IGA Library Prep Automated v2.1

Overview

IGA Library Prep Automated v2.1 contains preset protocols that support the preparation of samples and libraries used for sequencing. These protocols can be used with the IGA NovaSeq Sequencing v2.1 workflow and NextSeq 1000/2000 v2.3 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

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Samples

• Master Step Name = Select Samples (IGA v2.1)

• Step Type = No Outputs

Automations

Validate Sample Attributes (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2: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 v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '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 v2.1)

• 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 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--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'"

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
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in
    Project	Project Name	Built-in
    Submitted Sample	Illumina Universal Sample Identifier	Built-in
  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Submitted Sample	Sample Conc.	Numeric		Decimal Places Displayed = 2
    Submitted Sample	Units	Text

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 = 2.1.0.1
  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	Defaults = User tasks for this page: - Select Library Prep Method above - Select Next Steps
• Step File Placeholders

  • Set Library Prep Method Script Log - Automatically attached

• Sample Table (Table Columns - Global Fields)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Sample Name	Built-in
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Conc.	Numeric		Decimal Places Displayed = 2
  Submitted Sample	Submitted Sample Type	Text	Read Only
  Submitted Sample	Units	Text

Protocol 2: Sample Plating

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Plate Samples

• Master Step Name = Sample Plating (IGA v2.1)

• Step Type = Standard

• Derived Sample Generation = Variable

• Naming Convention = {InputItemlName}

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-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 python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

Sample Plating - Set Transfer Volume & Create Liquid Handler Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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_2.1/hamilton_fast_prep/templatefiles/PlatingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Sample Plating - Hamilton Output Plate Barcode Check, Store Instrument ID & Set Next Steps to Remove from Workflow before Custom Routing (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling 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 v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-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 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Blood (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Saliva (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Blood (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Saliva (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

• Defaults

  • Sample Grouping = Group by 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
    Submitted Sample	Library Prep Method	Text
    Submitted Sample	Sample Type	Text
    Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
    Submitted Sample	Submitted Sample Name	Built-in
  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Submitted Sample	Date Submitted	Built-in
    Submitted Sample	Sample Category	Text

Ice Bucket

• 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
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
  Submitted Sample	Submitted Sample Name	Built-in

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

  • Liquid Handler Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Liquid Handler Output File - Manually uploaded

• Sample Table (Table Columns - Global Fields)

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

Protocol 3: Blood Extraction

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Extraction - Blood

• Master Step Name = DNA Extraction - Blood (IGA v2.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-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 python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Extraction - Count Samples & Create LH Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/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_2.1/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i  'Liquid Handling Instrument ID' \
&& \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/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 v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-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 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Waiting	Built-in
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
  Submitted Sample	Submitted Sample 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
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Submitted Sample 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
  Ethanol	Text
  ITB	Text
  Liquid Handling Instrument ID	Text	Read Only
  MLB	Text
  ProK	Text
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0
  Step Sample Type	Text	Read Only
  Quick reference checklist: DNA Extraction - Blood. i) pre Liquid Handler	Multiline Text	Read Only	Default = User tasks for this page: - Download Liquid Handling Robot Input File - Enter reagent lots for MLB and ProK (not scanned by Liquid Handler as loaded as a mastermix)
  Quick reference checklist: DNA Extraction - Blood. ii) post Liquid Handler	Multiline Text	Read Only	Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
• Step File Placeholders

  • Liquid Handling Robot (Hamilton) Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Liquid Handling Robot Output File - Manually uploaded

• Sample Table (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
  Submitted Sample	Library Prep Method	Text

Protocol 4: Saliva Extraction

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Extraction - Saliva

• Master Step Name = DNA Extraction - Blood (IGA v2.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-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 python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Extraction - Count Samples & Create LH Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/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_2.1/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i  'Liquid Handling Instrument ID' \
&& \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/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 v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-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 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Waiting	Built-in
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
  Submitted Sample	Submitted Sample 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
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Submitted Sample 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
  Ethanol	Text
  ITB	Text
  Liquid Handling Instrument ID	Text	Read Only
  MLB	Text
  ProK	Text
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0
  Step Sample Type	Text	Read Only
  Quick reference checklist: DNA Extraction - Saliva. i) pre Liquid Handler	Multiline Text	Read Only	Default = User tasks for this page: - Download Liquid Handling Robot Input File - Enter reagent lots for MLB and ProK (not scanned by Liquid Handler as loaded as a mastermix)
  Quick reference checklist: DNA Extraction - Saliva. ii) post Liquid Handler	Multiline Text	Read Only	Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
• Step File Placeholders

  • Liquid Handling Robot (Hamilton) Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Liquid Handling Robot Output File - Manually uploaded

• Sample Table (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
  Submitted Sample	Library Prep Method	Text

Protocol 5: Illumina DNA PCR-Free

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Batching PCR-Free

• Master Step Name = DNA Batching NFPF (IGA v2.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}_DNA

Automations

DNA Batching PF - Set Final Volume and Validate Sample Type Combination (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-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 python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

DNA Batching PF - Generate LH Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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_2.1/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

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
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text

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
  Liquid Handling 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 Liquid Handler	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 'Liquid Handler Batching Input File'
  Quick reference checklist: DNA Batching IDPF. ii) post Liquid Handler	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting 'Output File from Liquid Handler' - Select 'Next Steps'
• Step File Placeholders

  • Liquid Handler Batching Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Output File from Liquid Handler - Manually uploaded

• Sample Table (Table Columns - Global Fields)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	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: Index Planning PCR-Free

• Master Step Name = Indexing Planning (IGA v2.1)

• Step Type = No Outputs

Automations

Register Step Started (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::Hamilton 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( ::[0-9]{8}-[A-Z]+[A-D]{1}$:: ) ) {fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format xxxxxxxx-S*(A/B/C/D), where 'x' is a digit 0-9 and 'S' is a sequence of uppercase letters, followed by 'A', 'B', 'C', or 'D'; e.g. 12345678-NXTA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/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 v2.1)' && \
/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.::Hamilton 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}"

Register Step Completed (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

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
  Hamilton Indexing Offset Column	Numeric		Default = 1 Range From 1 to 12
  Quick reference checklist: Indexing Planning	Multiline Text	Read Only	Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column) - Click 'Next Steps'
• Step File Placeholders

  • Script Log File (Aggregated) - Manually uploaded

• Sample Table (Table Columns - Global Fields)

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

Step 3: Library Prep - Indexing PCR-Free

• Master Step Name = Indexing NFPF (IGA v2.1)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

Automations

Indexing - Validate Index Category and Index Plate Barcode (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory.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'"

Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery (IGA v2.1)

• Trigger Location = Add Labels

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/04_B_autoAssignIndexesFromIndexPlanning.py -u {username} -p {password} -s {stepURI}"

Library Prep - Indexing PF - Validate/Copy LibPlate Barcode, Set Default Norm. Mol. if Applicable, and Generate LH Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/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/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'if ( !step.hasValue(::Library Plate Barcode::) || !step.::Library Plate Barcode::.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 scan a valid LIB plate barcode in the Record Details screen.:: ) }; output.container.name = step.::Library Plate Barcode::; 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]; if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) { output.::Normalized Molarity (nM):: = 3.5; }' \
-log {compoundOutputFileLuid1} \
&& /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/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_2.1/hamilton_fast_prep/templatefiles/LibInputFile_NFPF_template_withoffsets.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Library Prep - Indexing PF - Check for Valid, Unique LIB Plate Barcode & Match with Liquid Handler Output File & Parse Reagent Info & Set Next Steps to Remove from Workflow & Quant. Warning (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/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 python /opt/gls/clarity/extensions/IGA_2.1/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.'"

Library Prep - Indexing PF - Route Samples to Sequencing Platform Selection with Automatic Workflow Detection (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "bash /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/changeWorkflowScriptNoFieldChecks.sh {username} {password} {stepURI} {compoundOutputFileLuid1} /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/masterRoutingTable_NFPFtoSeqPlatSelect.csv 'v2.1' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_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	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 = Row

• Sample Table (Column Headers)

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

Add Labels

• Label Groups

  • Nextera UDP A

  • Nextera UDP B

  • Nextera UDP C

  • Nextera UDP D

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
  Library Plate Barcode	Text	Required Field
  Liquid Handling Instrument ID	Text	Read Only
  Quick reference checklist: Library Prep IDPF. i) pre Liquid Handler	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 'Liquid Handler Input File'
  Quick reference checklist: Library Prep IDPF. ii) post Liquid Handler	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting 'Hamilton 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
• Step File Placeholders

  • Liquid Handler Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Hamilton Output File - Manually uploaded

• Sample Table (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
  Submitted Sample	Library Prep Method	Text

Protocol 6: Illumina DNA with Enrichment

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Batching with Enrichment

• Master Step Name = DNA Batching NFE (IGA v2.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}_DNA

Automations

DNA Batching Enrichment - Set Final Volume (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-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 python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

DNA Batching Enrichment - Generate LH Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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_2.1/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

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
  Liquid Handling 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 Liquid Handler	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 'Liquid Handler Batching Input File'
  Quick reference checklist ii): DNA Batching IDE, post Liquid Handler	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting 'Output File from Liquid Handler' - Select 'Next Steps'
• Step File Placeholders

  • Liquid Handler Batching Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Output File from Liquid Handler - Manually uploaded

• Sample Table (Table Columns - Global Fields)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	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: Index Planning with Enrichment

• Master Step Name = Indexing Planning (IGA v2.1)

• Step Type = No Outputs

Automations

Register Step Started (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::Hamilton 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( ::[0-9]{8}-[A-Z]+[A-D]{1}$:: ) ) {fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format xxxxxxxx-S*(A/B/C/D), where 'x' is a digit 0-9 and 'S' is a sequence of uppercase letters, followed by 'A', 'B', 'C', or 'D'; e.g. 12345678-NXTA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/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 v2.1)' && \
/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.::Hamilton 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}"

Register Step Completed (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

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
  Hamilton Indexing Offset Column	Numeric		Default = 1 Range From 1 to 12
  Quick reference checklist: Indexing Planning	Multiline Text	Read Only	Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column) - Click 'Next Steps'
• Step File Placeholders

  • Script Log File (Aggregated) - Manually uploaded

• Sample Table (Table Columns - Global Fields)

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

Step 3: Library Prep - Indexing with Enrichment

• Master Step Name = Indexing NFE (IGA v2.1)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

Automations

Indexing - Validate Index Category and Index Plate Barcode (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory.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'"

Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery (IGA v2.1)

• Trigger Location = Add Labels

• Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/04_B_autoAssignIndexesFromIndexPlanning.py -u {username} -p {password} -s {stepURI}"

Library Prep - Indexing Enrichment - Copy Input Plate Barcode to Output Plate (IGA v2.1)

• Trigger Location = Add Labels

• 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} -t true -h false script:evaluateDynamicExpression -exp 'output.container.name = input.container.name;' -log {compoundOutputFileLuid0}"

Library Prep - Indexing Enrichment - Copy Indexing Metadata to Outputs & Set Next Steps to Advance (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2: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}"

Register Step Completed (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

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

  • Nextera UDP A

  • Nextera UDP B

  • Nextera UDP C

  • Nextera UDP D

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'
• Step File Placeholders

  • Script Log File (Aggregated) - Automatically attached

• Sample Table (Table Columns - Global Fields)

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

Step 4: Library Prep - Pre-Capture Pooling with Enrichment

• Master Step Name = Library Prep NFE - Pool Libraries (IGA v2.1)

• Step Type = Pooling

• Aliquot Generation = Fixed, 1

• Naming Convention = {PoolName}

Automations

Register Step Started (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Library Prep - Pooling Enrichment - Validate Pool Sizes (IGA v2.1)

• Trigger Location = Pooling

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-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 python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Library Prep - Pooling Enrichment - Create LH Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/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_2.1/hamilton_fast_prep/templatefiles/LibInputFile_NFE_template_withoffsets.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Library Prep - Pooling Enrichment - Validate LH Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/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 v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

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
  Liquid Handling Instrument ID	Text	Read Only
  Quick reference checklist: Library Prep IDE - pool libraries. i) pre Liquid Handler.	Multiline Text	Read Only	Default = User tasks for this page: - 'Run' Library Prep Pooling automation - Download resulting Liquid Handler Input File
  Quick reference checklist: Library Prep IDE - pool libraries. ii) post Liquid Handler.	Multiline Text	Read Only	Default = User tasks continued: - After running the Prep method on the Liquid Handler, upload resulting Liquid Handler 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
• Step File Placeholders

  • Liquid Handler Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Liquid Handler Output File - Manually uploaded

• Sample Table (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

• Master Step Name = Capture and Wash NFE (IGA v2.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

Automations

Register Step Started (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {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 v2.1)

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-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 python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Pool Count'"

Capture and Wash Enrichment - Create LH Input File (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/CaptureWashInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

Capture and Wash Enrichment - Validate LH Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/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 v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

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
  Liquid Handling 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 Liquid Handler.	Multiline Text	Read Only	Default = User tasks for this page: - 'Run' Capture and Wash automation - Download resulting Liquid Handler Input File
  Quick reference checklist: Capture and Wash IDE. ii) post Liquid Handler.	Multiline Text	Read Only	Default = User tasks continued: - After running Capture and Wash on the liquid handler, upload resulting Liquid Handler Output File - Click 'Next Steps'
• Step File Placeholders

  • Liquid Handler Input File - Automatically attached

  • Script Log File (Aggregated) - Automatically attached

  • Liquid Handler Output File - Manually uploaded

• Sample Table (Table Columns - Global Fields)

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

Step 6: Post-Capture Pool QC with Enrichment

• Master Step Name = Generic Pool QC NFE (IGA v2.1)

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName}

Automations

Register Step Started (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {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 v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '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 v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "bash /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/changeWorkflowScript_QCStep_RoutePassedInputs.sh {username} {password} {stepURI} {compoundOutputFileLuid1} /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/masterRoutingTable_NFEtoSeqPlatSelect.csv 'v2.1' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_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
  Quick reference checklist: Pool QC IDE.	Multiline Text	Read Only	Default = User tasks for this page: - 'Run' Capture and Wash automation - Download resulting Liquid Handler Input File
• Step File Placeholders

  • QC Instrument Results (Generic Placeholder) - Manually uploaded

  • Script Log File (Aggregated) - Automatically attached

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • File Column Options

    • File Column Display = Hide

    • File Attachment Method = Auto

  • 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	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	INTERNALFIELD_QCValue_forRouting	Text
    Measurement	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Measurement	INTERNALFIELD_QCValue_forRouting	Text	Read Only
    Project	Project Name	Built-in

Protocol 7: Sequencing Platform Selection

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Sequencing Platform

• Master Step Name = Sequencing Platform Selection (IGA v2.1)

• Step Type = No Outputs

Automations

Register Step Started (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Sequencing Platform Selection - Copy Instrument Type to Analyte & Set Next Steps to Remove from Workflow (IGA v2.1)

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'input.::Sequencing Platform:: = step.::Sequencing Platform:: ; nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"

Sequencing Platform Selection - Route to Sequencing Workflow by Type (IGA v2.1)

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "bash /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/changeWorkflowScript_SeqPlatform_RouteInputs.sh {username} {password} {stepURI} {compoundOutputFileLuid0} /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/masterRoutingTable_seqplatselection.csv \
&& /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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Sequencing Platform	Text Dropdown	Required Field	Presets NovaSeq_IGA NextSeq 1000/2000 v2.3 Default = NovaSeq_IGA
  Quick reference checklist: Sequencing Platform Selection	Multiline Text	Read Only	Default = User tasks for this page: - No actions for this page! The step serves to route all samples to the NovaSeq workflow
• Step File Placeholders

  • Set Sequencing Platform Script Log - Automatically attached

• Sample Table (Table Columns - Global Fields)

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