-z, A-Z, 0-9, -, and _::) }; if (step.::Workflow Type:: == ::No Index::) { if (step.::Index Read 1:: != 0) { fail(::Index Read 1 must be 0 if the Workflow Type is No Index.::) } } else { if (step.::Index Read 1:: == 0) { fail(::Index Read 1 must be greater than 0 if the Workflow Type is :: + step.::Workflow Type:: + ::.::) } }; if (step.::Paired End::.toBoolean() && step.::Read 2 Cycles:: == 0) { fail(::Read 2 Cycles must not be zero if it is Paired End read.::) }; if (step.::Workflow Type:: == ::Dual Index:: && step.::Index Read 2:: == 0) { fail(::Index Read 2 must not be zero if Workflow Type is Dual Index.::) }; if (step.::Workflow Type:: == ::No Index:: || step.::Workflow Type:: == ::Single Index::) { step.::Index Read 2:: = 0 }; if (!step.::Paired End::.toBoolean()) { step.::Read 2 Cycles:: = 0 }; if (input.::Flowcell Type::!=::SP:: && step.::Read 1 Cycles:: > 151) { fail(::Read 1 Cycles must not be larger than 151 if it is not SPrime Flowcell::) };if (input.::Flowcell Type::!=::SP:: && step.::Read 2 Cycles:: > 151) { fail(::Read 2 Cycles must not be larger than 151 if it is not SPrime Flowcell::) }; nextStep = ::REMOVE::' \ -log {compoundOutputFileLuid1} \ -t true \ && if [[ '{udf:SampleSheet Version}' == 'V2' && '{udf:Enable Secondary Analysis}' == 'false' ]]; then \ templateFilename='/opt/gls/clarity/extensions/IGA_2.1/ss_converter_templates/NovaSeq_BCL2FASTQ_Samplesheet_Std_V2.csv'; \ else \ templateFilename='/opt/gls/clarity/extensions/IGA_2.1/ss_converter_templates/NovaSeq_BCL2FASTQ_Samplesheet_Std_V1.csv'; \ fi \ && /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 $templateFilename \ -o {compoundOutputFileLuid0}.csv \ -q true \ -destLIMSID {compoundOutputFileLuid0} \ -l {compoundOutputFileLuid1} \ && if [[ '{udf:Enable Secondary Analysis}' == 'true' ]]; then \ PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 /opt/gls/clarity/extensions/IGA_2.1/ss_converter \ --input {compoundOutputFileLuid0}.csv \ --bssh-app {udf:BaseSpace App Slug} \ --stepURI {stepURI:v2} -u {username} -p {password} -q \ --destLIMSID {compoundOutputFileLuid0} 2>&1; \ fi && \ /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/IGA_2.1/iga_novaseq/Biosample_Manifest.csv \ -o {compoundOutputFileLuid4}.csv \ -q true \ -destLIMSID {compoundOutputFileLuid4} \ -l {compoundOutputFileLuid1}" ``` {% endcode %}
Dilute and Denature NovaSeq Standard - Set Next Steps to Remove from Workflow (IGA v2.1) * 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 'step.::Liquid Handling Instrument ID:: = ::::' -log {compoundOutputFileLuid1} \ && \ /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/02_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile_DiluteDenature.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid4} -i 'Liquid Handling Instrument ID' && \ /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.hasValue(::Liquid Handling Instrument ID::)) {step.::Liquid Handling Instrument ID:: = ::NO HAMILTON OUTPUT FILE UPLOADED:: } ; nextStep = ::REMOVE::' -log {compoundOutputFileLuid1}" ``` {% endcode %}
Dilute and Denature NovaSeq Standard - Routing Script (IGA v2.1) * 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/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid1} script:changeWorkflow \ \ --FIELD_NAME 'N/A' \ --FIELD_VALUE 'N/A' \ --WORKFLOW 'Illumina Genomics Architecture - NovaSeq Sequencing v2.1' \ --STEP 'AUTOMATED - NovaSeq Run (IGA v2.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' && \ /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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
#### Queue * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | -------------- | ------------------------------------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

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

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Placement Pattern = Column * Destination Containers * Library Tube
#### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ----------------------------------------------- | ---------------- | ------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Adapter | Text | | | | Adapter Read 2 | Text | | | | BaseSpace App Slug | Text Dropdown | | | | BaseSpace Sequence Hub Analysis Workflow | Text | | | | BaseSpace Sequence Hub Configuration | Text Dropdown | | | | BaseSpace Sequence Hub Project Name | Text | | | | Custom Recipe Path | Text | | | | Enable Secondary Analysis | Toggle Switch | | | | Experiment Name | Text | | | | Index Read 1 | Numeric Dropdown | | | | Index Read 2 | Numeric Dropdown | | | | Liquid Handling Instrument ID | Text | | | | Output Folder | Text | | | | Paired End | Text Dropdown | | | | Quick reference checklist: Dilute and Denature. | Multiline Text | | | | Read 1 Cycles | Numeric Dropdown | | | | Read 2 Cycles | Numeric Dropdown | | | | Required Yield Gbp | Numeric | | | | Run Mode | Text Dropdown | | | | SampleSheet Version | Text Dropdown | | | | Use Custom Index Read 1 Primer | Toggle Switch | | | | Use Custom Read 1 Primer | Toggle Switch | | | | Use Custom Read 2 Primer | Toggle Switch | | | | Use Custom Recipe | Toggle Switch | | | | Workflow | Text | | | | Workflow Type | Text Dropdown | | | * Step File Placeholders * Sample Sheet - Automatically attached * Sample sheet Log File - Automatically attached * Hamilton Load to Library tube file - Automatically attached * Hamilton file log - Automatically attached * Biosample Manifest - Automatically attached * Sample Table (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 | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ## Protocol 3: NovaSeq Xp Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Make Bulk Pool for NovaSeq Xp * Master Step Name = Make Bulk Pool for NovaSeq Xp (IGA v2.1) * Step Type = Pooling * Aliquot Generation = Fixed, 1 * Naming Convention = {PoolName} #### Automations
Register Sample & Register Step Started (IGA v2.1) * 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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/register_sample.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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Validate Inputs Flowcell Type and Single Pool (IGA v2.1) * 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_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -validateSingleOutput true -poolType bulk" ``` {% endcode %}
NovaSeq Make Bulk Pool - Output Plate BPP Barcode Check (Duplicates Allowed) (IGA v2.1) * 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:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-BPP:: ) ) {fail ( ::Invalid BPP Plate Barcode. This plate ID must be in the format LPxxxxxxx-BPP, where 'x' is a digit 0-9, e.g. LP1234567-BPP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} \ && PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/validate_multiple_destination_plates.py -s {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0}" ``` {% endcode %}
Make Bulk Pool NovaSeq Xp - Reset Loading Workflow Type and Flowcell Type (IGA v2.1) * Trigger Location = Record Details * 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 -t false -h false -exp 'output.::Loading Workflow Type:: = input.::Loading Workflow Type::; output.::Flowcell Type:: = input.::Flowcell Type::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Make Bulk Pool NovaSeq Xp - Calculate Volumes and Generate Hamilton Input File (IGA v2.1) * 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} -t true -log {compoundOutputFileLuid0} \ script:evaluateDynamicExpression \ -h false \ -exp 'step.::Number of Samples in Pool:: = step.::Number of Samples in Pool:: + 1' \ script:evaluateDynamicExpression \ -h false \ -exp 'if ( input.::Flowcell Type:: == ::SP:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Lanes to Sequence:: * 18+ 30 } ; if ( input.::Flowcell Type:: == ::S1:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Lanes to Sequence:: * 18+ 30 } ; if ( input.::Flowcell Type:: == ::S2:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Lanes to Sequence:: * 22 + 30 } ; if ( input.::Flowcell Type:: == ::S4:: ) { step.::Bulk Pool Volume (ul):: = step.::Number of Lanes to Sequence:: * 30 + 30 } ; input.::Per Sample Volume (ul):: = ( ( (input.::Final Loading Concentration (pM):: * 5 / 1000) / input.::Normalized Molarity (nM):: ) * step.::Bulk Pool Volume (ul):: ) / step.::Number of Samples in Pool::' \ script:calculate_adjusted_per_sample_volume \ script:evaluateDynamicExpression \ -h false \ -exp 'step.::Total Sample Volume (ul):: = step.::Total Sample Volume (ul):: + input.::Adjusted Per Sample Volume (ul)::' \ script:evaluateDynamicExpression \ -h false \ -exp 'if (step.::Total Sample Volume (ul):: >= step.::Bulk Pool Volume (ul)::) {output.::RSB Volume (ul):: = 0} else {output.::RSB Volume (ul):: = step.::Bulk Pool Volume (ul):: - step.::Total Sample Volume (ul)::} ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' \ && \ /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -t true -log {compoundOutputFileLuid0} \ script:evaluateDynamicExpression \ -h false \ -exp 'step.::Number of Samples in Pool:: = step.::Number of Samples in Pool:: - 1; step.::Total Sample Volume (ul):: = step.::Total Sample Volume (ul):: - input.::Adjusted Per Sample Volume (ul)::' \ && \ /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \ script:driver_file_generator \ -i {stepURI:v2} \ -u {username} \ -p {password} \ -q true \ -destLIMSID {compoundOutputFileLuid1} \ -t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/MakeBPFile_NovaSeq_template.csv \ -o Output_plate_name.csv \ -l {compoundOutputFileLuid2} && \ PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 \ /opt/gls/clarity/extensions/IGA_2.1/make_bpp/apply_multiple_bulk_pools.py \ -s {stepURI:v2} \ -u {username} \ -p {password} \ --min-volume {udf:Minimum Per Sample Volume (ul)} \ --selected-cf {udf:Apply Correction Factors} \ --hamilton-limsid {compoundOutputFileLuid1} \ --custom-cf-limsid {compoundOutputFileLuid3} \ -l {compoundOutputFileLuid4} " ``` {% endcode %}
Set Flowcell Type and Next Step (IGA v2.1) * 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 'output.::Flowcell Type:: = input.::Flowcell Type:: ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Register Step Completed (IGA v2.1) * 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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/pooling.groovy'" ``` {% endcode %}
Validate Unique Indexes (IGA v2.1) * Trigger Location = Not Used {% 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:validateUniqueIndexes" ``` {% 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 | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | 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 | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Pooling * Label Uniqueness = On * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row #### Placement = Enabled * Defaults * Well Sort Order = Row * Placement Pattern = Column * Destination Containers * 96 well plate #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------------------------------------------------------- | -------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Number of Lanes to Sequence | Numeric | Required Field | | | Minimum Per Sample Volume (ul) | Numeric | Required Field | | | Apply Correction Factors | Text Dropdown | Required Field | | | Quick reference checklist: Make Bulk Pool for NovaSeq Xp. i) pre Liquid Handler | Multiline Text | Read Only | | * Step File Placeholders * Log - Automatically attached * Hamilton Make Bulk Pool Input File - Automatically attached * Hamilton Input File Generation Log - Automatically attached * Custom Correction Factors - Manually uploaded * Index Correction Log - Automatically attached * Sample Table * Sample Display Default = Expand * 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 | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow 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 2: Dilute, Denature & ExAmp * Master Step Name = Dilute, Denature & ExAmp (IGA v2.1) * Step Type = Standard * Derived Sample Generation = Variable * Naming Convention = {InputItemName}\_WP{OutputItemNumber} * Reagent Kits * DPX1 * Supplier = Illumina * Catalog Number = 20019916 * DPX2 * Supplier = Illumina * Catalog Number = 20019917 * DPX3 * Supplier = Illumina * Catalog Number = 20019918 * NaOH * Resuspension Buffer (RSB) * Tris-HCl #### Automations
Dil/Den/ExAmp NovaSeq Xp - Generate Hamilton Consolidated Bulk Pool MakeBPP Input File and Validate Input Flowcell Type (IGA v2.1) * Trigger Location = Step * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/03_NovaSeqXp_consolidateBulkPoolFiles.py \ -u {username} -p {password} -s {stepURI} -o consolidated.csv --destLIMSID {compoundOutputFileLuid2} && \ /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:validate_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Dil/Den/ExAmp NovaSeq Xp - Validate Hamilton BPP Output File Name & Parse Instrument ID (IGA v2.1) * Trigger Location = Placement * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/03_NovaSeqXp_confirmBPPPlateAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid3} -i 'Liquid Handling Instrument ID'" ``` {% endcode %}
Dil/Den/ExAmp NovaSeq Xp - Output Plate WPP Barcode Uniqueness Check (IGA v2.1) * 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:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-WPP:: ) ) {fail ( ::Invalid WPP Plate Barcode. This plate ID must be in the format LPxxxxxxx-WPP, where 'x' is a digit 0-9, e.g. LP1234567-WPP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}" ``` {% endcode %}
Dil/Den/ExAmp NovaSeq Xp - Calculate Volumes and Generate Incomplete WPP Driver File for Next Step (IGA v2.1) * Trigger Location = Record Details * 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 \ -t true \ -h false \ -exp 'if ( input.::Flowcell Type:: == ::SP:: ) { output.::BP Aliquot Volume (ul):: = 18 ; output.::NaOH Volume (ul):: = 4.50 ; output.::Tris-HCl Volume (ul):: = 4.50 ; step.::DPX1 Volume (ul):: = 126 ; step.::DPX2 Volume (ul):: = 18 ; step.::DPX3 Volume (ul):: = 66 ; output.::Mastermix per Lane (ul):: = 63} ; if ( input.::Flowcell Type:: == ::S1:: ) { output.::BP Aliquot Volume (ul):: = 18 ; output.::NaOH Volume (ul):: = 4.50 ; output.::Tris-HCl Volume (ul):: = 4.50 ; step.::DPX1 Volume (ul):: = 126 ; step.::DPX2 Volume (ul):: = 18 ; step.::DPX3 Volume (ul):: = 66 ; output.::Mastermix per Lane (ul):: = 63} ; if ( input.::Flowcell Type:: == ::S2:: ) { output.::BP Aliquot Volume (ul):: = 22 ; output.::NaOH Volume (ul):: = 5.50 ; output.::Tris-HCl Volume (ul):: = 5.50 ; step.::DPX1 Volume (ul):: = 126 ; step.::DPX2 Volume (ul):: = 18 ; step.::DPX3 Volume (ul):: = 66 ; output.::Mastermix per Lane (ul):: = 77} ; if ( input.::Flowcell Type:: == ::S4:: ) { output.::BP Aliquot Volume (ul):: = 30 ; output.::NaOH Volume (ul):: = 7.50 ; output.::Tris-HCl Volume (ul):: = 7.50 ; step.::DPX1 Volume (ul):: = 315 ; step.::DPX2 Volume (ul):: = 45 ; step.::DPX3 Volume (ul):: = 165 ; output.::Mastermix per Lane (ul):: = 105} ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' \ -log {compoundOutputFileLuid1} \ && /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/NovaSeq_Xp_Working_Pool.csv \ -o {compoundOutputFileLuid0}.csv \ script:driver_file_generator \ -t /opt/gls/clarity/extensions/conf/driverfiletemplates/NovaSeq_Xp_Working_Pool2.csv \ -o append.csv \ && cat append.csv >> {compoundOutputFileLuid0}.csv \ && \ /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \ script:driver_file_generator \ -i {stepURI:v2} \ -u {username} \ -p {password} \ -q true \ -destLIMSID {compoundOutputFileLuid4} \ -t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/LoadToFlowcell_NovaSeqXp_Incomplete_template.csv \ -o Output_plate_name.csv \ -l {compoundOutputFileLuid1}" ``` {% endcode %}
Dil/Den/ExAmp NovaSeq Xp - Set Next Steps to Advance (IGA v2.1) * 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 'output.::Flowcell Type:: = input.::Flowcell Type:: ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}" ``` {% endcode %}
Register Step Completed (IGA v2.1) * 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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
Set Flowcell Type and Next Step (IGA v2.1) * Trigger Location = Not Used {% 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 'output.::Flowcell Type:: = input.::Flowcell Type:: ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}" ``` {% 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 | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | 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 | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Step Setup = Enabled * File Placeholders 1. Hamilton Consolidated MakeBPP Bulk Pool Input File * Description = This file contains consolidated Bulk Pool information to run the Hamilton MakeBPP method. It refers to previous Xp Make Bulk Pool steps in Clarity that all use the same BPP output plate name. Please run this file with the Hamilton MakeBPP method before continuing with this step. * Attachment = Auto 2. Upload Hamilton MakeBPP Output File * Description = Please upload the Hamilton output file from the MakeBPP run. * Attachment = Manual #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Column * Destination Containers * 96 well plate #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ----------------------------------------------------- | -------------- | ----------- | ----------------------------------------------------------------------------------------------------------- | | DPX1 Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 0 | | DPX2 Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 0 | | DPX3 Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 0 | | Liquid Handling Instrument ID | Text | Read Only | | | Quick reference checklist: Dilute, Denature and ExAmp | Multiline Text | Read Only |

Defaults =
User tasks for this page:
- Input DPX/NaOH/RSB/TrisHCl lots
- Click 'Next Steps'

| * Step File Placeholders * Calculation File - Automatically attached * Log File - Automatically attached * Incomplete WPP Hamilton Files (DO NOT USE; REQUIRED FOR NEXT STEP!) - Automatically attached * Sample Table * Sample Display Default = Expand * 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 | BP Aliquot Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 0 | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Mastermix per Lane (ul) | Numeric | Read Only | Decimal Places Displayed = 0 | | Derived Sample | NaOH Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Tris-HCl Volume (ul) | Numeric | Read Only | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 3: Load to Flowcell * Master Step Name = Load to Flowcell (IGA v2.1) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations
Validate Inputs and Selected Container (IGA v2.1) * 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 script:validate_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -validateSelectedContainer true && \ /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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'" ``` {% endcode %}
Validate Flowcell Barcode with New Mask Fixes (IGA v2.1) * 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:evaluateDynamicExpression \ -exp 'if (input.::Flowcell Type:: == ::SP:: && !output.container.name.matches( ::[A-Z0-9]{5}DR[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S1:: && !output.container.name.matches( ::[A-Z0-9]{5}DR[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S2:: && !output.container.name.matches( ::[A-Z0-9]{5}DM[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S4:: && !output.container.name.matches( ::[A-Z0-9]{5}DS[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' \ -log {compoundOutputFileLuid1} && \ /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/validate_floorcell_container.py -u {username} -p {password} -s {stepURI}" ``` {% endcode %}
Validate Run Setup and Generate Sample Sheet (IGA v2.1) * 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 'step.::Run Mode:: = input.::Flowcell Type:: ; if (!step.::Experiment Name::.matches(::[a-zA-Z0-9-_]+::)) { fail(::Experiment Name contains prohibited characters. Allowed characters are: a-z, A-Z, 0-9, -, and _::) }; if (step.::Workflow Type:: == ::No Index::) { if (step.::Index Read 1:: != 0) { fail(::Index Read 1 must be 0 if the Workflow Type is No Index.::) } } else { if (step.::Index Read 1:: == 0) { fail(::Index Read 1 must be greater than 0 if the Workflow Type is :: + step.::Workflow Type:: + ::.::) } }; if (step.::Paired End::.toBoolean() && step.::Read 2 Cycles:: == 0) { fail(::Read 2 Cycles must not be zero if it is Paired End read.::) }; if (step.::Workflow Type:: == ::Dual Index:: && step.::Index Read 2:: == 0) { fail(::Index Read 2 must not be zero if Workflow Type is Dual Index.::) }; if (step.::Workflow Type:: == ::No Index:: || step.::Workflow Type:: == ::Single Index::) { step.::Index Read 2:: = 0 }; if (!step.::Paired End::.toBoolean()) { step.::Read 2 Cycles:: = 0 }; if (input.::Flowcell Type::!=::SP:: && step.::Read 1 Cycles:: > 151) { fail(::Read 1 Cycles must not be larger than 151 if it is not SPrime Flowcell::) };if (input.::Flowcell Type::!=::SP:: && step.::Read 2 Cycles:: > 151) { fail(::Read 2 Cycles must not be larger than 151 if it is not SPrime Flowcell::) }; nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid1} \ -t true \ && if [[ '{udf:SampleSheet Version}' == 'V2' && '{udf:Enable Secondary Analysis}' == 'false' ]]; then \ templateFilename='/opt/gls/clarity/extensions/IGA_2.1/ss_converter_templates/NovaSeq_BCL2FASTQ_Samplesheet_XP_V2.csv'; \ else \ templateFilename='/opt/gls/clarity/extensions/IGA_2.1/ss_converter_templates/NovaSeq_BCL2FASTQ_Samplesheet_XP_V1.csv'; \ fi \ && /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 $templateFilename \ -o {compoundOutputFileLuid0}.csv \ -q true \ -destLIMSID {compoundOutputFileLuid0} \ -l {compoundOutputFileLuid1} \ && if [[ '{udf:Enable Secondary Analysis}' == 'true' ]]; then \ PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 /opt/gls/clarity/extensions/IGA_2.1/ss_converter \ --input {compoundOutputFileLuid0}.csv \ --bssh-app {udf:BaseSpace App Slug} \ --stepURI {stepURI:v2} -u {username} -p {password} -q \ --destLIMSID {compoundOutputFileLuid0} 2>&1; \ fi && \ /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/IGA_2.1/iga_novaseq/Biosample_Manifest.csv \ -o {compoundOutputFileLuid3}.csv \ -q true \ -destLIMSID {compoundOutputFileLuid3} \ -l {compoundOutputFileLuid1}" ``` {% endcode %}
Load to Flowcell NovaSeq Xp - Generate Hamilton WPP Input File (IGA v2.1) * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/04_NovaSeqXp_completeAndConsolidateWPPZipFile.py -u {username} -p {password} -s {stepURI} -o wpp_output --destLIMSID {compoundOutputFileLuid2}" ``` {% endcode %}
Register Step Completed (IGA v2.1) * 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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'" ``` {% endcode %}
Validate Flowcell Barcode (IGA v2.1) * Trigger Location = Not Used {% 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 (input.::Flowcell Type:: == ::SP:: && !output.container.name.matches( ::[A-Za-z0-9]{5}DRXX:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S1:: && !output.container.name.matches( ::[A-Za-z0-9]{5}DRXX:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S2:: && !output.container.name.matches( ::[A-Za-z0-9]{5}DMXX:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S4:: && !output.container.name.matches( ::[A-Za-z0-9]{5}DSXX:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' \ -log {compoundOutputFileLuid1}" ``` {% 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 | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | 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 | Well | Built-in | | | | Derived Sample | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Column * Destination Containers * SP
* S1
* S2
* S4
#### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------------------------------------- | ---------------- | ------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Adapter | Text | | | | Adapter Read 2 | Text | | | | BaseSpace App Slug | Text Dropdown | | | | BaseSpace Sequence Hub Analysis Workflow | Text | | | | BaseSpace Sequence Hub Configuration | Text Dropdown | | | | BaseSpace Sequence Hub Project Name | Text | | | | Custom Recipe Path | Text | | | | Enable Secondary Analysis | Toggle Switch | | | | Experiment Name | Text | | | | Index Read 1 | Numeric Dropdown | | | | Index Read 2 | Numeric Dropdown | | | | Library Tube Barcode | Text | | | | Output Folder | Text | | | | Paired End | Text Dropdown | | | | Quick reference checklist: Load To Flowcell. | Multiline Text | | | | Read 1 Cycles | Numeric Dropdown | | | | Read 2 Cycles | Numeric Dropdown | | | | Required Yield Gbp | Numeric | | | | SampleSheet Version | Text Dropdown | | | | Use Custom Index Read 1 Primer | Toggle Switch | | | | Use Custom Read 1 Primer | Toggle Switch | | | | Use Custom Read 2 Primer | Toggle Switch | | | | Use Custom Recipe | Toggle Switch | | | | Workflow | Text | | | | Workflow Type | Text Dropdown | | | * Step File Placeholders * Sample Sheet - Automatically attached * Log File - Automatically attached * Hamilton Input File (BPP to WPP to Flow Cell) - Automatically attached * Biosample Manifest - Automatically attached * Sample Table * Sample Display Default = Expand * 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 | Flowcell Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ## Protocol 4: AUTOMATED - NovaSeq Run Protocol Type = Sequencing **Next Steps Configuration**
### Step 1: AUTOMATED - NovaSeq Run * Master Step Name = AUTOMATED - NovaSeq Run (IGA v2.1) * Step Type = Analysis * Measurement Generation = Variable * Naming Convention = Lane {OutputItemNumber} * Reagent Kits * Buffer Cartridge * Supplier = Illumina * Cluster Cartridge * Supplier = Illumina * SBS Cartridge * Supplier = Illumina #### Automations
Register Step Completed (IGA v2.1) * 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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/novaseq6000/automated_sequencing_run_step_completed.groovy'" ``` {% endcode %}
Set Next Steps (IGA v2.1) * Trigger Location = Not Used {% 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 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Show warning message and register step started at AUTOMATED step (IGA v2.1) * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 \ /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/NovaSeq_automated_warning.py \ -s {stepURI:v2} \ -u {username} \ -p {password} \ -l {compoundOutputFileLuid0} && \ /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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/register_sample.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} -l {compoundOutputFileLuid0} -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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/novaseq6000/register_novaseq_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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/novaseq6000/novaseq_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} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/novaseq6000/novaseq_seqrun_started.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 | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | 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 | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | 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 | Numeric | Read Only | Decimal Places Displayed = 0 | | Current Read | Numeric | Read Only | Decimal Places Displayed = 0 | | Firmware Version | Text | Read Only | | | Flow Cell Expiration Date | Date | Read Only | | | Flow Cell ID | Text | Read Only | | | Flow Cell Lot Number | Text | Read Only | | | Flow Cell Mode | Text | Read Only | | | Flow Cell Part Number | Text | Read Only | | | Flow Cell Side | Text | Read Only | | | Instrument Control Software Version | Text | Read Only | | | Instrument ID | Text | Read Only | | | Instrument Type | Text | Read Only | | | Loading Workflow Type | Text | Read Only | | | Output Folder | Text | Read Only | | | RTA Version | Text | Read Only | | | Run ID | Text | Read Only | | | Run Status | Text | Read Only | | | Sequencing Log | Multiline Text | Read Only | | * Step File Placeholders * Log File - Automatically attached * Sample Table * File Column Options * File Column Display = Hide * File Attachment Method = Manual * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | --------------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Cluster Density (K/mm^2) R1 | Numeric | Read Only | | | Container | Cluster Density (K/mm^2) R2 | Numeric | Read Only | | | 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 | Read PF (M) R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | Read PF (M) R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | Well | Built-in | | | | Container | Yield PF (Gb) R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | Yield PF (Gb) R2 | Numeric | Read Only | Decimal Places Displayed = 2 | | 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 | %PF R1 | Numeric | Read Only | Decimal Places Displayed = 2 | | Container | %PF R2 | 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 | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | |