# IGA Library Prep Automated v3.0
## Overview
IGA Library Prep Automated v3.0 contains preset protocols that support the preparation of samples and libraries used for sequencing. These protocols can be used with the NovaSeq X Series Sequencing v2.0 workflow (which is installed separately). The protocols provide the following functions:
* File-based integration with the Hamilton robots that are used for liquid handling steps.
* Automated calculation of sample and buffer volumes.
* Automated calculation or display of reagents.
* When required, automatic step transition.
## Protocol 1: Sample Selection (IGA v3.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
* Step(s):
* 1: Select Samples (IGA v3.0)
* Assign Next Step = Automatic
### Step 1: Select Samples (IGA v3.0)
* Master Step Name = Sample Selection (IGA v3.0)
* Step Type = No Outputs
{% hint style="info" %}
The version of Sample Selection (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Validate Sample Attributes (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Sample Selection - Set Library prep method and Next steps (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Sample Selection - Route plated gDNA (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (submittedSample.::Sample Type:: == ::Genomic DNA::) {if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA PCR-Free:: ) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::} ; if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA with Enrichment::) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment::}}' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------------------- | -------------- | -------------- | ---------------------------------------------------------------------------------------------------------- |
| IGA WF Build Version | Text | Read Only | Default = 3.0.0.5-SNAPSHOT |
| Library Prep Method | Text Dropdown | Required Field |
Presets
Illumina DNA PCR-Free
Illumina DNA with Enrichment
|
| Quick reference checklist: Sample Selection | Multiline Text | Read Only |
Default = User tasks for this page: - Select Library Prep Method above - Select Next Steps
|
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | Sample Name | Built-in | | |
## Protocol 2: Sample Plating (IGA v3.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
* Step(s):
* 1: Plate Samples (IGA v3.0)
* Assign Next Step = Automatic
### Step 1: Plate Samples (IGA v3.0)
* Master Step Name = Sample Plating (IGA v3.0)
* Step Type = Standard
* Derived Sample Generation = Variable, 3
* Naming Convention = {InputItemName}
{% hint style="info" %}
The version of Sample Plating (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Placement Reminder (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"
```
{% endcode %}
Sample Plating - Sample Placement SAM Plate Barcode Uniqueness Check (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-SAM:: ) ) {fail ( ::Invalid SAM Plate Barcode format. This plate ID must be in the format LPxxxxxxx-SAM, where 'x' is a digit 0-9, e.g. LP1234567-SAM. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"
```
{% endcode %}
Sample Plating - Set Transfer Volume & Create LHR Input File (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Manual button
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Sample Type:: == ::Blood::) {output.::Transfer Volume (ul):: = 30} ; if (submittedSample.::Sample Type:: == ::Saliva::) {output.::Transfer Volume (ul):: = 60}; if (submittedSample.::Sample Type:: == ::Genomic DNA::) {output.::Transfer Volume (ul):: = 45}' \
-log {compoundOutputFileLuid1} &&
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/PlatingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"
```
{% endcode %}
Sample Plating - LHR Output Plate Barcode Check, Store Instrument ID & Set Next Steps to Remove from Workflow before Custom Routing (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::REMOVE:: ' \
-log {compoundOutputFileLuid1}"
```
{% endcode %}
Sample Plating - Route samples (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Blood (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Saliva (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Blood (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Extraction - Saliva (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
#### Queue
* Defaults
* Sample Grouping = Group by Projects
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | Waiting | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Projects
* Well Sort Order = Column
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Projects
* Well Sort Order = Column
* Placement Pattern = Column
* Destination Containers
* 96 well plate
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------------------------------- | -------------- | ----------- | -------------------------------------------------------------------------------------------------------- |
| LHR Instrument ID | Text | Read Only | |
| Quick reference checklist: Sample Plating. i) pre LHR | Multiline Text | Read Only |
Default = User tasks for this page: - Select blue 'Run' button - Download LHR Input File
|
| Quick reference checklist: Sample Plating. ii) post LHR | Multiline Text | Read Only |
Default = User tasks continued: - Upload resulting LHR Output File - Select Next Steps
|
| Step Sample Type | Text | Read Only | |
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Submitted Sample Type | Text | Read Only | |
| Derived Sample | Transfer Volume (ul) | Numeric | | |
## Protocol 3: Blood Extraction (IGA v3.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
* Step(s):
* 1: DNA Extraction - Blood (IGA v3.0)
* Assign Next Step = Automatic
### Step 1: DNA Extraction - Blood (IGA v3.0)
* Master Step Name = DNA Extraction - Blood (IGA v3.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
{% hint style="info" %}
The version of DNA Extraction - Blood (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-EDP:: ) ) {fail ( ::Update: Invalid EDP (Extracted DNA Plate) barcode format. This plate ID must be in the format LPxxxxxxx-EDP, where 'x' is a digit 0-9, e.g. LP1234567-EDP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"
```
{% endcode %}
Extraction - Count Samples & Create LHR Input File (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"
```
{% endcode %}
Extraction - Check LHR Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' \
&& \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \
-log {compoundOutputFileLuid1}"
```
{% endcode %}
Extraction - Routing (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) { output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | Waiting | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Placement Pattern = Column
* Destination Containers
* 96 well plate
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| --------------------------------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Ethanol | Text | | |
| ITB | Text | | |
| LHR Instrument ID | Text | Read Only | |
| MLB | Text | | |
| ProK | Text | | |
| Quick reference checklist: DNA Extraction - Blood. i) pre LHR | Multiline Text | Read Only |
Default = User tasks for this page: - Download LHR Input File - Enter reagent lots for MLB and ProK (not scanned by LHR as loaded as a mastermix)
|
| Quick reference checklist: DNA Extraction - Blood. ii) post LHR | Multiline Text | Read Only |
Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting LHR Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
|
| RSB | Text | | |
| Sample Count | Numeric | Read Only | Default = 0 |
| Step Sample Type | Text | Read Only | |
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container | Built-in | | |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Submitted Sample Type | Text | Read Only | |
| Project | Project Name | Built-in | | |
## Protocol 4: Saliva Extraction (IGA v3.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
* Step(s):
* 1: DNA Extraction - Saliva (IGA v3.0)
* Assign Next Step = Automatic
### Step 1: DNA Extraction - Saliva (IGA v3.0)
* Master Step Name = DNA Extraction - Saliva (IGA v3.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
{% hint style="info" %}
The version of DNA Extraction - Saliva (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-EDP:: ) ) {fail ( ::Update: Invalid EDP (Extracted DNA Plate) barcode format. This plate ID must be in the format LPxxxxxxx-EDP, where 'x' is a digit 0-9, e.g. LP1234567-EDP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"
```
{% endcode %}
Extraction - Count Samples & Create LHR Input File (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Sample Count' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/ExtractionInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"
```
{% endcode %}
Extraction - Check LHR Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' \
&& \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_extraction.csv \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp ' if (!step.hasValue (::MLB::) || !step.hasValue(::ProK::)) { fail(::Please scan barcodes for MLB and ProK before proceeding.::) } ; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { nextStep = ::REMOVE:: }' \
-log {compoundOutputFileLuid1}"
```
{% endcode %}
Extraction - Routing (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (submittedSample.::Library Prep Method::.toLowerCase().contains(::enrichment::)) { output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment:: } else if (submittedSample.::Library Prep Method::.contains(::PCR-Free::)) {output.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::}' \
-log {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching PCR-Free (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Blood_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Saliva_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'DNA Batching with Enrichment (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | Waiting | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Placement Pattern = Column
* Destination Containers
* 96 well plate
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------------------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Ethanol | Text | | |
| ITB | Text | | |
| LHR Instrument ID | Text | | |
| MLB | Text | | |
| ProK | Text | | |
| Quick reference checklist: DNA Extraction - Saliva. i) pre LHR | Multiline Text | Read Only |
Default = User tasks for this page: - Download LHR Input File - Enter reagent lots for MLK and ProK (not scanned by LHR as loaded as a mastermix)
|
| Quick reference checklist: DNA Extraction - Saliva. ii) post LHR | Multiline Text | Read Only |
Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting LHR Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
|
| RSB | Text | | |
| Sample Count | Numeric | Read Only | Default = 0 |
| Step Sample Type | Text | Read Only | |
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container | Built-in | | |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Submitted Sample Type | Text | Read Only | |
| Project | Project Name | Built-in | | |
## Protocol 5: Illumina DNA PCR-Free (IGA v3.0)
Protocol Type = Library Prep
**Next Steps Configuration**
* Step(s):
* 1: DNA Batching PCR-Free (IGA v3.0)
* Start Next Step = Manual
* Assign Next Step = Manual
* 2: Indexing Planning PCR-Free (IGA v3.0)
* Start Next Step = Manual
* Assign Next Step = Manual
* 3: Library Prep - Indexing PCR-Free (IGA v3.0)
* Assign Next Step = Automatic
| **Step** | **To Step 1** | **To Step 2** | **To Step 3** |
| -------- | ------------- | ------------- | ------------- |
| 1 | | ✓ | ❌ |
| 2 | | | ✓ |
| 3 | | | |
### Step 1: DNA Batching PCR-Free (IGA v3.0)
* Master Step Name = DNA Batching NFPF (IGA v3.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}\_DNA
{% hint style="info" %}
The version of DNA Batching NFPF (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
DNA Batching PF - Set Final Volume and Validate Sample Type Combination (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Placement Reminder (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"
```
{% endcode %}
DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"
```
{% endcode %}
DNA Batching PF - Generate LHR Input File (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Manual button
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Warnings:: = :::: ; if ( submittedSample.hasValue (::Sample Conc.::) ) { output.::Sample Needed (uL):: = (step.::DNA (ng) required for tagmentation:: * step.::Batching Well Volume (uL)::) / (25 * submittedSample.::Sample Conc.::) ; \
if ( output.::Sample Needed (uL):: > step.::Batching Well Volume (uL):: ) { output.::Sample Needed (uL):: =
step.::Batching Well Volume (uL):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (uL):: < 2.0 )
{ output.::Sample Needed (uL):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (uL):: =
step.::Batching Well Volume (uL):: - output.::Sample Needed (uL):: ; output.::Initial Input DNA (ng):: = output.::Sample Needed (uL):: * submittedSample.::Sample Conc.::} \
else \
{output.::Sample Needed (uL):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (uL):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (uL):: = step.::Batching Well Volume (uL)::; output.::Diluent Volume (uL):: = 0 }' \
-log {compoundOutputFileLuid1} &&
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"
```
{% endcode %}
DNA Batching - Check LHR Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"
```
{% endcode %}
Register Step Completed (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Placement Pattern = Column
* Destination Containers
* 96 well plate
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------------------------------------------- | -------------- | -------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Batching Well Volume (uL) | Numeric | Required Field | Default = 40 |
| DNA (ng) required for tagmentation | Numeric | Required Field | Default = 350 |
| LHR Instrument ID | Text | Read Only | |
| Notes: | Multiline Text | Read Only |
Default = - DNA (ng) required for tagmentation is 300-2000 ng. - A fixed 25uL is aliquoted from the total volume of 40uL (default) to carry out Library Prep and subsequent steps.
|
| Quick reference checklist: DNA Batching IDPF. i) pre LHR | Multiline Text | Read Only |
Default = User tasks for this page: - For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred - 'Run' DNA Batching PF automation, and download resulting 'LHR Input File'
|
| Quick reference checklist: DNA Batching IDPF. ii) post LHR | Multiline Text | Read Only |
|
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ---------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Diluent Volume (uL) | Numeric | | Decimal Places Displayed = 1 |
| Derived Sample | Initial Input DNA (ng) | Numeric | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Needed (uL) | Numeric | | Decimal Places Displayed = 1 |
| Derived Sample | Warnings | Text | Read Only | |
| Project | Project Name | Built-in | | |
### Step 2: Indexing Planning PCR-Free (IGA v3.0)
* Master Step Name = Indexing Planning (IGA v3.0)
* Step Type = No Outputs
{% hint style="info" %}
The version of Indexing Planning (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Register Step Started (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::LHR Indexing Offset Column::)) + 8) < step.node.::input-output-maps::.::input-output-map::.input.size()) { fail(::The column offset will not yield enough indexes for the number of samples! Please increase the number of available indexes by changing the offset.::) }' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if ( !step.::Index Plate Barcode::.matches( ::UD[A-D]{1}+[0-9]{11}$:: ) ) { fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format of UD{A/B/C/D} followed by 11-digit number xxxxxxxxxxx; e.g. UDA12345678912. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning (IGA v3.0)' && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'input.::INTERNALFIELD_IndexPlanning_Metadata:: = step.::Index Plate Barcode:: + ::_:: + (int) step.::LHR Indexing Offset Column::' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
Register Step Completed (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------------------------- | -------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| Index Plate Barcode | Text | Required Field | |
| LHR Indexing Offset Column | Numeric | | Default = 1 |
| Quick reference checklist: Indexing Planning | Multiline Text | Read Only |
Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the LHR Indexing Offset column (required start column) - Click 'Next Steps'
|
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | INTERNALFIELD\_IndexPlanning\_Metadata | Text | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 3: Library Prep - Indexing PCR-Free (IGA v3.0)
* Master Step Name = Indexing NFPF (IGA v3.0)
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
{% hint style="info" %}
The version of Indexing NFPF (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Indexing - Custom Indexing with LHR Offsets and Dynamic Index Category Discovery (IGA v3.0)
* Trigger Location = Add Labels
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_autoAssignIndexesFromIndexPlanning.py -u {username} -p {password} -s {stepURI} \
&& /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_storeIndexSetSetting.py -u {username} -p {password} -s {stepURI} -n 'Index Set A/B/C/D' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -log {compoundOutputFileLuid1} \
script:evaluateDynamicExpression \
-exp 'submittedSample.::INTERNALFIELD_IndexPlanning_Metadata:: = input.::INTERNALFIELD_IndexPlanning_Metadata::' -t true \
"
```
{% endcode %}
Library Prep - Indexing PF - Route Samples to Sequencing Platform Selection with Automatic Workflow Detection (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI} -l {compoundOutputFileLuid1} script:changeWorkflow \
--FIELD_NAME 'N/A' \
--FIELD_VALUE 'N/A' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'Select Sequencing Platform (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
Indexing - Validate Index Category and Index Plate Barcode (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory_UD.py -u {username} -p {password} -s {stepURI} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"
```
{% endcode %}
Library Prep - Indexing PF - Check for Valid, Unique LIB Plate Barcode & Match with LHR Output File & Parse Reagent Info & Set Next Steps to Remove from Workflow & Quant. Warning (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_libprep.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'WARNING' --message 'This protocol recommends performing a pooled quant. (per prep) at this stage. Please quant. and update the Normalized Molarity (nM) across all samples in the table below before proceeding.'"
```
{% endcode %}
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | INTERNALFIELD\_IndexPlanning\_Metadata | Text | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | INTERNALFIELD\_IndexPlanning\_Metadata | Text | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Add Labels
* Label Groups
* Illumina DNA-RNA UD Indexes Set A Tagmentation
* Illumina DNA-RNA UD Indexes Set B Tagmentation
* Illumina DNA-RNA UD Indexes Set C Tagmentation
* Illumina DNA-RNA UD Indexes Set D Tagmentation
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------------------------------------------- | -------------- | -------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Adapter | Text |
| Default = CTGTCTCTTATACACATCT |
| BLT-PF | Text | | |
| ELM-T | Text | | |
| HP3 | Text | | |
| Index Plate Barcode (read from input samples) | Text | Read Only | |
| Index Plate Offset (read from input samples) | Text | Read Only | |
| IPB | Text | | |
| LHR Instrument ID | Text | Read Only | |
| Library Plate Barcode | Text | Required Field | |
| Quick reference checklist: Library Prep IDPF. i) pre LHR | Multiline Text | Read Only |
Default = User tasks for this page: - Above, scan in the 'Library Plate Barcode' to be used - Click blue button to 'Run' the Library Prep automation, and download the resulting 'LHR Input File'
|
| Quick reference checklist: Library Prep IDPF. ii) post LHR | Multiline Text | Read Only |
Default = User tasks continued: - Upload resulting 'LHR Output File' - Perform a pooled quant for the prep, and apply the yield 'Normalized Molarity (nM)' to all samples - Click 'Next Steps'
|
| RSB | Text | | |
| Sample Count | Numeric | Read Only |
Default = 0
Decimal Places Displayed = 0
|
| ST2 | Text | | |
| TB1 | Text | | |
| TWB | Text | | |
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------------ | -------------- | ----------- | ----------------------------------------- |
| Container | Container | Built-in | | |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
## Protocol 6: Illumina DNA with Enrichment (IGA v3.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
* Step(s):
* 1: DNA Batching with Enrichment (IGA v3.0)
* Start Next Step = Manual
* Assign Next Step = Manual
* 2: Indexing Planning with Enrichment (IGA v3.0)
* Start Next Step = Manual
* Assign Next Step = Manual
* 3: Library Prep - Indexing with Enrichment (IGA v3.0)
* Start Next Step = Manual
* Assign Next Step = Manual
* 4: Library Prep - Pre-Capture Pooling with Enrichment (IGA v3.0)
* Start Next Step = Manual
* Assign Next Step = Manual
* 5: Library Prep - Capture and Wash with Enrichment (IGA v3.0)
* Start Next Step = Manual
* Assign Next Step = Manual
* 6: Post-Capture Pool QC with Enrichment (IGA v3.0)
* Assign Next Step = Automatic
| **Step** | **To Step 1** | **To Step 2** | **To Step 3** | **To Step 4** | **To Step 5** | **To Step 6** |
| -------- | ------------- | ------------- | ------------- | ------------- | ------------- | ------------- |
| 1 | | ✓ | ❌ | ❌ | ❌ | ❌ |
| 2 | | | ✓ | ❌ | ❌ | ❌ |
| 3 | | | | ✓ | ❌ | ❌ |
| 4 | | | | | ✓ | ❌ |
| 5 | | | | | | ✓ |
| 6 | | | | | | |
### Step 1: DNA Batching with Enrichment (IGA v3.0)
* Master Step Name = DNA Batching NFE (IGA v3.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}\_DNA
{% hint style="info" %}
The version of DNA Batching NFE (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
DNA Batching Enrichment - Set Final Volume (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Placement Reminder (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"
```
{% endcode %}
DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"
```
{% endcode %}
DNA Batching Enrichment - Generate LHR Input File (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Manual button
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Warnings:: = :::: ; if ( submittedSample.hasValue (::Sample Conc.::) ) {output.::Sample Needed (uL):: = (step.::DNA (ng) required for tagmentation:: * step.::Batching Well Volume (uL)::) / (30 * submittedSample.::Sample Conc.::) ; \
if ( output.::Sample Needed (uL):: > step.::Batching Well Volume (uL):: ) { output.::Sample Needed (uL):: =
step.::Batching Well Volume (uL):: ; output.::Warnings:: = ::Low concentration - Sample Vol set to total volume::} ; if (output.::Sample Needed (uL):: < 2.0 )
{ output.::Sample Needed (uL):: = 2.0 ; output.::Warnings:: = ::High concentration - Sample Vol set to 2ul:: } ; output.::Diluent Volume (uL):: =
step.::Batching Well Volume (uL):: - output.::Sample Needed (uL):: ; output.::Initial Input DNA (ng):: = output.::Sample Needed (uL):: * submittedSample.::Sample Conc.::} \
else \
{output.::Sample Needed (uL):: = 40 ; output.::Warnings:: = ::No Sample Conc. provided, setting Sample vol. to 40ul:: ; output.::Diluent Volume (uL):: = 0}; if (submittedSample.::Sample Type:: == ::Blood:: || submittedSample.::Sample Type:: == ::Saliva::) { output.::Sample Needed (uL):: = step.::Batching Well Volume (uL)::; output.::Diluent Volume (uL):: = 0 }' \
-log {compoundOutputFileLuid1} &&
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/BatchingInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"
```
{% endcode %}
DNA Batching - Check LHR Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' \
&& \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"
```
{% endcode %}
Register Step Completed (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Placement Pattern = Column
* Destination Containers
* 96 well plate
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| --------------------------------------------------------- | -------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| Batching Well Volume (uL) | Numeric | Required Field | Default = 45 |
| DNA (ng) required for tagmentation | Numeric | Required Field | Default = 450 |
| LHR Instrument ID | Text | Read Only | |
| Notes: | Multiline Text | Read Only |
Default = - DNA (ng) required for tagmentation is 50-1000 ng. - A fixed 30uL is aliquoted from the total volume of 45uL (default) to carry out Library Prep and subsequent steps.
|
| Quick reference checklist i): DNA Batching IDE, pre LHR | Multiline Text | Read Only |
Default = User tasks for this page: - For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred - 'Run' DNA Batching Enrichment automation, and download resulting 'LHR Input File'
|
| Quick reference checklist ii): DNA Batching IDE, post LHR | Multiline Text | Read Only |
|
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ---------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Diluent Volume (uL) | Numeric | | Decimal Places Displayed = 1 |
| Derived Sample | Initial Input DNA (ng) | Numeric | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Needed (uL) | Numeric | | Decimal Places Displayed = 1 |
| Derived Sample | Warnings | Text | Read Only | |
| Project | Project Name | Built-in | | |
### Step 2: Indexing Planning with Enrichment (IGA v3.0)
* Master Step Name = Indexing Planning (IGA v3.0)
* Step Type = No Outputs
{% hint style="info" %}
The version of Indexing Planning (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Register Step Started (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if (((96 - (8 * (int)step.::LHR Indexing Offset Column::)) + 8) < step.node.::input-output-maps::.::input-output-map::.input.size()) { fail(::The column offset will not yield enough indexes for the number of samples! Please increase the number of available indexes by changing the offset.::) }' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -h true script:evaluateDynamicExpression -exp 'if ( !step.::Index Plate Barcode::.matches( ::UD[A-D]{1}+[0-9]{11}$:: ) ) { fail ( ::Invalid Index Plate Barcode. This plate ID must be in the format of UD{A/B/C/D} followed by 11-digit number xxxxxxxxxxx; e.g. UDA12345678912. Please verify and try again.:: ) }' -log {compoundOutputFileLuid0} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/05_reusedIndexPlateWarning.py -u {username} -p {password} -s {stepURI} -f 'Index Plate Barcode' -v '{udf:Index Plate Barcode}' -t 'Indexing Planning (IGA v3.0)' && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'input.::INTERNALFIELD_IndexPlanning_Metadata:: = step.::Index Plate Barcode:: + ::_:: + (int) step.::LHR Indexing Offset Column::' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
Register Step Completed (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------------------------- | -------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| Index Plate Barcode | Text | Required Field | |
| LHR Indexing Offset Column | Numeric | | Default = 1 |
| Quick reference checklist: Indexing Planning | Multiline Text | Read Only |
Default = User tasks for this page: - Scan in Indexing Plate Barcode and set the LHR Indexing Offset column (required start column) - Click 'Next Steps'
|
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | INTERNALFIELD\_IndexPlanning\_Metadata | Text | | |
| Derived Sample | Sample Name | Built-in | | |
### Step 3: Library Prep - Indexing with Enrichment (IGA v3.0)
* Master Step Name = Indexing NFE (IGA v3.0)
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
{% hint style="info" %}
The version of Indexing NFE (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Indexing - Custom Indexing with LHR Offsets and Dynamic Index Category Discovery (IGA v3.0)
* Trigger Location = Add Labels
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_autoAssignIndexesFromIndexPlanning.py -u {username} -p {password} -s {stepURI} \
&& /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_B_storeIndexSetSetting.py -u {username} -p {password} -s {stepURI} -n 'Index Set A/B/C/D' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -log {compoundOutputFileLuid1} \
script:evaluateDynamicExpression \
-exp 'submittedSample.::INTERNALFIELD_IndexPlanning_Metadata:: = input.::INTERNALFIELD_IndexPlanning_Metadata::' -t true \
"
```
{% endcode %}
Indexing - Validate Index Category and Index Plate Barcode (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/04_A_checkIndexPlateBarcodeWithCategory_UD.py -u {username} -p {password} -s {stepURI} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_started.groovy'"
```
{% endcode %}
Library Prep - Indexing Enrichment - Copy Indexing Metadata to Outputs & Set Next Steps to Advance (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Add Labels
* Label Groups
* Illumina DNA-RNA UD Indexes Set A Tagmentation
* Illumina DNA-RNA UD Indexes Set B Tagmentation
* Illumina DNA-RNA UD Indexes Set C Tagmentation
* Illumina DNA-RNA UD Indexes Set D Tagmentation
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| --------------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------ |
| Index Plate Barcode (read from input samples) | Text | Read Only | |
| Index Plate Offset (read from input samples) | Text | Read Only | |
| Quick reference checklist: Library Prep IDE. | Multiline Text | Read Only |
Default = User tasks for this step: - No user tasks, click 'Next Steps'
| Default = CTGTCTCTTATACACATCT |
| eBLT | Text | | |
| EPM | Text | | |
| Index Plate Barcode (read from input samples) | Text | Read Only | |
| Index Plate Offset (read from input samples) | Text | Read Only | |
| LHR Instrument ID | Text | Read Only | |
| Quick reference checklist: Library Prep IDE - pool libraries. i) pre LHR. | Multiline Text | Read Only |
Default = User tasks for this page: - 'Run' Library Prep Pooling automation - Download resulting LHR Input File
|
| Quick reference checklist: Library Prep IDE - pool libraries. ii) post LHR. | Multiline Text | Read Only |
Default = User tasks continued: - After running the Prep method on the Liquid Handler, upload resulting LHR Output File - Click on 'Next Steps'
|
| RSB | Text | | |
| Sample Count | Numeric | Read Only | Default = 0 |
| SPB | Text | | |
| ST2 | Text | | |
| TB1 | Text | | |
| Total Pool Volume (ul) | Numeric | | Default = 30 |
| TWB | Text | | |
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | Diluent Volume (uL) | Numeric | | Decimal Places Displayed = 1 |
| Derived Sample | Number of Samples in Pool | Numeric | | Default = 0 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Needed (uL) | Numeric | | Decimal Places Displayed = 1 |
### Step 5: Library Prep - Capture and Wash with Enrichment (IGA v3.0)
* Master Step Name = Capture and Wash NFE (IGA v3.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
{% hint style="info" %}
The version of Capture and Wash NFE (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Register Step Started (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Capture and Wash Enrichment - Sample Placement LIB Plate Barcode Uniqueness Check & Update Pool Count (IGA v3.0)
* Trigger Location = Placement
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-LIB:: ) ) {fail ( ::Invalid LIB plate barcode format. This plate ID must be in the format LPxxxxxxx-LIB, where 'x' is a digit 0-9, e.g. LP1234567-LIB. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/countSamples.py -u {username} -p {password} -s {stepURI} -f 'Pool Count'"
```
{% endcode %}
Capture and Wash Enrichment - Create LHR Input File (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Manual button
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-t /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/templatefiles/CaptureWashInputFile_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid1}"
```
{% endcode %}
Capture and Wash Enrichment - Validate LHR Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -i 'LHR Instrument ID' && /usr/bin/env python3 /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/02_ReagentParsing.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid2} -m /opt/gls/clarity/extensions/IGA_3.0/hamilton_fast_prep/reagent_parsing/fieldmap_captureandwash.csv && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"
```
{% endcode %}
Register Step Completed (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Placement Pattern = Same Shape
* Destination Containers
* 96 well plate
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| EE1 | Text | | |
| EEW | Text | | |
| EHB2 | Text | | |
| EPM | Text | | |
| ET2 | Text | | |
| HP3 | Text | | |
| LHR Instrument ID | Text | Read Only | |
| Pool Count | Numeric | Read Only | Default = 0 |
| PPC | Text | | |
| Probes | Text | | |
| Quick reference checklist: Capture and Wash IDE. i) pre LHR | Multiline Text | Read Only |
Default = User tasks for this page: - 'Run' Capture and Wash automation - Download resulting LHR Input File
|
| Quick reference checklist: Capture and Wash IDE. ii) post LHR | Multiline Text | Read Only |
Default = User tasks continued: - After running Capture and Wash on the liquid handler, upload resulting LHR Output File - Click 'Next Steps'
|
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 6: Post-Capture Pool QC with Enrichment (IGA v3.0)
* Master Step Name = Generic Pool QC NFE (IGA v3.0)
* Step Type = Standard QC
* Measurement Generation = Fixed, 1
* Naming Convention = {InputItemName}
{% hint style="info" %}
The version of Generic Pool QC NFE (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Register Step Started (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Pool QC - Generic - Enrichment - Copy Normalized Molarity from Output to Input, Copy QC Value to Inputs & Set QC Passed Sample Next Steps to Remove from Workflow (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Pool QC - Generic - Enrichment - Route QC Passed Samples to Sequencing Platform Selection (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI} -l {compoundOutputFileLuid0} script:changeWorkflow \
--FIELD_NAME 'INTERNALFIELD_QCValue_forRouting' \
--FIELD_VALUE 'true' \
--WORKFLOW 'IGA LibraryPrep Automated (IGA v3.0)' \
--STEP 'Select Sequencing Platform (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| --------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Quick reference checklist: Pool QC IDE. | Multiline Text | Read Only |
Default = User tasks for this page: - After running QC on the pools, upload a QC instrument result file, or input Normalized Molarity (nM) and QC flags below - For any QC fails, assign next steps - Click 'Next Steps'
|
* Sample Table
* Enable QC Flags = Yes
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ---------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | INTERNALFIELD\_QCValue\_forRouting | Text | | |
| Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Measurement | INTERNALFIELD\_QCValue\_forRouting | Text | Read Only | |
| Measurement | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
## Protocol 7: Sequencing Platform Selection (IGA v3.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
* Step(s):
* 1: Select Sequencing Platform (IGA v3.0)
* Assign Next Step = Automatic
### Step 1: Select Sequencing Platform (IGA v3.0)
* Master Step Name = Sequencing Platform Selection (IGA v3.0)
* Step Type = No Outputs
{% hint style="info" %}
The version of Sequencing Platform Selection (IGA) master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Register Step Started (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
Sequencing Platform Selection - Copy Instrument Type to Analyte & Set Next Steps to Remove from Workflow (IGA v3.0)
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Sequencing Platform Selection - Route to Sequencing Workflow by Type (IGA v3.0)
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI} -l {compoundOutputFileLuid0} script:changeWorkflow \
--FIELD_NAME 'Sequencing Platform' \
--FIELD_VALUE 'NovaSeq X IGA' \
--WORKFLOW 'NovaSeq X Series v2.0' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Sequencing Platform' \
--FIELD_VALUE 'NovaSeq 6K IGA' \
--WORKFLOW 'Illumina Genomics Architecture - NovaSeq Sequencing v3.0' \
--STEP 'Define Run Format (IGA v3.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Sequencing Platform' \
--FIELD_VALUE 'NextSeq 1000/2000 v2.3' \
--WORKFLOW 'NextSeq 1000/2000 Sequencing v2.3' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"
```
{% endcode %}
> ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.
#### Queue
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Sample Table (Column Headers)
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------------------------------------- | -------------- | -------------- | ----------------------------------------------------------------------------------------------------------------------------------------- |
| Quick reference checklist: Sequencing Platform Selection | Multiline Text | Read Only |
Default = User tasks for this step: - No actions for this page! The step serves to route all samples to the NovaSeq workflow
|
| Sequencing Platform | Text Dropdown | Required Field |
Presets
NovaSeq X IGA
NovaSeq 6K IGA
|
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sequencing Platform | Text | | |
| Project | Project Name | Built-in | | |
---
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```
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