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
- Expanded View Fields

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log file - Automatically attached
Sample Table (Table Columns - Global Fields)

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
- Expanded View Fields

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

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)
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)

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
- Expanded View Fields

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

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)
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)

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
- Expanded View Fields

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

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)
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

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
- Expanded View Fields

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

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)
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

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
- Expanded View Fields

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

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)
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

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
- Expanded View Fields

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Manual
- Table Columns - Global Fields