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

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

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}"

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

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}"

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}"

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}"

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

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

PreviousIGA Library Prep Automated v2.1 NextViral Pathogen Protocols

Last updated 8 months ago

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