IGA Library Prep Automated v3.0

Overview

IGA Library Prep Automated v3.0 contains preset protocols that support the preparation of samples and libraries used for sequencing. These protocols can be used with the NovaSeq X Series Sequencing v2.0 workflow (which is installed separately). The protocols 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: Sample Selection (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: Select Samples (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: Select Samples (IGA v3.0)

• Master Step Name = Sample Selection (IGA v3.0)

• Step Type = No Outputs

The version of Sample Selection (IGA) master step name may be different depending on the version of IPP installed.

Automations

Validate Sample Attributes (IGA v3.0)

• 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:http} -u {username} -p {password} -t false -h false script:evaluateDynamicExpression \
-exp 'if (! submittedSample.hasValue(::Sample Type::)) { \
    fail(::Sample Type must be non-empty. Please update :: + submittedSample.::name::); \
}; \
acceptedSampleTypes = [::Genomic DNA::, ::Saliva::, ::Blood::]; \
if (! acceptedSampleTypes.contains(submittedSample.::Sample Type::)) { \
  fail(::Invalid Sample Type found for :: + submittedSample.::name:: + ::. Must be one of :: + acceptedSampleTypes.join(::, ::)); \
}; \
if (! submittedSample.hasValue(::Submitted Sample Labware Type::)) { \
    fail(::Submitted Sample Labware Type must be non-empty. Please update :: + submittedSample.::name::); \
}; \
acceptedSampleLabwareTypes = [::gDNA::, ::Saliva::, ::Blood1.3::, ::Blood2.7::, ::Blood7.5::, ::Blood10::]; \
if (! acceptedSampleLabwareTypes.contains(submittedSample.::Submitted Sample Labware Type::)) { \
  fail(::Invalid Submitted Sample Labware Type found for :: + submittedSample.::name:: + ::. Must be one of :: + acceptedSampleLabwareTypes.join(::, ::)); \
}; \
if (! submittedSample.hasValue(::Units::)) { \
    fail(::Units must be non-empty. Please update :: + submittedSample.::name::); \
}; \
if (submittedSample.::Sample Type:: == ::Genomic DNA:: && ! submittedSample.hasValue(::Sample Conc.::)) { \
    fail(::Sample Conc. must be non-empty for Genomic DNA samples. Please update :: + submittedSample.::name::); \
};' -log {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'"

Sample Selection - Set Library prep method and Next steps (IGA v3.0)

• 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 'submittedSample.::Library Prep Method:: = step.::Library Prep Method::' -log {compoundOutputFileLuid0} && /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 (submittedSample.::Sample Type:: == ::Genomic DNA:: && input.container.node.type[0].@name == ::96 well plate::) {nextStep = ::REMOVE::} else nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"

Sample Selection - Route plated gDNA (IGA v3.0)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (submittedSample.::Sample Type:: == ::Genomic DNA::) {if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA PCR-Free:: ) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::} ; if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA with Enrichment::) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment::}}' -log {compoundOutputFileLuid0} && /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 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
&& /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'"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  IGA WF Build Version	Text	Read Only	Default = 3.0.0.5-SNAPSHOT
  Library Prep Method	Text Dropdown	Required Field	Presets Illumina DNA PCR-Free Illumina DNA with Enrichment
  Quick reference checklist: Sample Selection	Multiline Text	Read Only	Default = User tasks for this page: - Select Library Prep Method above - Select Next Steps

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Sample Name	Built-in

Protocol 2: Sample Plating (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: Plate Samples (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: Plate Samples (IGA v3.0)

• Master Step Name = Sample Plating (IGA v3.0)

• Step Type = Standard

• Derived Sample Generation = Variable, 3

• Naming Convention = {InputItemName}

The version of Sample Plating (IGA) master step name may be different depending on the version of IPP installed.

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!step.hasValue(::Step Sample Type::)) {step.::Step Sample Type:: = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]::} else {if ( step.::Step Sample Type:: != submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ) { fail(::Samples must be of the same type and marked for same library prep method::) }}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Placement Reminder (IGA v3.0)

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"

Sample Plating - Sample Placement SAM Plate Barcode Uniqueness Check (IGA v3.0)

• 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}-SAM:: ) ) {fail ( ::Invalid SAM Plate Barcode format. This plate ID must be in the format LPxxxxxxx-SAM, where 'x' is a digit 0-9, e.g. LP1234567-SAM. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

Sample Plating - Set Transfer Volume & Create LHR Input File (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Sample Type:: == ::Blood::) {output.::Transfer Volume (ul):: = 30} ;  if (submittedSample.::Sample Type:: == ::Saliva::) {output.::Transfer Volume (ul):: = 60}; if (submittedSample.::Sample Type:: == ::Genomic DNA::) {output.::Transfer Volume (ul):: = 45}' \
-log {compoundOutputFileLuid1} &&
/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 {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/PlatingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Sample Plating - LHR Output Plate Barcode Check, Store Instrument ID & Set Next Steps to Remove from Workflow before Custom Routing (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::REMOVE:: ' \
-log {compoundOutputFileLuid1}"

Sample Plating - Route samples (IGA v3.0)

• 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 \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /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 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Blood (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Saliva (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Blood (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Saliva (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--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'"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Queue

• Defaults

  • Sample Grouping = Group by Projects

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Waiting	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Projects

  • Well Sort Order = Column

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Projects

  • 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
  LHR Instrument ID	Text	Read Only
  Quick reference checklist: Sample Plating. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - Select blue 'Run' button - Download LHR Input File
  Quick reference checklist: Sample Plating. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting LHR Output File - Select Next Steps
  Step Sample Type	Text	Read Only

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Submitted Sample Type	Text	Read Only
    Derived Sample	Transfer Volume (ul)	Numeric

Protocol 3: Blood Extraction (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: DNA Extraction - Blood (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: DNA Extraction - Blood (IGA v3.0)

• Master Step Name = DNA Extraction - Blood (IGA v3.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

The version of DNA Extraction - Blood (IGA) master step name may be different depending on the version of IPP installed.

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!step.hasValue(::Step Sample Type::)) {step.::Step Sample Type:: = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]::} else {if ( step.::Step Sample Type:: != submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ) { fail(::Samples must be of the same type and marked for same library prep method::) }}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v3.0)

• 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}-EDP:: ) ) {fail ( ::Update: Invalid EDP (Extracted DNA Plate) barcode format. This plate ID must be in the format LPxxxxxxx-EDP, where 'x' is a digit 0-9, e.g. LP1234567-EDP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Extraction - Count Samples & Create LHR Input File (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' \
&& \
/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 {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Extraction - Check LHR Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i  'LHR Instrument ID' \
&& \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \
&& \
/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 \
-t false \
-h false \
-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \
-log {compoundOutputFileLuid1}"

Extraction - Routing (IGA v3.0)

• 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 \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) { output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /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 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--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'"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

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
  Derived Sample	Waiting	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • 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
  Ethanol	Text
  ITB	Text
  LHR Instrument ID	Text	Read Only
  MLB	Text
  ProK	Text
  Quick reference checklist: DNA Extraction - Blood. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - Download LHR Input File - Enter reagent lots for MLB and ProK (not scanned by LHR as loaded as a mastermix)
  Quick reference checklist: DNA Extraction - Blood. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting LHR Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0
  Step Sample Type	Text	Read Only

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container	Built-in
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Submitted Sample Type	Text	Read Only
    Project	Project Name	Built-in

Protocol 4: Saliva Extraction (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: DNA Extraction - Saliva (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: DNA Extraction - Saliva (IGA v3.0)

• Master Step Name = DNA Extraction - Saliva (IGA v3.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

The version of DNA Extraction - Saliva (IGA) master step name may be different depending on the version of IPP installed.

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!step.hasValue(::Step Sample Type::)) {step.::Step Sample Type:: = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]::} else {if ( step.::Step Sample Type:: != submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ) { fail(::Samples must be of the same type and marked for same library prep method::) }}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v3.0)

• 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}-EDP:: ) ) {fail ( ::Update: Invalid EDP (Extracted DNA Plate) barcode format. This plate ID must be in the format LPxxxxxxx-EDP, where 'x' is a digit 0-9, e.g. LP1234567-EDP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Extraction - Count Samples & Create LHR Input File (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' \
&& \
/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 {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Extraction - Check LHR Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i  'LHR Instrument ID' \
&& \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \
&& \
/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 \
-t false \
-h false \
-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \
-log {compoundOutputFileLuid1}"

Extraction - Routing (IGA v3.0)

• 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 \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) { output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /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 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--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'"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

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
  Derived Sample	Waiting	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • 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
  Ethanol	Text
  ITB	Text
  LHR Instrument ID	Text
  MLB	Text
  ProK	Text
  Quick reference checklist: DNA Extraction - Saliva. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - Download LHR Input File - Enter reagent lots for MLK and ProK (not scanned by LHR as loaded as a mastermix)
  Quick reference checklist: DNA Extraction - Saliva. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting LHR Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0
  Step Sample Type	Text	Read Only

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container	Built-in
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Submitted Sample Type	Text	Read Only
    Project	Project Name	Built-in

Protocol 5: Illumina DNA PCR-Free (IGA v3.0)

Protocol Type = Library Prep

Next Steps Configuration

• Step(s):

  • 1: DNA Batching PCR-Free (IGA v3.0)

    • Start Next Step = Manual

    • Assign Next Step = Manual

  • 2: Indexing Planning PCR-Free (IGA v3.0)

    • Start Next Step = Manual

    • Assign Next Step = Manual

  • 3: Library Prep - Indexing PCR-Free (IGA v3.0)

    • Assign Next Step = Automatic

Step	To Step 1	To Step 2	To Step 3
1		✓	❌
2			✓
3

Step 1: DNA Batching PCR-Free (IGA v3.0)

• Master Step Name = DNA Batching NFPF (IGA v3.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}_DNA

The version of DNA Batching NFPF (IGA) master step name may be different depending on the version of IPP installed.

Automations

DNA Batching PF - Set Final Volume and Validate Sample Type Combination (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Sample Type:: == ::Genomic DNA::) {step.::Batching Well Volume (uL):: = 40} ; if (submittedSample.::Sample Type:: == ::Blood::) {step.::Batching Well Volume (uL):: = 40} ; if (submittedSample.::Sample Type:: == ::Saliva::) {step.::Batching Well Volume (uL):: = 40}' \
-log {compoundOutputFileLuid1} \
&& \
/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 \
-t false -h false -exp \
'String matchTargetGDNA = ::genomic dna:: ; \
String submittedSampleType = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::] | :: ; \
if (!step.hasValue(::Step Sample Type::)) { \
    step.::Step Sample Type:: = submittedSampleType; \
} else { \
    String stepType = step.::Step Sample Type:: ; \
    String smpType = submittedSampleType.toLowerCase(); \
    stepType = stepType.toLowerCase(); \
    if ( (stepType.contains(matchTargetGDNA) && !smpType.contains(matchTargetGDNA)) || (!stepType.contains(matchTargetGDNA) && smpType.contains(matchTargetGDNA)) ) { \
        fail(::Genomic DNA samples can only be plated together and not combined with any other sample type!::); \
    }; \
    if ( (stepType.contains(::blood::) && smpType.contains(::saliva::)) || (stepType.contains(::saliva::) && smpType.contains(::blood::)) ) { \
        step.::Step Sample Type:: = ::Blood + Saliva:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ; \
    }; \
}' \
 -log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Placement Reminder (IGA v3.0)

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v3.0)

• 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}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

DNA Batching PF - Generate LHR Input File (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Warnings:: = :::: ; if ( submittedSample.hasValue (::Sample Conc.::) ) {        output.::Sample Needed (uL):: = (step.::DNA (ng) required for tagmentation:: * step.::Batching Well Volume (uL)::) / (25 * submittedSample.::Sample Conc.::) ; \
if ( output.::Sample Needed (uL):: > step.::Batching Well Volume (uL):: ) { output.::Sample Needed (uL):: =
 step.::Batching Well Volume (uL):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (uL):: < 2.0 )
{ output.::Sample Needed (uL):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (uL):: =
step.::Batching Well Volume (uL):: - output.::Sample Needed (uL):: ; output.::Initial Input DNA (ng)::  = output.::Sample Needed (uL):: * submittedSample.::Sample Conc.::} \
else \
{output.::Sample Needed (uL):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (uL):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (uL):: = step.::Batching Well Volume (uL)::; output.::Diluent Volume (uL):: = 0 }' \
-log {compoundOutputFileLuid1} &&
/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 {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

DNA Batching - Check LHR Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR 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 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed (IGA v3.0)

• 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'"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • 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
  Batching Well Volume (uL)	Numeric	Required Field	Default = 40
  DNA (ng) required for tagmentation	Numeric	Required Field	Default = 350
  LHR Instrument ID	Text	Read Only
  Notes:	Multiline Text	Read Only	Default = - DNA (ng) required for tagmentation is 300-2000 ng. - A fixed 25uL is aliquoted from the total volume of 40uL (default) to carry out Library Prep and subsequent steps.
  Quick reference checklist: DNA Batching IDPF. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred - 'Run' DNA Batching PF automation, and download resulting 'LHR Input File'
  Quick reference checklist: DNA Batching IDPF. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting 'LHR Output File' - Select 'Next Steps'

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • 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	Diluent Volume (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Initial Input DNA (ng)	Numeric
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Needed (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Warnings	Text	Read Only
    Project	Project Name	Built-in

Step 2: Indexing Planning PCR-Free (IGA v3.0)

• Master Step Name = Indexing Planning (IGA v3.0)

• Step Type = No Outputs

The version of Indexing Planning (IGA) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started (IGA v3.0)

• 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/step_started.groovy'"

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v3.0)

• 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:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::LHR Indexing Offset Column::)) + 8) < step.node.::input-output-maps::.::input-output-map::.input.size()) { fail(::The column offset will not yield enough indexes for the number of samples! Please increase the number of available indexes by changing the offset.::) }' -log {compoundOutputFileLuid0} && \
/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} -h true script:evaluateDynamicExpression -exp 'if ( !step.::Index Plate Barcode::.matches( ::UD[A-D]{1}+[0-9]{11}$:: ) ) { fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format of UD{A/B/C/D} followed by 11-digit number xxxxxxxxxxx; e.g. UDA12345678912. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning (IGA v3.0)' && \
/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 'input.::INTERNALFIELD_IndexPlanning_Metadata:: = step.::Index Plate Barcode:: + ::_:: + (int) step.::LHR Indexing Offset Column::' -log {compoundOutputFileLuid0} && \
/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 'nextStep = ::ADVANCE::'   -log {compoundOutputFileLuid0}"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Register Step Completed (IGA v3.0)

• 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'"

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	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Index Plate Barcode	Text	Required Field
  LHR Indexing Offset Column	Numeric		Default = 1
  Quick reference checklist: Indexing Planning	Multiline Text	Read Only	Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the LHR Indexing Offset column (required start column) - Click 'Next Steps'

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • 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	INTERNALFIELD_IndexPlanning_Metadata	Text
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 3: Library Prep - Indexing PCR-Free (IGA v3.0)

• Master Step Name = Indexing NFPF (IGA v3.0)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

The version of Indexing NFPF (IGA) master step name may be different depending on the version of IPP installed.

Automations

Indexing - Custom Indexing with LHR Offsets and Dynamic Index Category Discovery (IGA v3.0)

• Trigger Location = Add Labels

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_autoAssignIndexesFromIndexPlanning.py -u {username} -p {password} -s {stepURI} \
&& /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_storeIndexSetSetting.py -u {username} -p {password} -s {stepURI}  -n 'Index Set A/B/C/D' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -log {compoundOutputFileLuid1} \
  script:evaluateDynamicExpression \
  -exp 'submittedSample.::INTERNALFIELD_IndexPlanning_Metadata:: = input.::INTERNALFIELD_IndexPlanning_Metadata::' -t true \
"

Library Prep - Indexing PF - Route Samples to Sequencing Platform Selection with Automatic Workflow Detection (IGA v3.0)

• 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} -l {compoundOutputFileLuid1} script:changeWorkflow \
--FIELD_NAME 'N/A' \
--FIELD_VALUE 'N/A' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'Select Sequencing Platform (IGA v3.0)' \
--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'"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Indexing - Validate Index Category and Index Plate Barcode (IGA v3.0)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory_UD.py -u {username} -p {password} -s {stepURI} \
&& /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'"

Library Prep - Indexing PF - Check for Valid, Unique LIB Plate Barcode & Match with LHR Output File & Parse Reagent Info & Set Next Steps to Remove from Workflow & Quant. Warning (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_libprep.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'WARNING' --message 'This protocol recommends performing a pooled quant. (per prep) at this stage. Please quant. and update the Normalized Molarity (nM) across all samples in the table below before proceeding.'"

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	INTERNALFIELD_IndexPlanning_Metadata	Text
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = 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	INTERNALFIELD_IndexPlanning_Metadata	Text
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Add Labels

• Label Groups

  • Illumina DNA-RNA UD Indexes Set A Tagmentation

  • Illumina DNA-RNA UD Indexes Set B Tagmentation

  • Illumina DNA-RNA UD Indexes Set C Tagmentation

  • Illumina DNA-RNA UD Indexes Set D Tagmentation

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Adapter	Text	Required Field Read Only	Default = CTGTCTCTTATACACATCT
  Adapter Read 2	Text	Required Field Read Only	Default = CTGTCTCTTATACACATCT
  BLT-PF	Text
  ELM-T	Text
  HP3	Text
  Index Plate Barcode (read from input samples)	Text	Read Only
  Index Plate Offset (read from input samples)	Text	Read Only
  IPB	Text
  LHR Instrument ID	Text	Read Only
  Library Plate Barcode	Text	Required Field
  Quick reference checklist: Library Prep IDPF. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - Above, scan in the 'Library Plate Barcode' to be used - Click blue button to 'Run' the Library Prep automation, and download the resulting 'LHR Input File'
  Quick reference checklist: Library Prep IDPF. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting 'LHR Output File' - Perform a pooled quant for the prep, and apply the yield 'Normalized Molarity (nM)' to all samples - Click 'Next Steps'
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0 Decimal Places Displayed = 0
  ST2	Text
  TB1	Text
  TWB	Text

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container	Built-in
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in

Protocol 6: Illumina DNA with Enrichment (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: DNA Batching with Enrichment (IGA v3.0)

    • Start Next Step = Manual

    • Assign Next Step = Manual

  • 2: Indexing Planning with Enrichment (IGA v3.0)

    • Start Next Step = Manual

    • Assign Next Step = Manual

  • 3: Library Prep - Indexing with Enrichment (IGA v3.0)

    • Start Next Step = Manual

    • Assign Next Step = Manual

  • 4: Library Prep - Pre-Capture Pooling with Enrichment (IGA v3.0)

    • Start Next Step = Manual

    • Assign Next Step = Manual

  • 5: Library Prep - Capture and Wash with Enrichment (IGA v3.0)

    • Start Next Step = Manual

    • Assign Next Step = Manual

  • 6: Post-Capture Pool QC with Enrichment (IGA v3.0)

    • Assign Next Step = Automatic

Step	To Step 1	To Step 2	To Step 3	To Step 4	To Step 5	To Step 6
1		✓	❌	❌	❌	❌
2			✓	❌	❌	❌
3				✓	❌	❌
4					✓	❌
5						✓
6

Step 1: DNA Batching with Enrichment (IGA v3.0)

• Master Step Name = DNA Batching NFE (IGA v3.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}_DNA

The version of DNA Batching NFE (IGA) master step name may be different depending on the version of IPP installed.

Automations

DNA Batching Enrichment - Set Final Volume (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Batching Well Volume (uL):: = 45' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Placement Reminder (IGA v3.0)

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v3.0)

• 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}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

DNA Batching Enrichment - Generate LHR Input File (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Warnings:: = :::: ; if ( submittedSample.hasValue (::Sample Conc.::) ) {output.::Sample Needed (uL):: = (step.::DNA (ng) required for tagmentation:: * step.::Batching Well Volume (uL)::) / (30 * submittedSample.::Sample Conc.::) ; \
if ( output.::Sample Needed (uL):: > step.::Batching Well Volume (uL):: ) { output.::Sample Needed (uL):: =
 step.::Batching Well Volume (uL):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (uL):: < 2.0 )
{ output.::Sample Needed (uL):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (uL):: =
step.::Batching Well Volume (uL):: - output.::Sample Needed (uL):: ; output.::Initial Input DNA (ng)::  = output.::Sample Needed (uL):: * submittedSample.::Sample Conc.::} \
else \
{output.::Sample Needed (uL):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (uL):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (uL):: = step.::Batching Well Volume (uL)::; output.::Diluent Volume (uL):: = 0 }' \
-log {compoundOutputFileLuid1} &&
/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 {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

DNA Batching - Check LHR Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR 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 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed (IGA v3.0)

• 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'"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

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
  Batching Well Volume (uL)	Numeric	Required Field	Default = 45
  DNA (ng) required for tagmentation	Numeric	Required Field	Default = 450
  LHR Instrument ID	Text	Read Only
  Notes:	Multiline Text	Read Only	Default = - DNA (ng) required for tagmentation is 50-1000 ng. - A fixed 30uL is aliquoted from the total volume of 45uL (default) to carry out Library Prep and subsequent steps.
  Quick reference checklist i): DNA Batching IDE, pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred - 'Run' DNA Batching Enrichment automation, and download resulting 'LHR Input File'
  Quick reference checklist ii): DNA Batching IDE, post LHR	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting 'LHR Output File' - Select 'Next Steps'

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Diluent Volume (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Initial Input DNA (ng)	Numeric
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Needed (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Warnings	Text	Read Only
    Project	Project Name	Built-in

Step 2: Indexing Planning with Enrichment (IGA v3.0)

• Master Step Name = Indexing Planning (IGA v3.0)

• Step Type = No Outputs

The version of Indexing Planning (IGA) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started (IGA v3.0)

• 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/step_started.groovy'"

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v3.0)

• 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:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::LHR Indexing Offset Column::)) + 8) < step.node.::input-output-maps::.::input-output-map::.input.size()) { fail(::The column offset will not yield enough indexes for the number of samples! Please increase the number of available indexes by changing the offset.::) }' -log {compoundOutputFileLuid0} && \
/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} -h true script:evaluateDynamicExpression -exp 'if ( !step.::Index Plate Barcode::.matches( ::UD[A-D]{1}+[0-9]{11}$:: ) ) { fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format of UD{A/B/C/D} followed by 11-digit number xxxxxxxxxxx; e.g. UDA12345678912. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning (IGA v3.0)' && \
/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 'input.::INTERNALFIELD_IndexPlanning_Metadata:: = step.::Index Plate Barcode:: + ::_:: + (int) step.::LHR Indexing Offset Column::' -log {compoundOutputFileLuid0} && \
/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 'nextStep = ::ADVANCE::'   -log {compoundOutputFileLuid0}"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Register Step Completed (IGA v3.0)

• 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'"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Index Plate Barcode	Text	Required Field
  LHR Indexing Offset Column	Numeric		Default = 1
  Quick reference checklist: Indexing Planning	Multiline Text	Read Only	Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the LHR Indexing Offset column (required start column) - Click 'Next Steps'

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	INTERNALFIELD_IndexPlanning_Metadata	Text
    Derived Sample	Sample Name	Built-in

Step 3: Library Prep - Indexing with Enrichment (IGA v3.0)

• Master Step Name = Indexing NFE (IGA v3.0)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

The version of Indexing NFE (IGA) master step name may be different depending on the version of IPP installed.

Automations

Indexing - Custom Indexing with LHR Offsets and Dynamic Index Category Discovery (IGA v3.0)

• Trigger Location = Add Labels

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_autoAssignIndexesFromIndexPlanning.py -u {username} -p {password} -s {stepURI} \
&& /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_storeIndexSetSetting.py -u {username} -p {password} -s {stepURI}  -n 'Index Set A/B/C/D' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -log {compoundOutputFileLuid1} \
  script:evaluateDynamicExpression \
  -exp 'submittedSample.::INTERNALFIELD_IndexPlanning_Metadata:: = input.::INTERNALFIELD_IndexPlanning_Metadata::' -t true \
"

Indexing - Validate Index Category and Index Plate Barcode (IGA v3.0)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory_UD.py -u {username} -p {password} -s {stepURI} \
&& /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'"

Library Prep - Indexing Enrichment - Copy Indexing Metadata to Outputs & Set Next Steps to Advance (IGA v3.0)

• 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:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'tkns = input.::INTERNALFIELD_IndexPlanning_Metadata::.split(::_::); step.::Index Plate Barcode (read from input samples):: = tkns[0]; step.::Index Plate Offset (read from input samples):: = tkns[1]; output.::INTERNALFIELD_IndexPlanning_Metadata:: = input.::INTERNALFIELD_IndexPlanning_Metadata:: ; nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Add Labels

• Label Groups

  • Illumina DNA-RNA UD Indexes Set A Tagmentation

  • Illumina DNA-RNA UD Indexes Set B Tagmentation

  • Illumina DNA-RNA UD Indexes Set C Tagmentation

  • Illumina DNA-RNA UD Indexes Set D Tagmentation

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Index Plate Barcode (read from input samples)	Text	Read Only
  Index Plate Offset (read from input samples)	Text	Read Only
  Quick reference checklist: Library Prep IDE.	Multiline Text	Read Only	Default = User tasks for this step: - No user tasks, click 'Next Steps'

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	INTERNALFIELD_IndexPlanning_Metadata	Text
    Derived Sample	Sample Name	Built-in

Step 4: Library Prep - Pre-Capture Pooling with Enrichment (IGA v3.0)

• Master Step Name = Library Prep NFE - Pool Libraries (IGA v3.0)

• Step Type = Pooling

• Aliquot Generation = Fixed, 1

• Naming Convention = {PoolName}

The version of Library Prep NFE - Pool Libraries (IGA) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started (IGA v3.0)

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

Library Prep - Pooling Enrichment - Validate Pool Sizes (IGA v3.0)

• 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 \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!output.hasValue(::Number of Samples in Pool::)) { output.::Number of Samples in Pool:: = 0; }; output.::Number of Samples in Pool::++; if (output.::Number of Samples in Pool:: > 12) { fail(::Pools cannot contain more than 12 samples each.::) }' \
-log {compoundOutputFileLuid1}"

Library Prep - Pooling Enrichment - Sample Placement PCPP Plate Barcode Uniqueness Check (IGA v3.0)

• 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}-PCPP:: ) ) {fail ( ::Invalid PCPP (Pre-Capture Pool Plate) barcode format. This plate ID must be in the format LPxxxxxxx-PCPP, where 'x' is a digit 0-9, e.g. LP1234567-PCPP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Library Prep - Pooling Enrichment - Create LHR Input File (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/countSamplesInPools.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' && /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 \
-t true \
-h false \
-exp 'tkns = input.::INTERNALFIELD_IndexPlanning_Metadata::.split(::_::); step.::Index Plate Barcode (read from input samples):: = tkns[0]; step.::Index Plate Offset (read from input samples):: = tkns[1]; ' \
-log {compoundOutputFileLuid1} \ && \
/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 \
-t true \
-h false \
-exp 'output.::Sample Needed (uL):: = 5.0 * output.::Number of Samples in Pool:: ; if (output.::Number of Samples in Pool:: >= 6) {output.::Diluent Volume (uL):: = 0} else {output.::Diluent Volume (uL):: = 30.0 - output.::Sample Needed (uL):: } ; ' \
-log {compoundOutputFileLuid1} \
&& /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 {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/LibInputFile_NFE_template_withoffsets.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Library Prep - Pooling Enrichment - Validate LHR Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_precap_pooling.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed (IGA v3.0)

• 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'"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Pooling

• Label Uniqueness = On

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

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
  Adapter	Text	Required Field Read Only	Default = CTGTCTCTTATACACATCT
  Adapter Read 2	Text	Required Field Read Only	Default = CTGTCTCTTATACACATCT
  eBLT	Text
  EPM	Text
  Index Plate Barcode (read from input samples)	Text	Read Only
  Index Plate Offset (read from input samples)	Text	Read Only
  LHR Instrument ID	Text	Read Only
  Quick reference checklist: Library Prep IDE - pool libraries. i) pre LHR.	Multiline Text	Read Only	Default = User tasks for this page: - 'Run' Library Prep Pooling automation - Download resulting LHR Input File
  Quick reference checklist: Library Prep IDE - pool libraries. ii) post LHR.	Multiline Text	Read Only	Default = User tasks continued: - After running the Prep method on the Liquid Handler, upload resulting LHR Output File - Click on 'Next Steps'
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0
  SPB	Text
  ST2	Text
  TB1	Text
  Total Pool Volume (ul)	Numeric		Default = 30
  TWB	Text

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Diluent Volume (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Number of Samples in Pool	Numeric		Default = 0
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Needed (uL)	Numeric		Decimal Places Displayed = 1

Step 5: Library Prep - Capture and Wash with Enrichment (IGA v3.0)

• Master Step Name = Capture and Wash NFE (IGA v3.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

The version of Capture and Wash NFE (IGA) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started (IGA v3.0)

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

Capture and Wash Enrichment - Sample Placement LIB Plate Barcode Uniqueness Check & Update Pool Count (IGA v3.0)

• 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}-LIB:: ) ) {fail ( ::Invalid LIB plate barcode format. This plate ID must be in the format LPxxxxxxx-LIB, where 'x' is a digit 0-9, e.g. LP1234567-LIB. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Pool Count'"

Capture and Wash Enrichment - Create LHR Input File (IGA v3.0)

• 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 {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/CaptureWashInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Capture and Wash Enrichment - Validate LHR Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_captureandwash.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed (IGA v3.0)

• 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'"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Same Shape

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  EE1	Text
  EEW	Text
  EHB2	Text
  EPM	Text
  ET2	Text
  HP3	Text
  LHR Instrument ID	Text	Read Only
  Pool Count	Numeric	Read Only	Default = 0
  PPC	Text
  Probes	Text
  Quick reference checklist: Capture and Wash IDE. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - 'Run' Capture and Wash automation - Download resulting LHR Input File
  Quick reference checklist: Capture and Wash IDE. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - After running Capture and Wash on the liquid handler, upload resulting LHR Output File - Click 'Next Steps'

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 6: Post-Capture Pool QC with Enrichment (IGA v3.0)

• Master Step Name = Generic Pool QC NFE (IGA v3.0)

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName}

The version of Generic Pool QC NFE (IGA) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started (IGA v3.0)

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

Pool QC - Generic - Enrichment - Copy Normalized Molarity from Output to Input, Copy QC Value to Inputs & Set QC Passed Sample Next Steps to Remove from Workflow (IGA v3.0)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (!output.hasValue(::Normalized Molarity (nM)::)) { fail(::Please set/check Normalized Molarity (nM) field values manually on each sample, or set up this step to parse this value from QC instrument output to automatically set QC pass/fail flags.::) } else { input.::Normalized Molarity (nM):: = output.::Normalized Molarity (nM):: }; input.::INTERNALFIELD_QCValue_forRouting:: = output.QC ; output.::INTERNALFIELD_QCValue_forRouting:: = output.QC ; if (output.QC == true) { nextStep = ::REMOVE:: }' -log {compoundOutputFileLuid1}"

Pool QC - Generic - Enrichment - Route QC Passed Samples to Sequencing Platform Selection (IGA v3.0)

• 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} -l {compoundOutputFileLuid0} script:changeWorkflow \
--FIELD_NAME 'INTERNALFIELD_QCValue_forRouting' \
--FIELD_VALUE 'true' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'Select Sequencing Platform (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
&& /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'"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Quick reference checklist: Pool QC IDE.	Multiline Text	Read Only	Default = User tasks for this page: - After running QC on the pools, upload a QC instrument result file, or input Normalized Molarity (nM) and QC flags below - For any QC fails, assign next steps - Click 'Next Steps'

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	INTERNALFIELD_QCValue_forRouting	Text
    Derived Sample	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	INTERNALFIELD_QCValue_forRouting	Text	Read Only
    Measurement	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Protocol 7: Sequencing Platform Selection (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: Select Sequencing Platform (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: Select Sequencing Platform (IGA v3.0)

• Master Step Name = Sequencing Platform Selection (IGA v3.0)

• Step Type = No Outputs

The version of Sequencing Platform Selection (IGA) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started (IGA v3.0)

• 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/step_started.groovy'"

Sequencing Platform Selection - Copy Instrument Type to Analyte & Set Next Steps to Remove from Workflow (IGA v3.0)

• 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 'input.::Sequencing Platform:: = step.::Sequencing Platform:: ; nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"

Sequencing Platform Selection - Route to Sequencing Workflow by Type (IGA v3.0)

• 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} -l {compoundOutputFileLuid0} script:changeWorkflow \
--FIELD_NAME 'Sequencing Platform' \
--FIELD_VALUE 'NovaSeq X IGA' \
--WORKFLOW 'NovaSeq X Series v2.0' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Sequencing Platform' \
--FIELD_VALUE 'NovaSeq 6K IGA' \
--WORKFLOW 'Illumina Genomics Architecture - NovaSeq Sequencing v3.0' \
--STEP 'Define Run Format (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Sequencing Platform' \
--FIELD_VALUE 'NextSeq 1000/2000 v2.3' \
--WORKFLOW 'NextSeq 1000/2000 Sequencing v2.3' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
&& /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'"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

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	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Quick reference checklist: Sequencing Platform Selection	Multiline Text	Read Only	Default = User tasks for this step: - No actions for this page! The step serves to route all samples to the NovaSeq workflow
  Sequencing Platform	Text Dropdown	Required Field	Presets NovaSeq X IGA NovaSeq 6K IGA

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sequencing Platform	Text
    Project	Project Name	Built-in