IGA Library Prep Automated v2.1

Illumina Genomics Architecture (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.

IGA Library Prep Automated v2.1 includes the following protocols:

• Protocol 1: Sample Selection
• Protocol 2: Sample Plating
• Protocol 3: Blood Extraction
• Protocol 4: Saliva Extraction
• Protocol 5: Illumina DNA PCR-Free
• Protocol 6: Illumina DNA with Enrichment
• Protocol 7: Sequencing Platform Selection

Protocol 1: Sample Selection

Master Step: Sample Selection

Step Type: No Outputs

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting

Illumina Universal Sample Identifier

 

Expanded View Fields

Units

Sample Conc.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Library Prep Method

Text Dropdown

Required Field

Presets

• Illumina DNA PCR-Free (Default)
• Illumina DNA with Enrichment
   

IGA WF Build Version

Text

Read Only

Inherited from master step.

Default

• 2.1.0.1

 

Multiline Text Fields

Quick reference checklist: Sample Selection

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– Select Library Prep Method.
– Select Next Steps.

Step File Placeholders

  

File Name

Set Library Prep Method Script

Auto

Configured on master step.

Sample Table

Table Columns

Sample Name

Built_ In

 
   

Library Prep Method

Text

 

 

  

Units

Text

 
   

Sample Conc.

Numeric Dropdown

Decimal places displayed = 2
   

Submitted Sample Type

Text

Read Only
Automation

Automation Name

Setting

Value

Specification

Sample Selection - Route Plated gDNA

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Sample Selection - Set Library Prep Method and Next Steps

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Register Sample & Register Step Started

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Validate Sample Attributes

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Protocol 2: Sample Plating

Master Step: Sample Plating

Step Type: Standard

Output = Derived Sample

Derived Sample Generation = Variable

Naming Convention = {InputItemlName}

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Type

Sequencing Method

Submitted Sample Name

Library Prep Method

Waiting

 

Expanded View Fields

Date Submitted

Sample Category
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Step Sample Type

Text

Read Only

Inherited from master step.
   

Liquid Handler Instrument ID

Text

Read Only

Inherited from master step.

 

Multiline Text Fields

Quick reference checklist: Sample Plating i) pre-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• 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

Inherited from master step.

Default

• User tasks for this page:
– Upload resulting Liquid Handler Output File.
– Select Next Steps.

Step File Placeholders

  

File Name

Liquid Handler Input File

Auto

Configured on master step.
     

Script Log File (Aggregated)

Auto

Configured on master step.
     

Liquid Handler Output File

Manual

Configured on master step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Sample Type

Text

Inherited from master step.

 

  

Submitted Sample Type

Text

Read Only

Configured on step.
   

Container Name

Built_In

  

 

  

Well

Built_In

  
   

Transfer Volume (µl)

Numeric

Inherited from master step.
   

Submitted Sample Labware Type

Text

Inherited from master step.
   

LIMS ID (Container)

Built_In

  
Automation

Automation Name

Setting

Value

Specification

Placement Reminder

Trigger Location

Placement

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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 & Extraction - Validate Single Sample Type and Library Prep Method

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"

Sample Plating - Hamilton Output Plate Barcode Check, Store Instrument ID & Set Next Steps to Remove from Workflow before Custom Routing

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Sample Plating - Sample Placement SAM Plate Barcode Uniqueness Check

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Record Details

 
 

Trigger Style

Manual

  
     

Command line

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}"
Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Protocol 3: Blood Extraction

Master Step: DNA Extraction - Blood

Step Type: Standard

Output = Derived Sample

Derived Sample Generation = Fixed 1

Naming Convention = {InputItemName}

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Submitted Sample Name

Sample Type

Library Prep Method

Sequencing Method

Waiting
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

MLB

Text

 
   

ProK

Text

 
   

ITB

Text

 
   

RSB

Text

 
   

Ethanol

Text

 
   

Step Sample Type

Text

Read Only
   

Sample Count

Numeric

Read Only

Default

• 0
   

Liquid Handling Instrument ID

Text

Read Only

 

Multiline Text Fields

Quick reference checklist: DNA Extraction - Blood i) pre-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

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 this is loaded as a master mix).
   

Quick reference checklist: DNA Extraction - Blood i) post-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– After running extraction on Liquid Handler, upload the resulting Liquid Handler Robot Output File.
– Select Next Steps (RSB, ITB, and Ethanol lots populate automatically on the next screen).

Step File Placeholders

  

Liquid Handling Robot (Hamilton) Input File

  

Auto

Configured on the master step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.
   

Liquid Handling Robot Output File

  

Manual

Configured on the step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Library Prep Method

Text

Inherited from the master step.
   

Submitted Sample Type

Text

Read Only

Configured on step.
   

Container Name

Built_In

  

 

  

Well

Built_In

  
   

LIMS ID (Container)

Built_In

  
   

Project Name

Built_In

  
   

Container

Built_In

  
Automation

Automation Name

Setting

Value

Specification

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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 - Count Samples & Create LH Input File

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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 - Routing

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Protocol 4: Saliva Extraction

• Master Step: DNA Extraction - Saliva
• Step Type: Standard
• Output = Derived Sample
• Derived Sample Generation = Fixed 1
• Naming Convention = {InputItemName}
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Submitted Sample Name

Sample Type

Sequencing Method

Library Prep Method

Waiting
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

MLB

Text

 
   

ProK

Text

 
   

ITB

Text

 
   

RSB

Text

 
   

Ethanol

Text

 
   

Step Sample Type

Text

Read Only
   

Sample Count

Numeric

Read Only

Default

• 0
   

Liquid Handling Instrument ID

Text

Read Only

 

Multiline Text Fields

Quick reference checklist: DNA Extraction - Saliva i) pre-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

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 this is loaded as a master mix).
   

Quick reference checklist: DNA Extraction - Saliva i) post-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– After running extraction on Liquid Handler, upload the resulting Liquid Handler Robot Output File.
– Select Next Steps (RSB, ITB, and Ethanol lots populate automatically on the next screen).

Step File Placeholders

  

Liquid Handling Robot (Hamilton) Input File

  

Auto

Configured on the master step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.
   

Liquid Handling Robot Output File

  

Manual

Configured on the step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Library Prep Method

Text

Inherited from the master step.
   

Submitted Sample Type

Text

Read Only

Configured on step.
   

Container Name

Built_In

  

 

  

Well

Built_In

  
   

LIMS ID (Container)

Built_In

  
   

Project Name

Built_In

  
   

Container

Built_In

  
Automation

Automation Name

Setting

Value

Specification

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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 - Count Samples & Create LH Input File

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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 - Routing

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Protocol 5: Illumina DNA PCR-Free

• Master Step: DNA Batching NFPF
• Step Type: Standard
• Output = Derived Sample
• Derived Sample Generation = Fixed 1
• Naming Convention = {InputItemName}_DNA
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

Sample Type

Library Prep Method

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Batching Well Volume (µl)

Numeric

Required Field

Default

• 40
   

DNA (ng) Required for Tagmentation

Numeric

Required Field

Default

• 350
   

Liquid Handling Instrument ID

Text

Read Only

 

Multiline Text Fields

Notes

Multiline Text

Read Only

Inherited from master step.

Default

• DNA (ng) required for tagmentation is 300–2000 ng.
• A fixed 25 µl is aliquoted from the total volume of 40 µl (default) to carry out Library Prep and subsequent steps.
   

Quick reference checklist: DNA Batching IDPF i) post-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– For gDNA samples, enter the library prep input amount (ng). This field is ignored for samples that arrive as raw blood or saliva, as a set volume is transferred.
– Run DNA Batching PF automation and download the resulting Liquid Handler Batching Input File.

Step File Placeholders

  

Liquid Handler Batching Input File

  

Auto

Configured on the master step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.
   

Liquid Handler Output File

  

Manual

Configured on the master step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Sample Needed (µl)

Numeric

Inherited from the master step.

Decimal places displayed = 1
   

Diluent Volume (µl)

Numeric

Inherited from the master step.

Decimal places displayed = 1
   

Warnings

Built_In

  
   

LIMS ID (Container)

Built_In

  
   

Project Name

Built_In

  

 

  

Well

Built_In

  
   

Container Name

Built_In

  
   

Initial Input DNA (ng)

Numeric

Inherited from the master step.
Automation

Automation Name

Setting

Value

Specification

DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Record Details

 
 

Trigger Style

Manual

  
     

Command line

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):: < 2.1 ) { output.::Sample Needed (uL):: = 2.1 ; 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 PF - Set Final Volume and Validate Sample Type Combination

Trigger Location

Started

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Placement

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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.'"

Register Step Completed

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"
Next Step

Setting

Value

Index Planning PCR-Free

 

Start Next Step

Manual

Assign Next Step

Manual
• Master Step: Index Planning
• Step Type: No Outputs
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Index Plate Barcode

Text

Required Field

Inherited from the master step.
   

Hamilton Indexing Offset Column

Numeric

Inherited from the master step.

Range: 1.0–12.0

Default

• 1

 

Multiline Text Fields

Quick reference checklist: Index Planning

Multiline Text

Read Only

Inherited from the master step.

Default

• User tasks for this page:
– Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column).
– Select Next Steps.

Step File Placeholders

  

Script Log File (Aggregated)

  

Manual

Configured on the step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Container Name

Built_In

  

 

  

Well

Built_In

  
   

LIMS ID (Container)

Built_In

  
   

Project Name

Built_In

  
   

INTERNALFIELD_IndexPlanning_Metadata

Text

Custom Entries

Inherited from the master step.
Automation

Automation Name

Setting

Value

Specification

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Register Step Started

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Library Prep - Indexing PCR-Free

 

Start Next Step

Manual

Assign Next Step

Manual
• Master Step: Indexing NFPF
• Step Type: Add Labels
• Output = Derived Sample
• Derived Sample Generation = Fixed 1
• Naming Convention = {SubmittedSampleName}
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

INTERNALFIELD_IndexPlanning_Metadata

Container Name

Well

Project Name

Waiting

Add Labels - Label Groups

• Nextera UDP A
• Nextera UDP B
• Nextera UDP C
• Nextera UDP D
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Sample Count

Numeric

Read Only

Decimal places displayed = 0

Inherited from the master step.

Default

• 0
   

TB1

Text

Inherited from the master step.
   

ST2

Text

Inherited from the master step.
   

TWB

Text

Inherited from the master step.
   

ELM-T

Text

Inherited from the master step.
   

HP3

Text

Inherited from the master step.
   

IPB

Numeric

Inherited from the master step.
   

RSB

Text

Inherited from the master step.
   

BLT-PF

Text

Inherited from the master step.
   

Library Plate Barcode

Text

Required Field

Inherited from the master step.
   

Index Plate Barcode (read from input samples)

Text

Read Only

Inherited from the master step.
   

Index Plate Offset (read from input samples)

Text

Read Only

Inherited from the master step.
   

Liquid Handling Instrument ID

Text

Read Only

Inherited from the master step.
   

Adapter

Text

Required Field

Read Only

Inherited from the master step.

Default

• CTGTCTCTTATACACATCT
   

Adapter Read 2

Text

Required Field

Read Only

Inherited from the master step.

Default

• CTGTCTCTTATACACATCT

 

Multiline Text Fields

Quick reference checklist: Library Prep IDPF i) pre-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– Scan in the Library Plate Barcode to be used.
– Select blue Run button to run the Library Prep automation and download the resulting Liquid Handler Input File.
   

Quick reference checklist: Library Prep IDPF i) post-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– Upload resulting Hamilton Output File.
– Perform a pooled quant for the prep and apply the yield Normalized Molarity (nM) to all samples.
– Select Next Steps.

Step File Placeholders

  

Liquid Handler Input File

  

Auto

Configured on the master step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.
   

Hamilton Output File

  

Manual

Configured on the master step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Library Prep Method

Text

Inherited from the master step.
   

Normalized Molarity (nM)

Numeric

Configured on the step.

Decimal places displayed = 2
   

Container Name

Built_In

  

 

  

Well

Built_In

  
   

LIMS ID (Container)

Built_In

  
   

Container

Built_In

  
Automation

Automation Name

Setting

Value

Specification

Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery

Trigger Location

Add Labels

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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}"

Indexing - Validate Index Category and Index Plate Barcode

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"

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

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

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

Trigger Location

Record Details

 
 

Trigger Style

Manual

  
     

Command line

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}"
Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Protocol 6: Illumina DNA with Enrichment

• Master Step: DNA Batching NFE
• Step Type: Standard
• Output = Derived Sample
• Derived Sample Generation = Fixed 1
• Naming Convention = {InputItemName}_DNA
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Batching Well Volume (µl)

Numeric

Required Field

Inherited from the master step.

Default

• 45
   

DNA (ng) Required for Tagmentation

Numeric

Required Field

Inherited from the master step.

Default

• 450
   

Liquid Handling Instrument ID

Text

Read Only

Inherited from the master step.

 

Multiline Text Fields

Notes

Multiline Text

Read Only

Inherited from the master step.

Default

• DNA (ng) required for tagmentation is 50–1000 ng.
• A fixed 30 µl is aliquoted from the total volume of 45 µl (default) to carry out Library Prep and subsequent steps.
   

Quick reference checklist: DNA Batching IDE i) pre-Liquid Handler

Multiline Text

Read Only

Inherited from the master step.

Default

• User tasks for this page:
– For gDNA samples, enter the library prep input amount (ng). This field is ignored for samples that arrive as raw blood or saliva, as a set volume is transferred.
– Run DNA Batching Enrichment automation and download the resulting Liquid Handler Batching Input File.
   

Quick reference checklist: DNA Batching IDE i) post-Liquid Handler

Multiline Text

Read Only

Inherited from the master step.

Default

• User tasks for this page:
– Upload the resulting Output File from Liquid Handler.
– Select Next Steps.

Step File Placeholders

  

Liquid Handler Batching Input File

  

Auto

Configured on the master step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.
   

Output File from Liquid Handler

  

Manual

Configured on the master step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Sample Needed (µl)

Numeric

Inherited from the master step.

Decimal places displayed = 1
   

Diluent Volume (µl)

Numeric

Inherited from the master step.

Decimal places displayed = 1
   

Warnings

Built_In

Read Only
   

LIMS ID (Container)

Built_In

  
   

Project Name

Built_In

  

 

  

Well

Built_In

  
   

Container Name

Built_In

  
   

Initial Input DNA (ng)

Numeric

Inherited from the master step.
Automation

Automation Name

Setting

Value

Specification

DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Record Details

 
 

Trigger Style

Manual

  
     

Command line

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):: < 2.1 ) { output.::Sample Needed (uL):: = 2.1 ; 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 Enrichment - Set Final Volume

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Trigger Location

Placement

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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.'"

Register Step Completed

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"
Next Step

Setting

Value

Index Planning with Enrichment

 

Start Next Step

Manual

Assign Next Step

Manual
• Master Step: Index Planning
• Step Type: No Outputs
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers
• Sample Name
• LIMS ID (Container)
• Container Name
• Well
• Project Name
• Waiting
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Index Plate Barcode

Text

Required Field

Inherited from the master step.
   

Hamilton Indexing Offset Column

Numeric

Inherited from the master step.

Range: 1.0–12.0

Default

• 1

 

Multiline Text Fields

Quick reference checklist: Index Planning

Multiline Text

Read Only

Inherited from the master step.

Default

• User tasks for this page:
– Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column).
– Select Next Steps.

Step File Placeholders

  

Script Log File (Aggregated)

  

Manual

Configured on the step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

INTERNALFIELD_IndexPlanning_Metadata

Text

Inherited from the master step.
Automation

Automation Name

Setting

Value

Specification

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Register Step Started

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Library Prep - Indexing with Enrichment

 

Start Next Step

Manual

Assign Next Step

Manual
• Master Step: Indexing NFE
• Step Type: Add Labels
• Output = Derived Sample
• Derived Sample Generation = Fixed 1
• Naming Convention = {SubmittedSampleName}
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.

Add Labels - Label Groups

• Nextera UDP A
• Nextera UDP B
• Nextera UDP C
• Nextera UDP D
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Index Plate Barcode (read from input samples)

Text

Read Only

Inherited from the master step.
   

Index Plate Offset (read from input samples)

Text

Read Only

Inherited from the master step.

 

Multiline Text Fields

Quick reference checklist: Library Prep IDE

Multiline Text

Read Only

Inherited from the master step.

Default

• User tasks for this page:
– No user tasks, select Next Steps.

Step File Placeholders

  

Script Log File (Aggregated)

  

Auto

Configured on the master step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

INTERNALFIELD_IndexPlanning_Metadata

Text

Inherited from the master step.
Automation

Automation Name

Setting

Value

Specification

Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery

Trigger Location

Add Labels

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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}"

Indexing - Validate Index Category and Index Plate Barcode

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"

Library Prep - Indexing Enrichment - Copy Indexing Metadata to Outputs & Set Next Steps to Advance

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Library Prep - Indexing Enrichment - Copy Input Plate Barcode to Output Plate

Trigger Location

Add Labels

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Register Step Completed

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"
Next Step

Setting

Value

Library Prep - Pre-Capture Pooling with Enrichment

  

Start Next Step

Manual

Assign Next Step

Manual
• Master Step: Library Prep NFE - Pool Libraries
• Step Type: Pooling
• Output = Aliquot Generation
• Derived Sample Generation = Fixed 1
• Naming Convention = {PoolName}
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Pooling

Section

Subsection

Value

Pool Settings

Label Uniqueness

On
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Sample Count

Numeric

Read Only

Inherited from the master step.

Default

• 0
   

Liquid Handling Instrument ID

Text

Read Only

Inherited from the master step.
   

Index Plate Barcode (read from input samples)

Text

Read Only

Inherited from the master step.
   

Index Plate Offset (read from input samples)

Text

Read Only

Inherited from the master step.
   

Total Pool Volume (µl)

Numeric

Inherited from the master step.

Default

• 30
   

eBLT

Text

Inherited from the master step.
   

TB1

Text

Inherited from the master step.
   

ST2

Text

Inherited from the master step.
   

TWB

Text

Inherited from the master step.
   

SPB

Numeric

Inherited from the master step.
   

RSB

Text

Inherited from the master step.
   

Adapter

Text

Required Field

Read Only

Inherited from the master step.

Default

• CTGTCTCTTATACACATCT
   

Adapter Read 2

Text

Required Field

Read Only

Inherited from the master step.

Default

• CTGTCTCTTATACACATCT

 

Multiline Text Fields

Quick reference checklist: Library Prep IDE i) pre-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– Run Library Prep Pooling automation.
– Download the resulting Liquid Handler Input File.
   

Quick reference checklist: Library Prep IDE i) post-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– After running the Prep method on the Liquid Handler, upload the resulting Liquid Handler Output File.
– Select Next Steps.

Step File Placeholders

  

Liquid Handler Input File

  

Auto

Configured on the master step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.
   

Liquid Handler Output File

  

Manual

Configured on the step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Samples Needed (µl)

Numeric

Inherited from the master step.

Decimal places displayed = 1
   

Diluent Volume (µl)

Numeric

Inherited from the master step.

Decimal places displayed = 1
   

Number of Samples in Pool

Numeric

Inherited from the master step.

Default

• 0
Automation

Automation Name

Setting

Value

Specification

Library Prep - Pooling Enrichment - Create LH Input File

Trigger Location

Add Labels

 
 

Trigger Style

Manual

  
     

Command line

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 - Sample Placement PCPP Plate Barcode Uniqueness Check

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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 - Validate LH Output File Name, Parse Reagents & Set Next Steps to Advance

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Library Prep - Pooling Enrichment - Validate Pool Sizes

Trigger Location

Pooling

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Register Step Completed

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Register Step Started

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Library Prep - Capture and Wash with Enrichment

  

Start Next Step

Manual

Assign Next Step

Automatic
• Master Step: Capture and Wash NFE
• Step Type: Standard
• Output = Derived Sample
• Derived Sample Generation = Fixed 1
• Naming Convention = {InputItemName}
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Pool Count

Numeric

Read Only

Inherited from the master step.

Default

• 0
   

Liquid Handling Instrument ID

Text

Read Only

Inherited from the master step.
   

EHB2

Text

Inherited from the master step.
   

Probes

Text

Inherited from the master step.
   

EEW

Text

Inherited from the master step.
   

EE1

Text

Inherited from the master step.
   

HP3

Numeric

Inherited from the master step.
   

ET2

Text

Inherited from the master step.
   

EPM

Text

Inherited from the master step.
   

PPC

Text

Inherited from the master step.

 

Multiline Text Fields

Quick reference checklist: Capture and Wash IDE i) pre-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– Run Capture and Wash automation.
– Download the resulting Liquid Handler Input File.
   

Quick reference checklist: Capture and Wash IDE i) post-Liquid Handler

Multiline Text

Read Only

Inherited from master step.

Default

• User tasks for this page:
– After running the Capture and Wash on the Liquid Handler, upload the resulting Liquid Handler Output File.
– Select Next Steps.

Step File Placeholders

  

Liquid Handler Input File

  

Auto

Configured on the master step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.
   

Liquid Handler Output File

  

Manual

Configured on the step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Container Name

Built_In

  
   

Well

Built_In

  
   

LIMS ID (Container)

Built_In

 
   

Project Name

Built_In

 
Automation

Automation Name

Setting

Value

Specification

Capture and Wash Enrichment - Create LH Input File

Trigger Location

Record Details

 
 

Trigger Style

Manual

  
     

Command line

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 - Sample Placement LIB Plate Barcode Uniqueness Check & Update Pool Count

Trigger Location

Placement

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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 - Validate LH Output File Name, Parse Reagents & Set Next Steps to Advance

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Register Step Started

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Post-Capture Pool QC with Enrichment

  

Start Next Step

Manual

Assign Next Step

Automatic
• Master Step: Generic Pool QC NFE
• Step Type: Standard QC
• Output = Measurement
• Derived Sample Generation = Fixed 1
• Naming Convention = {InputItemName}
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Quick reference checklist: Pool QC IDE

Multiline Text

Read Only

Inherited from the master step.

Default

• User tasks for this page:
– After running QC on the pools, upload a QC instrument file or input Normalized Molarity (nM) and QC flags.
– For any QC fails, assign next steps.
– Select Next Steps.

Step File Placeholders

  

QC Instrument Results (Generic Placeholder)

  

Manual

Configured on the step.
   

Script Log File (Aggregated)

  

Auto

Configured on the master step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Container Name

Built_In

 
   

Well

Built_In

 
   

Normalized Molarity (nM)

Numeric

Derived Sample

Inherited from the master step.

Decimal places displayed = 2
   

Normalized Molarity (nM)

Numeric

Measurement

Inherited from the master step.

Decimal places displayed = 2
   

LIMS ID

Built_In

 
   

Project Name

Built_In

 
   

INTERNALFIELD_QCValue_forRouting

Text

Derived Sample

Inherited from the master step.
   

INTERNALFIELD_QCValue_forRouting

Text

Read Only

Measurement

Inherited from the master step.

 
Automation

Automation Name

Setting

Value

Specification

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

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Register Step Started

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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'"
Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Protocol 7: Sequencing Platform Selection

• Master Step: Sequencing Platform Selection
• Step Type: No Outputs
Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers

Sample Name

LIMS ID (Container)

Container Name

Well

Project Name

Waiting
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

Inherited from master step.
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Sequencing Platform

Text

Required Field

Inherited from the master step.

Presets

• NovaSeq_IGA (Default)
• NextSeq 1000/2000 v2.3

 

Multiline Text Fields

Quick reference checklist: Sequencing Platform Selection

Multiline Text

Read Only

Inherited from the master step.

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

  

Auto

Configured on the master step.

Sample Table

Table Columns

Sample Name

Built_In

 
   

Container Name

Built_In

  

 

  

Well

Built_In

  
   

LIMS ID (Container)

Built_In

  
   

Project Name

Built_In

  
   

Sequencing Platform

Text

Inherited from the master step.
Automation

Automation Name

Setting

Value

Specification

Register Step Started

Trigger Location

Step

 
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Trigger Location

Record Details

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Trigger Location

Step

 
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"
Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

End of Workflow