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

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'"

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

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}"

Define Run Format - Routing Script (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

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'"

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	Read Only	Decimal Places Displayed = 2
  Derived Sample	Final Loading Concentration (pM)	Numeric Dropdown	Required Field Custom Entries	Presets 225 400 Decimal Places Displayed = 0
  Derived Sample	Flowcell Type	Text Dropdown	Required Field	Presets SP S1 S2 S4
  Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
  Derived Sample	Minimum Molarity (nM)	Numeric		Decimal Places Displayed = 2
  Derived Sample	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
  Derived Sample	Per Sample Volume (ul)	Numeric	Read Only	Decimal Places Displayed = 2
  Derived Sample	Sample Name	Built-in
  Derived Sample	Warning	Text	Read Only
  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

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'"

Pooling NovaSeq Standard - Show Warning Message (IGA v2.1)

• Trigger Location = Pooling

• Trigger Style = Automatic upon entry

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}"

Validate Inputs Flowcell Type and Number of Pools (IGA v2.1)

• 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_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}"

NovaSeq Make Bulk Pool - Output Plate BPP Barcode Check (Duplicates Allowed) (IGA v2.1)

• 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: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}"

Make Bulk Pool NovaSeq Standard - Calculate Volumes and Generate Hamilton Input File (IGA v2.1)

• 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} -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} "

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

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}"

Register Step Completed (IGA v2.1)

• 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} -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'"

Validate Unique Indexes (IGA v2.1)

• Trigger Location = Not Used

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"

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 SP S1 S2 S4
    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 SP S1 S2 S4
    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	Default = 1 Range From 1 to 10 Decimal Places Displayed = 0
  Minimum Per Sample Volume (ul)	Numeric	Required Field	Default = 2 Decimal Places Displayed = 2
  Liquid Handling Instrument ID	Text	Read Only
  Apply Correction Factors	Text Dropdown	Required Field	Presets None IDPF Custom Default = None
  Quick reference checklist: Make Bulk Pool for NovaSeq Standard. i) pre Liquid Handler	Multiline Text	Read Only	Defaults = User tasks for this page: - Select 'Number Of Flowcells' and 'Min Per Sample Volume (ul)' - 'Run' the Make Bulk Pool automation, and download resulting Hamilton Make Bulk Pool Input File
  Quick reference checklist: Make Bulk Pool for NovaSeq Standard. ii) post Liquid Handler	Multiline Text	Read Only	Defaults = User tasks for this page: - After running MakeBPP on the liquid handler, upload resulting Hamilton Output File - Click on 'Next Steps'

• 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 SP S1 S2 S4
  Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
  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

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'"

Validate Library Tube Barcode (IGA v2.1)

• 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: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}"

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

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}"

Dilute and Denature NovaSeq Standard - Set Next Steps to Remove from Workflow (IGA v2.1)

• 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 '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}"

Dilute and Denature NovaSeq Standard - Routing Script (IGA v2.1)

• Trigger Location = Step

• 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 -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'"

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 SP S1 S2 S4
    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 SP S1 S2 S4
    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	Required Field	Default = CTGTCTCTTATACACATCT
  Adapter Read 2	Text	Required Field	Default = CTGTCTCTTATACACATCT
  BaseSpace App Slug	Text Dropdown	Required Field Custom Entries	Presets Illumina-inc.bcl-convert.1.3.0 Illumina-inc.bcl-convert.1.2.0
  BaseSpace Sequence Hub Analysis Workflow	Text	Required Field	Default = TSS Connect v1.1
  BaseSpace Sequence Hub Configuration	Text Dropdown	Required Field	Presets Run Monitoring And Storage Run Monitoring Only Not Used Default = Run Monitoring And Storage
  BaseSpace Sequence Hub Project Name	Text	Required Field
  Custom Recipe Path	Text
  Enable Secondary Analysis	Toggle Switch	Required Field	Default = Yes
  Experiment Name	Text	Required Field
  Index Read 1	Numeric Dropdown	Required Field Custom Entries	Presets 10 6 8 0 Default = 10 Range From 0 to 20 Decimal Places Displayed = 0
  Index Read 2	Numeric Dropdown	Required Field Custom Entries	Presets 10 6 8 0 Default = 10 Range From 0 to 20 Decimal Places Displayed = 0
  Liquid Handling Instrument ID	Text	Read Only
  Output Folder	Text	Required Field
  Paired End	Text Dropdown	Required Field	Presets True False Default = True
  Quick reference checklist: Dilute and Denature.	Multiline Text	Read Only	Defaults = User tasks for this page: - Select NaOH/TrisHCl/RSB lots, and input run configuration - 'Run' Dilute and Denature automation, download resulting input 'Hamilton Load to Library tube file' - Click 'Next Steps' and then 'Finish Step' to move library tube through to 'AUTOMATED - NovaSeq Run'.
  Read 1 Cycles	Numeric Dropdown	Required Field Custom Entries	Presets 151 251 101 51 Default = 151 Range From 1 to 301 Decimal Places Displayed = 0
  Read 2 Cycles	Numeric Dropdown	Required Field Custom Entries	Presets 151 251 101 51 Default = 151 Range From 0 to 301 Decimal Places Displayed = 0
  Required Yield Gbp	Numeric	Required Field	Default = 90
  Run Mode	Text Dropdown	Read Only	Presets S4 S1 S2 SP Default = S4
  SampleSheet Version	Text Dropdown	Required Field	Presets V2 V1 Default = V2
  Use Custom Index Read 1 Primer	Toggle Switch		Default = No
  Use Custom Read 1 Primer	Toggle Switch	Required Field	Default = No
  Use Custom Read 2 Primer	Toggle Switch	Required Field	Default = No
  Use Custom Recipe	Toggle Switch	Required Field	Default = No
  Workflow	Text	Read Only	Default = GenerateFASTQ
  Workflow Type	Text Dropdown	Required Field	Presets Dual Index Single Index No Index Custom Default = Dual Index

• 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 SP S1 S2 S4
  Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
  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

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'"

Validate Inputs Flowcell Type and Single Pool (IGA v2.1)

• 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_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -validateSingleOutput true -poolType bulk"

NovaSeq Make Bulk Pool - Output Plate BPP Barcode Check (Duplicates Allowed) (IGA v2.1)

• 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: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}"

Make Bulk Pool NovaSeq Xp - Reset Loading Workflow Type and Flowcell Type (IGA v2.1)

• Trigger Location = Record Details

• 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 -t false -h false -exp 'output.::Loading Workflow Type:: = input.::Loading Workflow Type::; output.::Flowcell Type:: = input.::Flowcell Type::' -log {compoundOutputFileLuid0}"

Make Bulk Pool NovaSeq Xp - Calculate Volumes and Generate Hamilton Input File (IGA v2.1)

• 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} -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} "

Set Flowcell Type and Next Step (IGA v2.1)

• 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 'output.::Flowcell Type:: = input.::Flowcell Type:: ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"

Register Step Completed (IGA v2.1)

• 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} -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'"

Validate Unique Indexes (IGA v2.1)

• Trigger Location = Not Used

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"

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 SP S1 S2 S4
    Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
    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 SP S1 S2 S4
    Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
    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	Decimal Places Displayed = 0
  Minimum Per Sample Volume (ul)	Numeric	Required Field	Default = 2 Decimal Places Displayed = 2
  Apply Correction Factors	Text Dropdown	Required Field	Presets None IDPF Custom Default = None
  Quick reference checklist: Make Bulk Pool for NovaSeq Xp. i) pre Liquid Handler	Multiline Text	Read Only	Defaults = User tasks for this page: - Select 'Number Of Lanes' and 'Min Per Sample Volume (ul)' - 'Run' the Make Bulk Pool automation - Click 'Next Steps' and 'Finish Steps'. To add another Bulk Pool to this BPP, repeat Make Bulk Pool for NovaSeq Xp. Once your BPP contains the pools you need, continue on to Dilute and Denature to get the collated MakeBPP Liquid Handler input file.

• 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 SP S1 S2 S4
    Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
    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

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'"

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

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'"

Dil/Den/ExAmp NovaSeq Xp - Output Plate WPP Barcode Uniqueness Check (IGA v2.1)

• 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: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}"

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

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}"

Dil/Den/ExAmp NovaSeq Xp - Set Next Steps to Advance (IGA v2.1)

• 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 'output.::Flowcell Type:: = input.::Flowcell Type:: ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed (IGA v2.1)

• 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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Set Flowcell Type and Next Step (IGA v2.1)

• Trigger Location = Not Used

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}"

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 SP S1 S2 S4
    Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
    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 SP S1 S2 S4
    Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
    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 SP S1 S2 S4
    Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
    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

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'"

Validate Flowcell Barcode with New Mask Fixes (IGA v2.1)

• 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: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}"

Validate Run Setup and Generate Sample Sheet (IGA v2.1)

• 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 '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}"

Load to Flowcell NovaSeq Xp - Generate Hamilton WPP Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Manual button

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}"

Register Step Completed (IGA v2.1)

• 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} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Validate Flowcell Barcode (IGA v2.1)

• Trigger Location = Not Used

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}"

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 SP S1 S2 S4
    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 SP S1 S2 S4
    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	Required Field	Default = CTGTCTCTTATACACATCT
  Adapter Read 2	Text	Required Field	Default = CTGTCTCTTATACACATCT
  BaseSpace App Slug	Text Dropdown	Required Field Custom Entries	Presets Illumina-inc.bcl-convert.1.3.0 Illumina-inc.bcl-convert.1.2.0
  BaseSpace Sequence Hub Analysis Workflow	Text	Required Field	Default = TSS Connect v1.1
  BaseSpace Sequence Hub Configuration	Text Dropdown	Required Field	Presets Run Monitoring And Storage Run Monitoring Only Not Used Default = Run Monitoring And Storage
  BaseSpace Sequence Hub Project Name	Text	Required Field
  Custom Recipe Path	Text
  Enable Secondary Analysis	Toggle Switch	Required Field	Default = Yes
  Experiment Name	Text	Required Field
  Index Read 1	Numeric Dropdown	Required Field Custom Entries	Presets 10 6 8 0 Default = 10 Range From 0 to 20 Decimal Places Displayed = 0
  Index Read 2	Numeric Dropdown	Required Field Custom Entries	Presets 10 6 8 0 Default = 10 Range From 0 to 20 Decimal Places Displayed = 0
  Library Tube Barcode	Text	Required Field
  Output Folder	Text	Required Field
  Paired End	Text Dropdown	Required Field	Presets True False Default = True
  Quick reference checklist: Load To Flowcell.	Multiline Text	Read Only	Defaults = User tasks for this page: - Populate run configuration settings above - 'Run' Load To Flowcell automation, download resulting 'Hamilton Input File (BPP to WPP to Flow Cell)' file - 'Run' Validate Run Setup and Generate Sample Sheet (IGA v2.1) automation - Click 'Next Steps' and then 'Finish Step' to move flowcell through to 'AUTOMATED - NovaSeq Run'
  Read 1 Cycles	Numeric Dropdown	Required Field Custom Entries	Presets 151 251 101 51 Default = 151 Range From 1 to 301 Decimal Places Displayed = 0
  Read 2 Cycles	Numeric Dropdown	Required Field Custom Entries	Presets 151 251 101 51 Default = 151 Range From 0 to 301 Decimal Places Displayed = 0
  Required Yield Gbp	Numeric		Default = 90
  SampleSheet Version	Text Dropdown	Required Field	Presets V2 V1 Default = V2
  Use Custom Index Read 1 Primer	Toggle Switch	Required Field	Default = No
  Use Custom Read 1 Primer	Toggle Switch	Required Field	Default = No
  Use Custom Read 2 Primer	Toggle Switch	Required Field	Default = No
  Use Custom Recipe	Toggle Switch	Required Field	Default = No
  Workflow	Text	Read Only	Default = GenerateFASTQ
  Workflow Type	Text Dropdown	Required Field	Presets Dual Index Single Index No Index Custom Default = Dual Index

• 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 SP S1 S2 S4
    Derived Sample	Loading Workflow Type	Text Dropdown	Required Field	Presets NovaSeq Standard NovaSeq Xp [Remove from workflow]
    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

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'"

Set Next Steps (IGA v2.1)

• Trigger Location = Not Used

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}"

Show warning message and register step started at AUTOMATED step (IGA v2.1)

• Trigger Location = Not Used

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' "

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