Illumina Genomics Architecture - Library Prep Automated v1.0

The Illumina Genomics Architecture - Library Prep Automated v1.0 includes the following functionality:

• Preset Illumina Genomics Architecture - Library Prep Automated v1.0 protocols that support the preparation of samples and libraries for sequencing.
• Can be used with the Illumina Genomics Architecture - NovaSeq Sequencing v1.0 workflow.
• Tight file-based integration with Hamilton robots for performing various steps of liquid handling.
• Automated calculation of sample and buffer volumes.
• Automated calculation or display of reagents.
• Automatic step transition when required.

Protocol 1: Sample Selection (IGA v1.0)

Master Step 1: Sample Selection

Step Type = No Outputs

Input = Blood, Saliva, or Genomic DNA (gDNA) samples (in any combination)

Output = None

Queue

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• Units
• Sample Conc.

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Library Prep Method

Text Dropdown

Required Field = Yes

Read Only = No

Custom Entries = No

Presets:

• Illumina DNA PCR-Free (Set as Default = Yes)
• Illumina DNA with Enrichment

 

Multiline Text Fields

Quick reference checklist: Sample Selection

Multiline Text

Required Fields = No

Read Only = Yes

Default

User tasks for this page:

• Select Library Prep Method.
• Select Next Steps.

Step File Placeholders

 

Set Library Prep Method Script

Log

Auto

Sample Table

 

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  
   

Well Sort Order

Row

  

 

Table Columns

 

 

 
   

Sample Name

    
   

Library Prep Method

Text

Global Field = Submitted Sample

Required field = No

Read Only = No
   

Units

Text

Global Field = Submitted Sample

Required Field = No

Read Only = No
   

Sample Conc.

Numeric

• Global Field = Submitted Sample
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 2
   

Submitted Sample Type

Text

• Global Field = Derived Sample & Submitted Sample
• Required Field = No
• Read Only = Yes
Automation - Script Description

Automation Name

Setting

Value

Specification

Validate Sample Attributes (IGA v1.0)

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}"

Sample Selection - Set Library prep method and Next steps (IGA v1.0)

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}"

Sample Selection - Route Plated gDNA (IGA v1.0)

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 v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' "

Next Step

Setting

Value

Plate Samples (IGA v1.0)

  

DNA Batching PCR-Free (IGA v1.0)

  

DNA Batching with Enrichment (IGA v1.0)

  

Assign Next Step

Automatic

Safe Stopping Point

 

Protocol 2: Sample Plating (IGA v1.0)

Master Step 1: Sample Plating

Step Type = Standard

Input = Blood, Saliva, or Genomic DNA (gDNA) samples (cannot be mixed sample types or mixed library preparation methods when step starts)

Output = Analytes plated on a 96-well plate

Queue

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

Defaults

Sample Grouping

Group by Projects
 

Well Sort Order

Column
Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers
• Submitted Sample Name
• Sample Type
• Sequencing Method
• Library Prep Method
 

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Projects
 

Well Sort Order

Column
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

 

Defaults

Sample Grouping

Group by Projects
 

Well Sort Order

Column

 

Placement Pattern

Column
 

Skip Alternating Rows

No
 

Skip Alternating Columns

No
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Step Sample Type

Text

Required Field = No

Read Only = Yes
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = Yes

 

Multiline Text Fields

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User tasks for this page:

• Select Run button.
• Download Liquid Handler Input File.
   

Quick reference checklist: Sample Plating. ii) post Liquid Handler

Multiline Text

Required Field = No

Read Only = Yes

Default

User tasks for this page:

• Upload resulting Liquid Handler Output File
• Select Next Steps.

Step File Placeholders

 

Liquid Handler Input File

File

Auto
   

Script Log File (Aggregated)

Log

Auto
   

Liquid Handler Output File

File

Manual

Sample Table

 

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  
   

Well Sort Order

Row

  

 

Table Columns

 

 

 
   

Sample Name

    
   

Sample Type

Text
• Global Field = Submitted Sample
• Required field = No
• Read Only = No
   

Submitted Sample Type

Text
• Global Field = Derived Sample & Submitted Sample
• Required field = No
• Read Only = Yes
   

Container Name

    
   

Well

    
   

Transfer Volume (ul)

Numeric
• Global Field = Derived Sample
• Required field = No
• Read Only = No
   

Submitted Sample Labware Type

Text
• Global Field = Submitted Sample
• Required field = No
• Read Only = No
   

LIMS ID (Container)

    
Automation - Script Description

Automation Name

Setting

Value

Specification

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v1.0)

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}"

Placement Reminder (IGA v1.0)

Trigger Location

Placement

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Sample Plating - Sample Placement SAM Barcode Uniqueness Check (IGA v1.0)

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/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \

/usr/bin/env python /opt/gls/clarity/extensions/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

Sample Plating - Set Transfer Volume & Create Liquid Handler Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Manual Button

  
     

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/hamilton_fast_prep/templatefiles/PlatingInputFile_template.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

Sample Plating - Hamilton Output Plate Barcode Check, Store Instrument ID & Set Next Steps to Remove from Workflow before Custom Routing (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \

-i {stepURI} \

-u {username} \

-p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp 'nextStep = ::REMOVE:: ' \

-log {compoundOutputFileLuid1}"

Sample Plating - Route Samples (IGA v1.0)

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 v1.0' \

--STEP 'DNA Extraction - Blood (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Extraction - Saliva (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Extraction - Blood (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Extraction - Saliva (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' "

Next Step

Setting

Value

DNA Extraction - Blood (IGA v1.0)

  

DNA Extraction - Saliva (IGA v1.0)

 

DNA Batching PCR-Free (IGA v1.0)

  

DNA Batching with Enrichment (IGA v1.0)

  

Assign Next Step

Automatic

Safe Stopping Point

 

Protocol 3: Blood Extraction (IGA v1.0)

Master Step 1: DNA Extraction - Blood

Step Type = Standard

Input = 96-well plates of Blood

Output = Analytes plated on a 96-well plate

Queue

Section

Subsection

Value

Sample Table

Column Headers
• Submitted Sample Name
• Sample Type
• Library Prep Method
• Sequencing Method
• Waiting
 

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Column
Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers
• Sample Type
• Submitted Sample Name
• Library Prep Method
 

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Column
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

 

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Column

 

Placement Pattern

Column
 

Skip Alternating Rows

No
 

Skip Alternating Columns

No
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

MLB

Text

Required Field = No

Read Only = No
   

ProK

Text

Required Field = No

Read Only = No
   

ITB

Text

Required Field = No

Read Only = No
   

RSB

Text

Required Field = No

Read Only = No
   

Ethanol

Text

Required Field = No

Read Only = No
   

Step Sample Type

Text

Required Field = No

Read Only = Yes
   

Sample Count

Numeric

Required Field = No

Read Only = Yes

Default = 0
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = Yes
 

Multiline Text Fields

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• Download Liquid Handling Robot Input File.
• Enter reagent lots for MLB and ProK (not scanned by Liquid Handler as loaded as a master mix).
   

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File.
• Select Next Steps (RSB, ITB, and Ethanol lots will populate automatically on the next screen).

Step File Placeholders

  

Liquid Handling Robot (Hamilton) Input File

File

Auto
   

Script Log File (Aggregated)

Log

Auto
   

Liquid Handling Robot Output File

File

Manual

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  

 

Table Columns

 

 

 
   

Sample Name

    
   

Library Prep Method

Text

• Global Field = Submitted Sample
• Required Field = No
• Read Only = No
   

Submitted Sample Type

Text

• Global Field = Derived Sample & Submitted Sample
• Required Field = No
• Read Only = Yes
   

Container Name

    
   

Well

    
   

LIMS ID (Container)

    
   

Project Name

    
   

Container

    
Automation - Script Description

Automation Name

Setting

Value

Specification

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v1.0)

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}"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v1.0)

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/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Extraction - Count Samples & Create LH Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \

&& \

/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \

-i {stepURI:v2:http} \

-u {username} \

-p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \

-log {compoundOutputFileLuid1}"

Extraction - Routing (IGA v1.0)

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 v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' "

Next Step

Setting

Value

DNA Batching PCR-Free (IGA v1.0)

  

DNA Batching with Enrichment (IGA v1.0)

Assign Next Step

Automatic

Must Move Forward

 

Protocol 4: Saliva Extraction (IGA v1.0)

Master Step 1: DNA Extraction - Saliva

Step Type = Standard

Input = 96-well plates of Saliva

Output = Analytes plated on a 96-well plate

Queue

Section

Subsection

Value

Sample Table

Column Headers
• Submitted Sample Name
• Sample Type
• Library Prep Method
• Sequencing Method
• Waiting
 

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Column
Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers
• Submitted Sample Name
• Sample Name
• Library Prep Method
 

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Column
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

 

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Column

 

Placement Pattern

Column
 

Skip Alternating Rows

No
 

Skip Alternating Columns

No
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

MLB

Text

Required Field = No

Read Only = No
   

ProK

Text

Required Field = No

Read Only = No
   

ITB

Text

Required Field = No

Read Only = No
   

RSB

Text

Required Field = No

Read Only = No
   

Ethanol

Text

Required Field = No

Read Only = No
   

Step Sample Type

Text

Required Field = No

Read Only = Yes
   

Sample Count

Numeric

Required Field = No

Read Only = Yes

Default = 0
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = No
 

Multiline Text Fields

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• Download Liquid Handling Robot Input File.
• Enter reagent lots for MLK and ProK (not scanned by Liquid Handler as loaded as a master mix).
   

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File.
• Select Next Steps (RSB, ITB, and Ethanol lots will populate automatically on the next screen).

Step File Placeholders

  

Liquid Handling Robot (Hamilton) Input File

File

Manual
   

Script Log File (Aggregated)

Log

Auto
   

Liquid Handling Robot Output File

File

Manual

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  

 

Table Columns

 

 

 
   

Sample Name

    
   

Library Prep Method

Text

• Global Field = Submitted Sample
• Required Field = No
• Read Only = No
   

Submitted Sample Type

Text

• Global Field = Derived Sample & Submitted Sample
• Required Field = No
• Read Only = Yes
   

Container Name

    
   

Well

    
   

LIMS ID (Container)

    
   

Project Name

    
   

Container

    
Automation - Script Description

Automation Name

Setting

Value

Specification

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v1.0)

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}"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v1.0)

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/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Extraction - Count Samples & Create LH Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \

&& \

/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \

-i {stepURI:v2:http} \

-u {username} \

-p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \

-log {compoundOutputFileLuid1}"

Extraction - Routing (IGA v1.0)

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 v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching PCR-Free (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'Submitted Sample Type' \

--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \

--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v1.0' \

--STEP 'DNA Batching with Enrichment (IGA v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' "

Next Step

Setting

Value

DNA Batching PCR-Free (IGA v1.0)

  

DNA Batching with Enrichment (IGA v1.0)

  

Assign Next Step

Automatic

Must Move Forward

  

Protocol 5: Illumina DNA PCR-Free (IGA v1.0)

Master Step 1: DNA Batching NFPF

Step Type = Standard

Input = Blood, Saliva, or Genomic DNA (gDNA) samples on 96-well plates (can mix Blood and Saliva, but not Genomic DNA)

Output = Analytes plated on a 96-well plate

Queue

Section

Subsection

Value

Sample Table

Column Headers
• Sample Name
• Sample Type
• Library Prep Method
• LIMS ID (Container)
• Container Name
• Well
• Project Name
• Waiting
 

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

 

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Column

 

Placement Pattern

Column
 

Skip Alternating Rows

No
 

Skip Alternating Columns

No
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Final Volume (µl)

Numeric

Required Field = Yes

Read Only = No

Default = 35
   

Input Amount (ng)

Numeric

Required Field = Yes

Read Only = No

Default = 350
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = Yes
 

Multiline Text Fields

Quick reference checklist: DNA Batching IDPF. i) pre Liquid Handler

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• For gDNA samples, enter library prep Input Amount (ng). This field is ignored for samples that arrived as raw blood or saliva, as a set volume is transferred.
• Run DNA Batching PF automation, and download resulting Liquid Handler Batching Input File.
   

Quick reference checklist: DNA Batching IDPF. ii) post Liquid Handler

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• Upload resulting Output File from Liquid Handler.
• Select Next Steps.

Step File Placeholders

  

Liquid Handler Batching Input File

File

Auto
   

Script Log File (Aggregated)

Log

Auto
   

Output File from Liquid Handler

File

Manual

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  

 

Table Columns

 

 

 
   

Sample Name

    
   

Sample Needed (µl)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Points Displayed = 1
   

Final Amount (ng)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
   

Diluent Volume (µl)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Points Displayed = 1
   

Warnings

Text
• Global Field = Derived Sample
• Required Field = No
• Read Only = Yes
   

LIMS ID (Container)

    
   

Project Name

    
   

Well

    
   

Container

    
Automation - Script Description

Automation Name

Setting

Value

Specification

DNA Batching PF - Set Final Volume and Validate Sample Type Combination (IGA v1.0)

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 (submittedSample.::Sample Type:: == ::Genomic DNA::) {step.::Final Volume (µl):: = 35} ; if (submittedSample.::Sample Type:: == ::Blood::) {step.::Final Volume (µl):: = 40} ; if (submittedSample.::Sample Type:: == ::Saliva::) {step.::Final Volume (µl):: = 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}"

Placement Reminder (IGA v1.0)

Trigger Location

Placement

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v1.0)

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/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \

/usr/bin/env python /opt/gls/clarity/extensions/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

DNA Batching PF - Generate LH Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Manual Button

  
     

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 (µl):: = step.::Input Amount (ng):: / submittedSample.::Sample Conc.:: ; \

if ( output.::Sample Needed (µl):: > step.::Final Volume (µl):: ) { output.::Sample Needed (µl):: =

step.::Final Volume (µl):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (µl):: < 2.0 )

{ output.::Sample Needed (µl):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (µl):: =

step.::Final Volume (µl):: - output.::Sample Needed (µl):: ; output.::Final Amount (ng):: = output.::Sample Needed (µl):: * submittedSample.::Sample Conc.::} \

else \

{output.::Sample Needed (µl):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (µl):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (µl):: = step.::Final Volume (µl)::; output.::Diluent Volume (µl):: = 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/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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}"

Next Step

Setting

Value

Indexing Planning PCR-Free (IGA v1.0)

  

Start Next Step

Manual

Assign Next Step

Manual

If Illumina extraction kit is used: Must Move Forward

  

If external extraction kit is used: Safe Stopping Point

  

Master Step 2: Indexing Planning

Step Type = No Outputs

Input = Blood, Saliva, or Genomic DNA (gDNA) 96-well batch plates

Output = No Outputs

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Index Plate Barcode

Text

Required Field = Yes

Read Only = No
   

Hamilton Indexing Offset Column

Numeric

Required Field = No

Read Only = No

Default = 1

Range = 1 to 12
 

Multiline Text Fields

Quick reference checklist:: Indexing Planning

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the 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)

Log

Manual

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

Container Name

    
   

Well

    
   

LIMS ID (Container)

    
   

Project Name

    
   

INTERNALFIELD_IndexPlanning_Metadata

Text
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
Automation - Script Description

Automation Name

Setting

Value

Specification

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v1.0)

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/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning' && \

/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}"

Next Step

Setting

Value

Library Prep - Indexing PCR-Free (IGA v1.0)

  

Start Next Step

Manual

Assign Next Step

Manual

If Illumina extraction kit is used: Must Move Forward

  

If external extraction kit is used: Safe Stopping Point

  

Master Step 3: Indexing NFPF

Step Type = Add Labels

Input = Blood, Saliva, or Genomic DNA (gDNA) 96-well batch plates

Output = Indexed 96-well plates

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

Column Headers
• Sample Name
• INTERNALFIELD_Indexplanning_Metadata
• Container Name
• Well
• Project Name
• Waiting
 

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Add Labels

Section

Subsection

Value

Label Groups

Nextera UDP A

96 Labels
 

Nextera UDP B

96 Labels
 

Nextera UDP C

96 Labels
 

Nextera UDP D

96 Labels
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Sample Count

Numeric

Required Field = No

Read Only = Yes

Default = 0

Decimal Places Displayed = 0
   

TB1

Text

Required Field = No

Read Only = No
   

ST2

Text

Required Field = No

Read Only = No
   

TWB

Text

Required Field = No

Read Only = No
   

ELM-T

Text

Required Field = No

Read Only = No
   

HP3

Text

Required Field = No

Read Only = No
   

IPB

Text

Required Field = No

Read Only = No
   

RSB

Text

Required Field = No

Read Only = No
   

BLT-PF

Text

Required Field = No

Read Only = No
   

Library Plate Barcode

Text

Required Field = Yes

Read Only = No
   

Index Plate Barcode (read from input samples)

Text

Required Field = No

Read Only = Yes
   

Index Plate Offset (read from input samples)

Text

Required Field = No

Read Only = Yes
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = Yes
   

Adapter

Text

Required Field = Yes

Read Only = Yes

Default = CTGTCTCTTATACACATCT
   

Adapter Read 2

Text

Required Field = Yes

Read Only = Yes

Default = CTGTCTCTTATACACATCT
 

Multiline Text Fields

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• Scan in the Library Plate Barcode to be used.
• Select blue button to Run the Library Prep automation, and download the resulting Liquid Handler Input File.
   

Quick reference checklist: Library Prep IDPF. ii) post Liquid Handler

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the 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

File

Auto
   

Script Log File (Aggregated)

Log

Auto
   

Hamilton Output File

File

Manual

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

Library Prep Method

Text
• Global Field = Submitted Sample
• Required Field = No
• Read Only = No
   

Normalized Molarity (nM)

Numeric
• Global Field = Derived Sample & Measurement
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 2
   

Container Name

    
   

Well

    
   

LIMS ID (Container)

    
   

Container

    
Automation - Script Description

Automation Name

Setting

Value

Specification

Indexing - Validate Index Category and Index Plate Barcode (IGA v1.0)

Trigger Location

Step

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery (IGA v1.0)

Trigger Location

Add Labels

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Library Prep - Indexing PF - Validate/Copy LibPlate Barcode, Set Default Norm. Mol. if Applicable, and Generate LH Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Manual Button

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/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/hamilton_fast_prep/templatefiles/LibInputFile_NFPF_template_withoffsets.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

Library Prep - Indexing PF - Check for Valid, Unique LIB Plate Barcode & Match with Liquid Handler Output File & Parse Reagent Info & Set Next Steps to Remove from Workflow & Quant. Warning (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/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_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'WARNING' --message 'This protocol recommends performing a pooled quant. (per prep) at this stage. Please quant. and update the Normalized Molarity (nM) across all samples in the table below before proceeding.'"

Library prep - Indexing PF - Route Samples to Sequencing Platform Selection with Automatic Workflow Detection (IGA v1.0)

Trigger Location

Step

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "bash /opt/gls/clarity/extensions/iga_workflow_routing/changeWorkflowScriptNoFieldChecks.sh {username} {password} {stepURI} {compoundOutputFileLuid1} /opt/gls/clarity/extensions/iga_workflow_routing/masterRoutingTable_NFPFtoSeqPlatSelect.csv 'v1.0'"

Next Step

Setting

Value

Select Sequencing Platform (IGA v1.0)

  

Assign Next Step

Automatic

Safe Stopping Point

  

Protocol 6: Illumina DNA with Enrichment (IGA v1.0)

Master Step 1: DNA Batching NFE

Step Type = Standard

Input = Blood, Saliva, or Genomic DNA (gDNA) samples on 96-well plates (can mix types)

Output = Analytes plated on a 96-well plate

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Placement

Section

Subsection

Value

Destination Containers

96 Well Plate

 

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row

 

Placement Pattern

Column
 

Skip Alternating Rows

No
 

Skip Alternating Columns

No
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Final Volume (µl)

Numeric

Required Field = Yes

Read Only = No

Default = 35
   

Input Amount (ng)

Numeric

Required Field = Yes

Read Only = No

Default = 450
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = Yes
 

Multiline Text Fields

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• For gDNA samples, enter library prep Input Amount (ng). This field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred.
• Run DNA Batching Enrichment automation, and download resulting Liquid Handler Batching Input File.
   

Quick reference checklist ii): DNA Batching IDE, post Liquid Handler

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• Upload resulting Output File from Liquid Handler.
• Select Next Steps.

Step File Placeholders

  

Liquid Handler Batching Input File

File

Auto
   

Script Log File (Aggregated)

Log

Auto
   

Output File from Liquid Handler

File

Manual

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

Sample Needed (µl)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 1
   

Final Amount (ng)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
   

Diluent Volume (µl)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 1
   

Warnings

Text
• Global Field = Derived Sample
• Required Field = No
• Read Only = Yes
   

LIMS ID (Container)

    
   

Project Name

    
   

Well

    
   

Container Name

    
Automation - Script Description

Automation Name

Setting

Value

Specification

DNA Batching Enrichment - Set Final Volume (IGA v1.0)

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.::Final Volume (µl):: = 40' \

-log {compoundOutputFileLuid1}"

Placement Reminder (IGA v1.0)

Trigger Location

Placement

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v1.0)

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/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \

/usr/bin/env python /opt/gls/clarity/extensions/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

DNA Batching Enrichment - Generate LH Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Manual Button

  
     

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 (µl):: = step.::Input Amount (ng):: / submittedSample.::Sample Conc.:: ; \

if ( output.::Sample Needed (µl):: > step.::Final Volume (µl):: ) { output.::Sample Needed (µl):: =

step.::Final Volume (µl):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (µl):: < 2.0 )

{ output.::Sample Needed (µl):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (µl):: =

step.::Final Volume (µl):: - output.::Sample Needed (µl):: ; output.::Final Amount (ng):: = output.::Sample Needed (µl):: * submittedSample.::Sample Conc.::} \

else \

{output.::Sample Needed (µl):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (µl):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (µl):: = step.::Final Volume (µl)::; output.::Diluent Volume (µl):: = 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/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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}"

Next Step

Setting

Value

Indexing Planning with Enrichment (IGA v1.0)

  

Start Next Step

Manual

Assign Next Step

Manual

If Illumina extraction kit used: Must Move Forward.

  

If external extraction kit used: Safe Stopping Point.

  

Master Step 2: Indexing Planning

Step Type = No Outputs

Input = Blood, Saliva, or Genomic DNA (gDNA) 96-well batch plates

Output = No Outputs

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Index Plate Barcode

Text

Required Field = Yes

Read Only = No
   

Hamilton Indexing Offset Column

Numeric

Required Field = No

Read Only = No

Default = 1

Range = 1 to 12
 

Multiline Text Fields

Quick reference checklist:: Indexing Planning

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the 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)

Log

Manual

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

INTERNALFIELD_IndexPlanning_Metadata

Text
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
Automation - Script Description

Automation Name

Setting

Value

Specification

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v1.0)

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/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning' && \

/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}"

Next Step

Setting

Value

Library Prep - Indexing with Enrichment (IGA v1.0)

  

Start Next Step

Manual

Assign Next Step

Manual

If Illumina extraction kit used: Must Move Forward.

  

If external extraction kit used: Safe Stopping Point.

  

Master Step 3: Indexing NFE

Step Type = Add Labels

Input = Blood, Saliva, or Genomic DNA (gDNA) 96-well batch plates

Output = Indexed 96-well plates

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Add Labels

Section

Subsection

Value

Label Groups

Nextera UDP A

96 Labels
 

Nextera UDP B

96 Labels
 

Nextera UDP C

96 Labels
 

Nextera UDP D

96 Labels
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Index Plate Barcode (read from input samples)

Text

Required Field = No

Read Only = Yes
   

Index Plate Offset (read from input samples)

Text

Required Field = No

Read Only = Yes
 

Multiline Text Fields

Quick reference checklist: Library Prep IDE

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• No user tasks, select Next Steps.

Step File Placeholders

  

Script Log File (Aggregated)

Log

Auto

Sample Table

  

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

INTERNALFIELD_IndexPlanning_Metadata

Text
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
Automation - Script Description

Automation Name

Setting

Value

Specification

Indexing - Validate Index Category and Index Plate Barcode (IGA v1.0)

Trigger Location

Step

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery (IGA v1.0)

Trigger Location

Add Labels

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

Library Prep - Indexing Enrichment - Copy Input Plate Barcode to Output Plate (IGA v1.0)

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}"

Library Prep - Indexing Enrichment - Copy Indexing Metadata to Outputs & Set Next Steps to Advance (IGA v1.0)

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}"

Next Step

Setting

Value

Library Prep - Pre-Capture Pooling with Enrichment (IGA v1.0)

  

Start Next Step

Manual

Assign Next Step

Manual

Must Move Forward

  

Master Step 4: Library Prep NFE - Pool Libraries

Step Type = Pooling

Input = Blood, Saliva, or Genomic DNA (gDNA) 96-well batch plates

Output = One 96-well plate of pooled samples

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Pooling

Section

Subsection

Value

Pooling Settings

Label Uniqueness

On

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

 

Defaults

Well Sort Order

Row

 

Placement Pattern

Column
 

Skip Alternating Rows

No
 

Skip Alternating Columns

No
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Sample Count

Numeric

Required Field = No

Read Only = Yes

Default = 0
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = Yes
   

Index Plate Barcode (read from input samples)

Text

Required Field = No

Read Only = Yes
   

Index Plate Offset (read from input samples)

Text

Required Field = No

Read Only = Yes
   

Total Pool Volume (µl)

Numeric

Required Field = No

Read Only = No

Default = 30
   

eBLT

Text

Required Field = No

Read Only = No
   

TB1

Text

Required Field = No

Read Only = No
   

ST2

Text

Required Field = No

Read Only = No
   

TWB

Text

Required Field = No

Read Only = No
   

EPM

Text

Required Field = No

Read Only = No
   

SPB

Text

Required Field = No

Read Only = No
   

RSB

Text

Required Field = No

Read Only = No
   

Adapter

Text

Required Field = Yes

Read Only = Yes

Default = CTGTCTCTTATACACATCT
   

Adapter Read 2

Text

Required Field = Yes

Read Only = No

Default = CTGTCTCTTATACACATCT
 

Multiline Text Fields

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• Run Library Prep Pooling automation.
• Download resulting Liquid Handler Input File.
   

Quick reference checklist: Library Prep IDE - pool libraries. ii) post Liquid Handler

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• After running the Prep method on the Liquid Handler, upload resulting Liquid Handler Output File.
• Select Next Steps.

Step File Placeholders

  

Liquid Handler Input File

File

Auto

 

  

Script Log File (Aggregated)

Log

Auto
   

Liquid Handler Output File

File

Manual

Sample Table

 

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

Sample Needed (µl)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 1
   

Diluent Volume (µl)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 1
   

Number of Samples in Pool

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 0
Automation - Script Description

Automation Name

Setting

Value

Specification

Library prep - Pooling Enrichment - Validate Pool Sizes (IGA v1.0)

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}"

Library Prep - Pooling Enrichment - Sample Placement PCPP Plate Barcode Uniqueness Check (IGA v1.0)

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/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

Library Prep - Pooling Enrichment - Create LH Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Manual Button

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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 µloutput.::Number of Samples in Pool:: ; if (output.::Number of Samples in Pool:: >= 6) {output.::Diluent Volume (uL):: = 0} eµle {output.::Diluent Volume (uL):: = 30.0µl output.::Sample Needed (uL):: } ; ' µl

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/hamilton_fast_prep/templatefiles/LibInputFile_NFE_template_withoffsets.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

Library Prep - Pooling Enrichment - Validate LH Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/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}"

Next Step

Setting

Value

Library Prep - Capture and Wash with Enrichment (IGA v1.0)

  

Start Next Step

Manual

Assign Next Step

Manual

Must Move Forward

  

Master Step 5: Capture and Wash NFE

Step Type = Standard

Input = Blood, Saliva, or Genomic DNA (gDNA) 96-well batch plates

Output = Indexed 96-well plates

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Placement

Setting

Value

Specification

Destination Containers

96 Well Plate

 

Defaults

Sample Grouping

Group by Containers

 

Well Sort Order

Row

 

Placement Pattern

Same Shape
 

Skip Alternating Rows

No
 

Skip Alternating Columns

No
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Pool Count

Numeric

Required Field = No

Read Only = Yes

Default = 0
   

Liquid Handling Instrument ID

Text

Required Field = No

Read Only = Yes
   

EHB2

Text

Required Field = No

Read Only = No
   

Probes

Text

Required Field = No

Read Only = No
   

EEW

Numeric

Required Field = No

Read Only = No
   

EE1

Text

Required Field = No

Read Only = No
   

HP3

Text

Required Field = No

Read Only = No
   

ET2

Text

Required Field = No

Read Only = No
   

EPM

Text

Required Field = No

Read Only = No
   

PPC

Text

Required Field = No

Read Only = No
 

Multiline Text Fields

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• Run Capture and Wash automation.
• Download resulting Liquid Handler Input File.
   

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

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• After running Capture and Wash on the liquid handler, upload resulting Liquid Handler Output File.
• Select Next Steps.

Step File Placeholders

  

Liquid Handler Input File

File

Auto

 

  

Script Log File (Aggregated)

Log

Auto
   

Liquid Handler Output File

File

Manual

Sample Table

 

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

Container Name

    
   

Well

    
   

LIMS ID (Container)

    
   

Project Name

    
Automation - Script Description

Automation Name

Setting

Value

Specification

Capture and Wash Enrichment - Sample Placement LIB Plate Barcode Uniqueness Check & Update Pool Count (IGA v1.0)

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/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \

/usr/bin/env python /opt/gls/clarity/extensions/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Pool Count'"

Capture and Wash Enrichment - Create LH Input File (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Manual Button

  
     

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/hamilton_fast_prep/templatefiles/CaptureWashInputFile_template.csv \

-o Output_plate_name.csv \

-l {compoundOutputFileLuid1}"

Capture and Wash Enrichment - Validate LH Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v1.0)

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/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/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/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}"

Next Step

Setting

Value

Post-Capture Pool QC with Enrichment (IGA v1.0)

  

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

  

Master Step 6: Generic Pool QC NFE

Step Type = Standard QC

Input = Blood, Saliva, or Genomic DNA (gDNA) 96-well captured plates

Output = No Outputs

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Quick reference checklist: Pool QC IDE

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the page:

• After running QC on the pools, upload a QC instrument result 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)

File

Manual

 

  

Script Log File (Aggregated)

Log

Auto

Sample Table

 

Table Heading

Sample Table

  
   

Enable QC Flags

Yes

  
   

Sample Display Default

Expand

  

 

  

Well Sort Order

Row

  
   

File Column Options

File Column Display

Hide
     

File Attachment Method

Auto
 

Table Columns

Sample Name

    
   

Container Name

    
   

Well

    
   

Normalized Molarity (nM)

Numeric
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 2
   

Normalized Molarity (nM)

Numeric
• Global Field = Meaurement
• Required Field = No
• Read Only = No
• Decimal Places Displayed = 2
   

LIMS ID (Container)

    
   

Project Name

    
   

INTERNALFIELD_QCValue_forRouting

Text
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
   

INTERNALFIELD_QCValue_forRouting

Text
• Global Field = Meaurement
• Required Field = No
• Read Only = Yes
Automation - Script Description

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 (IGA v1.0)

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 (IGA v1.0)

Trigger Location

Step

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c "bash /opt/gls/clarity/extensions/iga_workflow_routing/changeWorkflowScript_QCStep_RoutePassedInputs.sh {username} {password} {stepURI} {compoundOutputFileLuid1} /opt/gls/clarity/extensions/iga_workflow_routing/masterRoutingTable_NFEtoSeqPlatSelect.csv 'v1.0'"

Next Step

Setting

Value

Select Sequencing Platform (IGA v1.0)

  

Assign Next Step

Automatic

Safe Stopping Point

  

Protocol 7: Sequencing Platform Selection (IGA v1.0)

Master Step 1: Sequencing Platform Selection

Step Type = No Outputs

Input = Indexed or Pool/Captured 96-well plates

Output = None

Queue/Ice Bucket

Section

Subsection

Value

Sample Table

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

Expanded View Fields
• None

Defaults

Sample Grouping

Group by Containers
 

Well Sort Order

Row
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Sequencing Platform

Text

Required Field = Yes

Read Only = Yes

Default = NovaSeq_IGA

 

Multiline Text Fields

Quick reference checklist: Sequencing Platform Selection

Multiline Text

Required Field = No

Read Only = Yes

Default

User Tasks for the 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

Log

Auto

Sample Table

 

Table Heading

Sample Table

  
   

Enable QC Flags

No

  
   

Sample Display Default

Collapse

  

 

  

Well Sort Order

Row

  
 

Table Columns

Sample Name

    
   

Container Name

    
   

Well

    
   

LIMS ID (Container)

    
   

Project Name

    
   

Sequencing Platform

Text
• Global Field = Derived Sample
• Required Field = No
• Read Only = No
Automation - Script Description

Automation Name

Setting

Value

Specification

Sequencing Platform Selection - Copy Instrument Type to Analyte & Set Next Steps to Remove from Workflow (IGA v1.0)

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 (IGA v1.0)

Trigger Location

Step

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

Next Step

Setting

Value

Define Run Format (IGA v1.0)

  

Assign Next Step

Automatic

Safe Stopping Point