IGA Library Prep Automated v2.1

Overview

IGA Library Prep Automated v2.1 contains preset protocols that support the preparation of samples and libraries used for sequencing. These protocols can be used with the IGA NovaSeq Sequencing v2.1 workflow and NextSeq 1000/2000 v2.3 workflow (which is installed separately). The protocols provide the following functions:

File-based integration with the Hamilton robots that are used for liquid handling steps.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents.
When required, automatic step transition.

Protocol 1: Sample Selection

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Samples

Master Step Name = Select Samples (IGA v2.1)
Step Type = No Outputs

Automations

Validate Sample Attributes (IGA v2.1)

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -t false -h false script:evaluateDynamicExpression \
-exp 'if (! submittedSample.hasValue(::Sample Type::)) { \
    fail(::Sample Type must be non-empty. Please update :: + submittedSample.::name::); \
}; \
acceptedSampleTypes = [::Genomic DNA::, ::Saliva::, ::Blood::]; \
if (! acceptedSampleTypes.contains(submittedSample.::Sample Type::)) { \
  fail(::Invalid Sample Type found for :: + submittedSample.::name:: + ::. Must be one of :: + acceptedSampleTypes.join(::, ::)); \
}; \
if (! submittedSample.hasValue(::Submitted Sample Labware Type::)) { \
    fail(::Submitted Sample Labware Type must be non-empty. Please update :: + submittedSample.::name::); \
}; \
acceptedSampleLabwareTypes = [::gDNA::, ::Saliva::, ::Blood1.3::, ::Blood2.7::, ::Blood7.5::, ::Blood10::]; \
if (! acceptedSampleLabwareTypes.contains(submittedSample.::Submitted Sample Labware Type::)) { \
  fail(::Invalid Submitted Sample Labware Type found for :: + submittedSample.::name:: + ::. Must be one of :: + acceptedSampleLabwareTypes.join(::, ::)); \
}; \
if (! submittedSample.hasValue(::Units::)) { \
    fail(::Units must be non-empty. Please update :: + submittedSample.::name::); \
}; \
if (submittedSample.::Sample Type:: == ::Genomic DNA:: && ! submittedSample.hasValue(::Sample Conc.::)) { \
    fail(::Sample Conc. must be non-empty for Genomic DNA samples. Please update :: + submittedSample.::name::); \
};' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/register_sample.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Sample Selection - Set Library prep method and Next steps (IGA v2.1)

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'submittedSample.::Library Prep Method:: = step.::Library Prep Method::' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (submittedSample.::Sample Type:: == ::Genomic DNA:: && input.container.node.type[0].@name == ::96 well plate::) {nextStep = ::REMOVE::} else nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"

Sample Selection - Route plated gDNA (IGA v2.1)

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (submittedSample.::Sample Type:: == ::Genomic DNA::) {if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA PCR-Free:: ) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::} ; if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA with Enrichment::) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment::}}' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
  Project
  Project Name
  Built-in
  Submitted Sample
  Illumina Universal Sample Identifier
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Submitted Sample
  Sample Conc.
  Numeric
  Decimal Places Displayed = 2
  Submitted Sample
  Units
  Text

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
IGA WF Build Version
Text
Read Only
Default = 2.1.0.1
Library Prep Method
Text Dropdown
Required Field
Presets
Illumina DNA PCR-Free
Illumina DNA with Enrichment
Quick reference checklist: Sample Selection
Multiline Text
Read Only
Defaults = User tasks for this page: - Select Library Prep Method above - Select Next Steps
Step File Placeholders
- Set Library Prep Method Script Log - Automatically attached
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Sample Name
Built-in
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Conc.
Numeric
Decimal Places Displayed = 2
Submitted Sample
Submitted Sample Type
Text
Read Only
Submitted Sample
Units
Text

Protocol 2: Sample Plating

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Plate Samples

Master Step Name = Sample Plating (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Variable
Naming Convention = {InputItemlName}

Automations

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

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!step.hasValue(::Step Sample Type::)) {step.::Step Sample Type:: = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]::} else {if ( step.::Step Sample Type:: != submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ) { fail(::Samples must be of the same type and marked for same library prep method::) }}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Placement Reminder (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"

Sample Plating - Sample Placement SAM Plate Barcode Uniqueness Check (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-SAM:: ) ) {fail ( ::Invalid SAM Plate Barcode format. This plate ID must be in the format LPxxxxxxx-SAM, where 'x' is a digit 0-9, e.g. LP1234567-SAM. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

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

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Sample Type:: == ::Blood::) {output.::Transfer Volume (ul):: = 30} ;  if (submittedSample.::Sample Type:: == ::Saliva::) {output.::Transfer Volume (ul):: = 60}; if (submittedSample.::Sample Type:: == ::Genomic DNA::) {output.::Transfer Volume (ul):: = 45}' \
-log {compoundOutputFileLuid1} &&
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/PlatingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Sample Plating - Route samples (IGA v2.1)

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Blood (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Saliva (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Blood (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Extraction - Saliva (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

Defaults
- Sample Grouping = Group by Projects
- Well Sort Order = Column
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Derived Sample
  Waiting
  Built-in
  Submitted Sample
  Library Prep Method
  Text
  Submitted Sample
  Sample Type
  Text
  Submitted Sample
  Sequencing Method
  Text Dropdown
  Custom Entries
  Presets
  Single Read
  Paired End Read
  Indexed Single Read
  Indexed Paired End Read
  Submitted Sample
  Submitted Sample Name
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Submitted Sample
  Date Submitted
  Built-in
  Submitted Sample
  Sample Category
  Text

Ice Bucket

Defaults
- Sample Grouping = Group by Projects
- Well Sort Order = Column
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Type
Text
Submitted Sample
Sequencing Method
Text Dropdown
Custom Entries
Presets
Single Read
Paired End Read
Indexed Single Read
Indexed Paired End Read
Submitted Sample
Submitted Sample Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Projects
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Liquid Handling Instrument ID
Text
Read Only
Quick reference checklist: Sample Plating. i) pre Liquid Handler
Multiline Text
Read Only
Defaults = User tasks for this page: - Select blue 'Run' button - Download Liquid Handler Input File
Quick reference checklist: Sample Plating. ii) post Liquid Handler
Multiline Text
Read Only
Defaults = User tasks continued: - Upload resulting Liquid Handler Output File - Select Next Steps
Step Sample Type
Text
Read Only
Step File Placeholders
- Liquid Handler Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Liquid Handler Output File - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Submitted Sample Type
Text
Read Only
Derived Sample
Transfer Volume (ul)
Numeric
Submitted Sample
Sample Type
Text
Submitted Sample
Submitted Sample Labware Type
Text

Protocol 3: Blood Extraction

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Extraction - Blood

Master Step Name = DNA Extraction - Blood (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

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

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!step.hasValue(::Step Sample Type::)) {step.::Step Sample Type:: = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]::} else {if ( step.::Step Sample Type:: != submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ) { fail(::Samples must be of the same type and marked for same library prep method::) }}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-EDP:: ) ) {fail ( ::Update: Invalid EDP (Extracted DNA Plate) barcode format. This plate ID must be in the format LPxxxxxxx-EDP, where 'x' is a digit 0-9, e.g. LP1234567-EDP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i  'Liquid Handling Instrument ID' \
&& \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \
-log {compoundOutputFileLuid1}"

Extraction - Routing (IGA v2.1)

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) { output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Waiting
Built-in
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Type
Text
Submitted Sample
Sequencing Method
Text Dropdown
Custom Entries
Presets
Single Read
Paired End Read
Indexed Single Read
Indexed Paired End Read
Submitted Sample
Submitted Sample Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Type
Text
Submitted Sample
Submitted Sample Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Ethanol
Text
ITB
Text
Liquid Handling Instrument ID
Text
Read Only
MLB
Text
ProK
Text
RSB
Text
Sample Count
Numeric
Read Only
Default = 0
Step Sample Type
Text
Read Only
Quick reference checklist: DNA Extraction - Blood. i) pre Liquid Handler
Multiline Text
Read Only
Default = User tasks for this page: - Download Liquid Handling Robot Input File - Enter reagent lots for MLB and ProK (not scanned by Liquid Handler as loaded as a mastermix)
Quick reference checklist: DNA Extraction - Blood. ii) post Liquid Handler
Multiline Text
Read Only
Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
Step File Placeholders
- Liquid Handling Robot (Hamilton) Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Liquid Handling Robot Output File - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container
Built-in
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Submitted Sample Type
Text
Read Only
Project
Project Name
Built-in
Submitted Sample
Library Prep Method
Text

Protocol 4: Saliva Extraction

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Extraction - Saliva

Master Step Name = DNA Extraction - Blood (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

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

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!step.hasValue(::Step Sample Type::)) {step.::Step Sample Type:: = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]::} else {if ( step.::Step Sample Type:: != submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ) { fail(::Samples must be of the same type and marked for same library prep method::) }}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-EDP:: ) ) {fail ( ::Update: Invalid EDP (Extracted DNA Plate) barcode format. This plate ID must be in the format LPxxxxxxx-EDP, where 'x' is a digit 0-9, e.g. LP1234567-EDP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i  'Liquid Handling Instrument ID' \
&& \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \
-log {compoundOutputFileLuid1}"

Extraction - Routing (IGA v2.1)

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) { output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Waiting
Built-in
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Type
Text
Submitted Sample
Sequencing Method
Text Dropdown
Custom Entries
Presets
Single Read
Paired End Read
Indexed Single Read
Indexed Paired End Read
Submitted Sample
Submitted Sample Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Type
Text
Submitted Sample
Submitted Sample Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Ethanol
Text
ITB
Text
Liquid Handling Instrument ID
Text
Read Only
MLB
Text
ProK
Text
RSB
Text
Sample Count
Numeric
Read Only
Default = 0
Step Sample Type
Text
Read Only
Quick reference checklist: DNA Extraction - Saliva. i) pre Liquid Handler
Multiline Text
Read Only
Default = User tasks for this page: - Download Liquid Handling Robot Input File - Enter reagent lots for MLB and ProK (not scanned by Liquid Handler as loaded as a mastermix)
Quick reference checklist: DNA Extraction - Saliva. ii) post Liquid Handler
Multiline Text
Read Only
Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
Step File Placeholders
- Liquid Handling Robot (Hamilton) Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Liquid Handling Robot Output File - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container
Built-in
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Submitted Sample Type
Text
Read Only
Project
Project Name
Built-in
Submitted Sample
Library Prep Method
Text

Protocol 5: Illumina DNA PCR-Free

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Batching PCR-Free

Master Step Name = DNA Batching NFPF (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}_DNA

Automations

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

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Sample Type:: == ::Genomic DNA::) {step.::Batching Well Volume (uL):: = 40} ; if (submittedSample.::Sample Type:: == ::Blood::) {step.::Batching Well Volume (uL):: = 40} ; if (submittedSample.::Sample Type:: == ::Saliva::) {step.::Batching Well Volume (uL):: = 40}' \
-log {compoundOutputFileLuid1} \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} \
-p {password} script:evaluateDynamicExpression \
-t false -h false -exp \
'String matchTargetGDNA = ::genomic dna:: ; \
String submittedSampleType = submittedSample.::Sample Type:: + :: [:: + submittedSample.::Library Prep Method:: + ::] | :: ; \
if (!step.hasValue(::Step Sample Type::)) { \
    step.::Step Sample Type:: = submittedSampleType; \
} else { \
    String stepType = step.::Step Sample Type:: ; \
    String smpType = submittedSampleType.toLowerCase(); \
    stepType = stepType.toLowerCase(); \
    if ( (stepType.contains(matchTargetGDNA) && !smpType.contains(matchTargetGDNA)) || (!stepType.contains(matchTargetGDNA) && smpType.contains(matchTargetGDNA)) ) { \
        fail(::Genomic DNA samples can only be plated together and not combined with any other sample type!::); \
    }; \
    if ( (stepType.contains(::blood::) && smpType.contains(::saliva::)) || (stepType.contains(::saliva::) && smpType.contains(::blood::)) ) { \
        step.::Step Sample Type:: = ::Blood + Saliva:: + :: [:: + submittedSample.::Library Prep Method:: + ::]:: ; \
    }; \
}' \
 -log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Placement Reminder (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

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

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Warnings:: = :::: ; if ( submittedSample.hasValue (::Sample Conc.::) ) {        output.::Sample Needed (uL):: = (step.::DNA (ng) required for tagmentation:: * step.::Batching Well Volume (uL)::) / (25 * submittedSample.::Sample Conc.::) ; \
if ( output.::Sample Needed (uL):: > step.::Batching Well Volume (uL):: ) { output.::Sample Needed (uL):: =
 step.::Batching Well Volume (uL):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (uL):: < 2.0 )
{ output.::Sample Needed (uL):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (uL):: =
step.::Batching Well Volume (uL):: - output.::Sample Needed (uL):: ; output.::Initial Input DNA (ng)::  = output.::Sample Needed (uL):: * submittedSample.::Sample Conc.::} \
else \
{output.::Sample Needed (uL):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (uL):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (uL):: = step.::Batching Well Volume (uL)::; output.::Diluent Volume (uL):: = 0 }' \
-log {compoundOutputFileLuid1} &&
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Type
Text

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batching Well Volume (uL)
Numeric
Required Field
Default = 40
DNA (ng) required for tagmentation
Numeric
Required Field
Default = 350
Liquid Handling Instrument ID
Text
Read Only
Notes:
Multiline Text
Read Only
Default = - DNA (ng) required for tagmentation is 300-2000 ng. - A fixed 25uL is aliquoted from the total volume of 40uL (default) to carry out Library Prep and subsequent steps.
Quick reference checklist: DNA Batching IDPF. i) pre Liquid Handler
Multiline Text
Read Only
Default = User tasks for this page: - For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred - 'Run' DNA Batching PF automation, and download resulting 'Liquid Handler Batching Input File'
Quick reference checklist: DNA Batching IDPF. ii) post Liquid Handler
Multiline Text
Read Only
Default = User tasks continued: - Upload resulting 'Output File from Liquid Handler' - Select 'Next Steps'
Step File Placeholders
- Liquid Handler Batching Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Output File from Liquid Handler - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Diluent Volume (uL)
Numeric
Decimal Places Displayed = 1
Derived Sample
Initial Input DNA (ng)
Numeric
Derived Sample
Sample Name
Built-in
Derived Sample
Sample Needed (uL)
Numeric
Decimal Places Displayed = 1
Derived Sample
Warnings
Text
Read Only
Project
Project Name
Built-in

Step 2: Index Planning PCR-Free

Master Step Name = Indexing Planning (IGA v2.1)
Step Type = No Outputs

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::Hamilton Indexing Offset Column::)) + 8) < step.node.::input-output-maps::.::input-output-map::.input.size()) { fail(::The column offset will not yield enough indexes for the number of samples! Please increase the number of available indexes by changing the offset.::) }' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if ( !step.::Index Plate Barcode::.matches( ::[0-9]{8}-[A-Z]+[A-D]{1}$:: ) ) {fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format xxxxxxxx-S*(A/B/C/D), where 'x' is a digit 0-9 and 'S' is a sequence of uppercase letters, followed by 'A', 'B', 'C', or 'D'; e.g. 12345678-NXTA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning (IGA v2.1)' && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'input.::INTERNALFIELD_IndexPlanning_Metadata:: = step.::Index Plate Barcode:: + ::_:: + (int) step.::Hamilton Indexing Offset Column::' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::'   -log {compoundOutputFileLuid0}"

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Index Plate Barcode
Text
Required Field
Hamilton Indexing Offset Column
Numeric
Default = 1
Range From 1 to 12
Quick reference checklist: Indexing Planning
Multiline Text
Read Only
Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column) - Click 'Next Steps'
Step File Placeholders
- Script Log File (Aggregated) - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
INTERNALFIELD_QCValue_forRouting
Text
Derived Sample
Sample Name
Built-in
Project
Project Name
Built-in

Step 3: Library Prep - Indexing PCR-Free

Master Step Name = Indexing NFPF (IGA v2.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

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

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory.py -u {username} -p {password} -s {stepURI} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

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

Trigger Location = Add Labels
Trigger Style = Automatic upon entry

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

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

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'if ( !step.hasValue(::Library Plate Barcode::) || !step.::Library Plate Barcode::.matches( ::LP[0-9]{7}-LIB:: ) ) { fail( ::Invalid LIB plate barcode format. This plate ID must be in the format LPxxxxxxx-LIB, where 'x' is a digit 0-9, e.g. LP1234567-LIB. Please scan a valid LIB plate barcode in the Record Details screen.:: ) }; output.container.name = step.::Library Plate Barcode::; tkns = input.::INTERNALFIELD_IndexPlanning_Metadata::.split(::_::); step.::Index Plate Barcode (read from input samples):: = tkns[0]; step.::Index Plate Offset (read from input samples):: = tkns[1]; if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) { output.::Normalized Molarity (nM):: = 3.5; }' \
-log {compoundOutputFileLuid1} \
&& /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/LibInputFile_NFPF_template_withoffsets.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/reagent_parsing/fieldmap_libprep.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid1} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'WARNING' --message 'This protocol recommends performing a pooled quant. (per prep) at this stage. Please quant. and update the Normalized Molarity (nM) across all samples in the table below before proceeding.'"

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

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Well
Built-in
Derived Sample
INTERNALFIELD_IndexPlanning_Metadata
Text
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Well
Built-in
Derived Sample
INTERNALFIELD_IndexPlanning_Metadata
Text
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Add Labels

Label Groups
- Nextera UDP A
- Nextera UDP B
- Nextera UDP C
- Nextera UDP D

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Adapter
Text
Required Field
Read Only
Default = CTGTCTCTTATACACATCT
Adapter Read 2
Text
Required Field
Read Only
Default = CTGTCTCTTATACACATCT
BLT-PF
Text
ELM-T
Text
HP3
Text
Index Plate Barcode (read from input samples)
Text
Read Only
Index Plate Offset (read from input samples)
Text
Read Only
IPB
Text
Library Plate Barcode
Text
Required Field
Liquid Handling Instrument ID
Text
Read Only
Quick reference checklist: Library Prep IDPF. i) pre Liquid Handler
Multiline Text
Read Only
Default = User tasks for this page: - Above, scan in the 'Library Plate Barcode' to be used - Click blue button to 'Run' the Library Prep automation, and download the resulting 'Liquid Handler Input File'
Quick reference checklist: Library Prep IDPF. ii) post Liquid Handler
Multiline Text
Read Only
Default = User tasks continued: - Upload resulting 'Hamilton Output File' - Perform a pooled quant for the prep, and apply the yield 'Normalized Molarity (nM)' to all samples - Click 'Next Steps'
RSB
Text
Sample Count
Numeric
Read Only
Default = 0
Decimal Places Displayed = 0
ST2
Text
TB1
Text
TWB
Text
Step File Placeholders
- Liquid Handler Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Hamilton Output File - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container
Built-in
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Normalized Molarity (nM)
Numeric
Decimal Places Displayed = 2
Derived Sample
Sample Name
Built-in
Submitted Sample
Library Prep Method
Text

Protocol 6: Illumina DNA with Enrichment

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Batching with Enrichment

Master Step Name = DNA Batching NFE (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}_DNA

Automations

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

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Batching Well Volume (uL):: = 45' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Placement Reminder (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"

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

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Warnings:: = :::: ; if ( submittedSample.hasValue (::Sample Conc.::) ) {output.::Sample Needed (uL):: = (step.::DNA (ng) required for tagmentation:: * step.::Batching Well Volume (uL)::) / (30 * submittedSample.::Sample Conc.::) ; \
if ( output.::Sample Needed (uL):: > step.::Batching Well Volume (uL):: ) { output.::Sample Needed (uL):: =
 step.::Batching Well Volume (uL):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (uL):: < 2.0 )
{ output.::Sample Needed (uL):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (uL):: =
step.::Batching Well Volume (uL):: - output.::Sample Needed (uL):: ; output.::Initial Input DNA (ng)::  = output.::Sample Needed (uL):: * submittedSample.::Sample Conc.::} \
else \
{output.::Sample Needed (uL):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (uL):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (uL):: = step.::Batching Well Volume (uL)::; output.::Diluent Volume (uL):: = 0 }' \
-log {compoundOutputFileLuid1} &&
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batching Well Volume (uL)
Numeric
Required Field
Default = 45
DNA (ng) required for tagmentation
Numeric
Required Field
Default = 450
Liquid Handling Instrument ID
Text
Read Only
Notes:
Multiline Text
Read Only
Default = - DNA (ng) required for tagmentation is 50-1000 ng. - A fixed 30uL is aliquoted from the total volume of 45uL (default) to carry out Library Prep and subsequent steps.
Quick reference checklist i): DNA Batching IDE, pre Liquid Handler
Multiline Text
Read Only
Default = User tasks for this page: - For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred - 'Run' DNA Batching Enrichment automation, and download resulting 'Liquid Handler Batching Input File'
Quick reference checklist ii): DNA Batching IDE, post Liquid Handler
Multiline Text
Read Only
Default = User tasks continued: - Upload resulting 'Output File from Liquid Handler' - Select 'Next Steps'
Step File Placeholders
- Liquid Handler Batching Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Output File from Liquid Handler - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Diluent Volume (uL)
Numeric
Decimal Places Displayed = 1
Derived Sample
Initial Input DNA (ng)
Numeric
Derived Sample
Sample Name
Built-in
Derived Sample
Sample Needed (uL)
Numeric
Decimal Places Displayed = 1
Derived Sample
Warnings
Text
Read Only
Project
Project Name
Built-in

Step 2: Index Planning with Enrichment

Master Step Name = Indexing Planning (IGA v2.1)
Step Type = No Outputs

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::Hamilton Indexing Offset Column::)) + 8) < step.node.::input-output-maps::.::input-output-map::.input.size()) { fail(::The column offset will not yield enough indexes for the number of samples! Please increase the number of available indexes by changing the offset.::) }' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if ( !step.::Index Plate Barcode::.matches( ::[0-9]{8}-[A-Z]+[A-D]{1}$:: ) ) {fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format xxxxxxxx-S*(A/B/C/D), where 'x' is a digit 0-9 and 'S' is a sequence of uppercase letters, followed by 'A', 'B', 'C', or 'D'; e.g. 12345678-NXTA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning (IGA v2.1)' && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'input.::INTERNALFIELD_IndexPlanning_Metadata:: = step.::Index Plate Barcode:: + ::_:: + (int) step.::Hamilton Indexing Offset Column::' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::'   -log {compoundOutputFileLuid0}"

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Index Plate Barcode
Text
Required Field
Hamilton Indexing Offset Column
Numeric
Default = 1
Range From 1 to 12
Quick reference checklist: Indexing Planning
Multiline Text
Read Only
Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column) - Click 'Next Steps'
Step File Placeholders
- Script Log File (Aggregated) - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Sample Name
Built-in
Derived Sample
INTERNALFIELD_IndexPlanning_Metadata
Text

Step 3: Library Prep - Indexing with Enrichment

Master Step Name = Indexing NFE (IGA v2.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

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

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory.py -u {username} -p {password} -s {stepURI} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

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

Trigger Location = Add Labels
Trigger Style = Automatic upon entry

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

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

Trigger Location = Add Labels
Trigger Style = Automatic upon exit

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

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'tkns = input.::INTERNALFIELD_IndexPlanning_Metadata::.split(::_::); step.::Index Plate Barcode (read from input samples):: = tkns[0]; step.::Index Plate Offset (read from input samples):: = tkns[1]; output.::INTERNALFIELD_IndexPlanning_Metadata:: = input.::INTERNALFIELD_IndexPlanning_Metadata:: ; nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Add Labels

Label Groups
- Nextera UDP A
- Nextera UDP B
- Nextera UDP C
- Nextera UDP D

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Index Plate Barcode (read from input samples)
Text
Read Only
Index Plate Offset (read from input samples)
Text
Read Only
Quick reference checklist: Library Prep IDE.
Multiline Text
Read Only
Default = User tasks for this step: - No user tasks, click 'Next Steps'
Step File Placeholders
- Script Log File (Aggregated) - Automatically attached
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Sample Name
Built-in
Derived Sample
INTERNALFIELD_IndexPlanning_Metadata
Text

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

Master Step Name = Library Prep NFE - Pool Libraries (IGA v2.1)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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

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

Trigger Location = Pooling
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!output.hasValue(::Number of Samples in Pool::)) { output.::Number of Samples in Pool:: = 0; }; output.::Number of Samples in Pool::++; if (output.::Number of Samples in Pool:: > 12) { fail(::Pools cannot contain more than 12 samples each.::) }' \
-log {compoundOutputFileLuid1}"

Library Prep - Pooling Enrichment - Sample Placement PCPP Plate Barcode Uniqueness Check (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-PCPP:: ) ) {fail ( ::Invalid PCPP (Pre-Capture Pool Plate) barcode format. This plate ID must be in the format LPxxxxxxx-PCPP, where 'x' is a digit 0-9, e.g. LP1234567-PCPP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"

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

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/countSamplesInPools.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'tkns = input.::INTERNALFIELD_IndexPlanning_Metadata::.split(::_::); step.::Index Plate Barcode (read from input samples):: = tkns[0]; step.::Index Plate Offset (read from input samples):: = tkns[1]; ' \
-log {compoundOutputFileLuid1} \ && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'output.::Sample Needed (uL):: = 5.0 * output.::Number of Samples in Pool:: ; if (output.::Number of Samples in Pool:: >= 6) {output.::Diluent Volume (uL):: = 0} else {output.::Diluent Volume (uL):: = 30.0 - output.::Sample Needed (uL):: } ; ' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/LibInputFile_NFE_template_withoffsets.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/reagent_parsing/fieldmap_precap_pooling.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Pooling

Label Uniqueness = On
Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Placement = Enabled

Defaults
- Well Sort Order = Row
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Adapter
Text
Required Field
Read Only
Default = CTGTCTCTTATACACATCT
Adapter Read 2
Text
Required Field
Read Only
Default = CTGTCTCTTATACACATCT
eBLT
Text
EPM
Text
Index Plate Barcode (read from input samples)
Text
Read Only
Index Plate Offset (read from input samples)
Text
Read Only
Liquid Handling Instrument ID
Text
Read Only
Quick reference checklist: Library Prep IDE - pool libraries. i) pre Liquid Handler.
Multiline Text
Read Only
Default = User tasks for this page: - 'Run' Library Prep Pooling automation - Download resulting Liquid Handler Input File
Quick reference checklist: Library Prep IDE - pool libraries. ii) post Liquid Handler.
Multiline Text
Read Only
Default = User tasks continued: - After running the Prep method on the Liquid Handler, upload resulting Liquid Handler Output File - Click on 'Next Steps'
RSB
Text
Sample Count
Numeric
Read Only
Default = 0
SPB
Text
ST2
Text
TB1
Text
Total Pool Volume (ul)
Numeric
Default = 30
TWB
Text
Step File Placeholders
- Liquid Handler Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Liquid Handler Output File - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Diluent Volume (uL)
Numeric
Decimal Places Displayed = 1
Derived Sample
Number of Samples in Pool
Numeric
Default = 0
Derived Sample
Sample Name
Built-in
Derived Sample
Sample Needed (uL)
Numeric
Decimal Places Displayed = 1

Step 5: Library Prep - Capture and Wash with Enrichment

Master Step Name = Capture and Wash NFE (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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

Capture and Wash Enrichment - Sample Placement LIB Plate Barcode Uniqueness Check & Update Pool Count (IGA v2.1)

Trigger Location = Placement
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-LIB:: ) ) {fail ( ::Invalid LIB plate barcode format. This plate ID must be in the format LPxxxxxxx-LIB, where 'x' is a digit 0-9, e.g. LP1234567-LIB. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Pool Count'"

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

Trigger Location = Record Details
Trigger Style = Manual button

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

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'Liquid Handling Instrument ID' && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/reagent_parsing/fieldmap_captureandwash.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Same Shape
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
EE1
Text
EEW
Text
EHB2
Text
EPM
Text
ET2
Text
HP3
Text
Liquid Handling Instrument ID
Text
Read Only
Pool Count
Numeric
Read Only
Default = 0
PPC
Text
Probes
Text
Quick reference checklist: Capture and Wash IDE. i) pre Liquid Handler.
Multiline Text
Read Only
Default = User tasks for this page: - 'Run' Capture and Wash automation - Download resulting Liquid Handler Input File
Quick reference checklist: Capture and Wash IDE. ii) post Liquid Handler.
Multiline Text
Read Only
Default = User tasks continued: - After running Capture and Wash on the liquid handler, upload resulting Liquid Handler Output File - Click 'Next Steps'
Step File Placeholders
- Liquid Handler Input File - Automatically attached
- Script Log File (Aggregated) - Automatically attached
- Liquid Handler Output File - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Project
Project Name
Built-in

Step 6: Post-Capture Pool QC with Enrichment

Master Step Name = Generic Pool QC NFE (IGA v2.1)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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

Pool QC - Generic - Enrichment - Copy Normalized Molarity from Output to Input, Copy QC Value to Inputs & Set QC Passed Sample Next Steps to Remove from Workflow (IGA v2.1)

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Pool QC - Generic - Enrichment - Route QC Passed Samples to Sequencing Platform Selection (IGA v2.1)

Trigger Location = Step
Trigger Style = Automatic upon exit

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

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Quick reference checklist: Pool QC IDE.
Multiline Text
Read Only
Default = User tasks for this page: - 'Run' Capture and Wash automation - Download resulting Liquid Handler Input File
Step File Placeholders
- QC Instrument Results (Generic Placeholder) - Manually uploaded
- Script Log File (Aggregated) - Automatically attached
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Row
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Normalized Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  INTERNALFIELD_QCValue_forRouting
  Text
  Measurement
  Normalized Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Measurement
  INTERNALFIELD_QCValue_forRouting
  Text
  Read Only
  Project
  Project Name
  Built-in

Protocol 7: Sequencing Platform Selection

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Sequencing Platform

Master Step Name = Sequencing Platform Selection (IGA v2.1)
Step Type = No Outputs

Automations

Trigger Location = Step
Trigger Style = Automatic upon entry

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

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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

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

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -l -c "bash /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/changeWorkflowScript_SeqPlatform_RouteInputs.sh {username} {password} {stepURI} {compoundOutputFileLuid0} /opt/gls/clarity/extensions/IGA_2.1/iga_workflow_routing/masterRoutingTable_seqplatselection.csv \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Sequencing Platform
Text Dropdown
Required Field
Presets
NovaSeq_IGA
NextSeq 1000/2000 v2.3
Default = NovaSeq_IGA
Quick reference checklist: Sequencing Platform Selection
Multiline Text
Read Only
Default = User tasks for this page: - No actions for this page! The step serves to route all samples to the NovaSeq workflow
Step File Placeholders
- Set Sequencing Platform Script Log - Automatically attached
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Sequencing Platform
Text
Project
Project Name
Built-in