# TruSight Oncology 500 v1.1
## Protocol 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)
Protocol Type = Sample Prep
**Next Steps Configuration**
### Step 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)
* Master Step Name = DNA/RNA FFPE Extraction (TSO 500 HT v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 2
* Naming Convention = {LIST:{SubmittedSampleName}\_DNA,{SubmittedSampleName}\_RNA}
* Reagent Kits
* QIAGEN AllPrep DNA/RNA FFPE Kit
* Supplier = Qiagen
* Catalog Number = 80234
{% hint style="info" %}
The version of DNA/RNA FFPE Extraction master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Sample Type
* Trigger Location = Record Details
* 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} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (output.name.endsWith(::_RNA::)) {output.::Sample Type:: = ::RNA::}; if (output.name.endsWith(::_DNA::)) {output.::Sample Type:: = ::DNA::}' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Remove
* 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 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Route DNA/RNA samples
* 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:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
```
{% endcode %}
> ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Route DNA/RNA samples - HT
* Trigger Location = Not Used
{% 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:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
```
{% endcode %}
> ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* 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 | Sample Type | Text Dropdown | - Required Field
- Custom Entries
| Presets
|
| Project | Project Name | Built-in | | |
## Protocol 2: RNA QC and cDNA Synthesis (TruSight Oncology 500 v1.1)
Protocol Type = Library Prep
**Next Steps Configuration**
### Step 1: Qubit RNA QC (TruSight Oncology 500 v1.1)
* Master Step Name = Qubit RNA QC (TSO 500 v1.1)
* Step Type = Standard QC
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
{% hint style="info" %}
The version of Qubit RNA QC master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Assign QC flags - RNA
* 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 {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid2} && /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 true -h false -exp 'input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Sample Type | Text Dropdown | - Required Field
- Custom Entries
| Presets
|
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------ | -------------- | -------------- | --------------------------------------------------------------------------------------------------------- |
| Criteria 1 - Operator | Text Dropdown | Custom Entries | |
| Criteria 1 - Source Data Field | Text | | - Default = Concentration (ng/ul)
|
| Criteria 1 - Threshold Value | Numeric | | - Default = 4.7
- Decimal Places Displayed = 2
|
| Criteria 2 - Operator | Text Dropdown | Custom Entries | |
| Criteria 2 - Source Data Field | Text | | - Default = Concentration (ng/ul)
|
| Criteria 2 - Threshold Value | Numeric | | - Decimal Places Displayed = 2
|
* Step File Placeholders
* Log File - Automatically attached
* Qubit Result File - Manually uploaded
* Sample Table
* Enable QC Flags = Yes
* Sample Display Default = Expand
* Well Sort Order = Column
* File Column Options
* File Column Display = Hide
* File Attachment Method = Auto
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Measurement | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 2: Denature and Anneal RNA (TruSight Oncology 500 v1.1)
* Master Step Name = Denature and Anneal RNA (TSO 500 v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
{% hint style="info" %}
The version of Denature and Anneal RNA master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Count Samples and Calculate Master Mix
* Trigger Location = Record Details
* 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} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-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 'step.::FSM (uL):: = step.::Total Samples:: * (27/3) ; \
step.::RVT (uL):: = step.::Total Samples:: * (3/3) ' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
RNA Sample Dilution
* 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} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Sample Volume (uL):: = (step.::Dilution Concentration (ng/ul):: * 8.5) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 8.5 - output.::Sample Volume (uL)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------ | -------------- | -------------- | ------------------------------------------------------------------------ |
| Comment | Multiline Text | | |
| Dilution Concentration (ng/ul) | Numeric | Required Field | - Range = 4.7 To 10
- Decimal Places Displayed = 1
|
| EPH3 to each well (uL) | Numeric | | |
| FSM (uL) | Text | | |
| RVT (uL) | Text | | |
| Thermal Cycler Program | Text Dropdown | Custom Entries | |
| Total Samples | Numeric | | |
* Step File Placeholders
* Calculation Log File - Automatically attached
* NextStep Log File - Automatically attached
* 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 | Buffer Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 3: First Strand cDNA Synthesis (TruSight Oncology 500 v1.1)
* Master Step Name = First Strand cDNA Synthesis v2.0
* Step Type = No Outputs
{% hint style="info" %}
The version of First Strand cDNA Synthesis master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------- | -------------- | -------------- | ------------------------------------------------------------------- |
| Comment | Multiline Text | | |
| Thermal Cycler Program | Text Dropdown | Custom Entries | Presets
- Synthesize 1st Strand
- 1stSS
|
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 4: Second Strand cDNA Synthesis (TruSight Oncology 500 v1.1)
* Master Step Name = Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
* Step Type = No Outputs
* Reagent Kits
* TruSight Oncology 500, Box 1
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Second Strand cDNA Synthesis master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| Thermal Cycler Program | Text | Read Only | Default = 2ndSS |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 5: cDNA Clean Up (TruSight Oncology 500 v1.1)
* Master Step Name = cDNA Clean Up (TSO 500 v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}\_cDNA
* Reagent Kits
* TruSight Oncology 500, Box 4
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of cDNA Clean Up master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Assign Sample Type
* Trigger Location = Record Details
* 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} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Sample Type:: = ::cDNA::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Remove
* 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 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Routing cDNA Samples
* 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:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
```
{% endcode %}
> ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Routing cDNA Samples - HT
* Trigger Location = Not Used
{% 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:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
```
{% endcode %}
> ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| BIND1 Plate Barcode | Text | | |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* 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 | Sample Type | Text Dropdown | - Required Field
- Custom Entries
| Presets
|
| Project | Project Name | Built-in | | |
## Protocol 3: DNA QC and Fragmentation (TruSight Oncology 500 v1.1)
Protocol Type = Library Prep
**Next Steps Configuration**
### Step 1: Qubit DNA QC (TruSight Oncology 500 v1.1)
* Master Step Name = Qubit DNA QC (TruSight Oncology 500 HT v1.1)
* Step Type = Standard QC
* Measurement Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
{% hint style="info" %}
The version of Qubit DNA QC master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Assign QC flags - DNA
* 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 {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid1} && /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 true -h false -exp 'input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Sample Type | Text Dropdown | - Required Field
- Custom Entries
| Presets
|
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------ | -------------- | ----------- | --------------------------------------------------------------------------------------------------------- |
| Criteria 1 - Operator | Text Dropdown | | |
| Criteria 1 - Source Data Field | Text | | - Default = Concentration (ng/ul)
|
| Criteria 1 - Threshold Value | Numeric | | - Default = 3.3
- Decimal Places Displayed = 2
|
| Criteria 2 - Operator | Text Dropdown | | |
| Criteria 2 - Source Data Field | Text | | - Default = Concentration (ng/ul)
|
| Criteria 2 - Threshold Value | Numeric | | - Decimal Places Displayed = 2
|
* Step File Placeholders
* Log File - Automatically attached
* Qubit Result File - Automatically attached
* Sample Table
* Enable QC Flags = Yes
* Sample Display Default = Expand
* Well Sort Order = Column
* File Column Options
* File Column Display = Hide
* File Attachment Method = Auto
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Measurement | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 2: Fragment DNA (TruSight Oncology 500 v1.1)
* Master Step Name = Fragment DNA (TruSight Oncology 500 HT v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}\_DNA
* Reagent Kits
* TruSight Oncology 500, Box 4
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Fragment DNA master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Dilution Calculation
* 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} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Sample Volume (uL):: = (step.::Dilution Concentration (ng/ul):: * 12) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 12 - output.::Sample Volume (uL)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | 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** |
| ------------------------------ | -------------- | -------------- | ------------------------------------------------------------------------ |
| Comment | Multiline Text | | |
| Dilution Concentration (ng/ul) | Numeric | Required Field | - Range = 3.3 To 10
- Decimal Places Displayed = 0
|
* Step File Placeholders
* Log File - Automatically attached
* 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 | Buffer Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
## Protocol 4: Library Prep (TruSight Oncology 500 v1.1)
Protocol Type = Library Prep
**Next Steps Configuration**
### Step 1: End Repair and A-Tailing (TruSight Oncology 500 v1.1)
* Master Step Name = End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)
* Step Type = No Outputs
* Reagent Kits
* TruSight Oncology 500, Box 3
* Supplier = Illumina
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of End Repair and A-Tailing master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Count Samples and Calculate Master Mix
* Trigger Location = Record Details
* 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} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-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 'step.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| ERA1-A (uL) | Numeric | | Decimal Places Displayed = 0 |
| ERA1-B (uL) | Numeric | | Decimal Places Displayed = 0 |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 2: Ligate Adapters (TruSight Oncology 500 v1.1)
* Master Step Name = Ligate Adapters (TruSight Oncology 500 HT v1.1)
* Step Type = No Outputs
* Reagent Kits
* TruSight Oncology 500, Box 2
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 3
* Supplier = Illumina
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Ligate Adapters master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 3: Clean Up Ligation (TruSight Oncology 500 v1.1)
* Master Step Name = Clean Up v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* TruSight Oncology 500, Box 4
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Clean Up master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 4: Index PCR (TruSight Oncology 500 v1.1)
* Master Step Name = Index PCR (TruSight Oncology 500 HT v1.1)
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* TruSight Oncology 500, Box 5
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 4
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Index PCR master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Add Labels
* Label Groups
* TruSight Oncology 500 NextSeq
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| PCR Program | Text | Read Only | Default = I-PCR |
* Step File Placeholders
* Log File - Automatically attached
* 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 | Reagent Name | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
## Protocol 5: Hybridization (TruSight Oncology 500 v1.1)
Protocol Type = Library Prep
**Next Steps Configuration**
### Step 1: Set Up First Hybridization (TruSight Oncology 500 v1.1)
* Master Step Name = Hybridize v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* TruSight Oncology 500, Box 6
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 7
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 8
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 9
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Hybridize master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
Library Dilution
* Trigger Location = Not Used
{% 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 true -h false -exp 'output.::Library Volume (ul):: = 200 / input.::Concentration (ng/ul):: ; output.::RSB Volume (ul):: = 10 - output.::Library Volume (ul)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| PCR Program | Text | | Default = HYB1 |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 2: Capture Targets One (TruSight Oncology 500 v1.1)
* Master Step Name = Capture Targets One (TSO 500 v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* TruSight Oncology 500, Box 6
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 7
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Capture Targets One master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Count Samples and Calculate Master Mix
* Trigger Location = Record Details
* 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} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-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 'step.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| EE2 (uL) | Numeric | | Decimal Places Displayed = 0 |
| HP3 (uL) | Numeric | | Decimal Places Displayed = 0 |
| Total Samples | Numeric | | Default = 0 |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 3: Set Up Second Hybridization (TruSight Oncology 500 v1.1)
* Master Step Name = Set Up Second Hybridization (TSO 500 v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* TruSight Oncology 500, Box 6
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 7
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 8
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 9
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Set Up Second Hybridization master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| PCR Program | Text | Read Only | Default = HYB2 |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 4: Capture Targets Two (TruSight Oncology 500 v1.1)
* Master Step Name = Capture Targets Two (TSO 500 v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* TruSight Oncology 500, Box 6
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
* TruSight Oncology 500, Box 7
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Capture Targets Two master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Count Samples and Calculate Master Mix
* Trigger Location = Record Details
* 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} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-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 'step.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------- | -------------- | ----------- | ----------------------------------------- |
| BIND1 Plate Barcode | Text | | |
| Comment | Multiline Text | | |
| EE2 (uL) | Numeric | | Decimal Places Displayed = 0 |
| HP3 (uL) | Numeric | | Decimal Places Displayed = 0 |
* Step File Placeholders
* Log File - Automatically attached
* 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 5: Amplify Enriched Library (TruSight Oncology 500 v1.1)
* Master Step Name = Amplify Enriched Library v2.0
* Step Type = No Outputs
* Reagent Kits
* TruSight Oncology 500, Box 7
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Amplify Enriched Library master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| PCR | Text | | Default = EL-PCR |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |
### Step 6: Clean Up Amplified Enriched Library (TruSight Oncology 500 v1.1)
* Master Step Name = Clean Up v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* TruSight Oncology 500, Box 6
* Supplier = Illumina
* Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
* Website = [www.illumina.com](https://www.illumina.com)
{% hint style="info" %}
The version of Clean Up master step name may be different depending on the version of IPP installed.
{% endhint %}
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/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 | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------ | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* 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 | | |
| Project | Project Name | Built-in | | |