# Respiratory Virus Panel v1.0
## Overview
The Respiratory Virus Panel workflow includes the following functionality:
* Preconfigured protocols that support the preparation of upper and lower respiratory specimens for real-time RT-PCR qualitative detection of nucleic acid from the 2019-nCoV.
* Automated calculation of sample and buffer volumes.
* Automated calculation or display of reagents at every step in the protocol.
* Automatic step transition when required.
* Automatic placement of samples when necessary.
* Automated assignment of QC Pass/Fail, based on user-selected threshold values.
* Routing to iSeq, MiniSeq, MiSeq, NextSeq 550, NextSeq 2000.
## Protocol 1: Sort Sample Type (Respiratory Virus Panel v1.0)
Protocol Type = Other
**Next Steps Configuration**
### Step 1: Sort Sample Type (Respiratory Virus Panel v1.0)
* Master Step Name = Sort Sample Type (Respiratory Virus Panel v1.0)
* Step Type = No Outputs
#### Automations
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 Script - Extraction
* 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 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'QIAamp Viral Mini Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sample Concentration (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'AllPrep PowerViral DNA/RNA Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sort Sample (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"
```
{% 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 = 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** |
| -------------- | -------------- | ----------- | ---------------------------------------------------------------------------------- |
| Instruction | Multiline Text | Read Only | Default = Please select the Respiratory Virus Extraction Protocol for each sample. |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Respiratory Virus Extraction Protocol | Text Dropdown | Required Field | Presets
- QIAamp Viral Mini Kit
- AllPrep PowerViral DNA/RNA Kit
|
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
## Protocol 2: QIAamp Viral RNA Mini Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
### Step 1: Sample Concentration (Respiratory Virus Panel v1.0)
* Master Step Name = Sample Concentration (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
#### Automations
Set Next Step - Purification
* 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 (input.::Is Bead Beating Required?:: == ::Yes::) {nextStep = ::Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)::} \
else {if (input.::Is Bead Beating Required?:: == ::No::) {nextStep = ::Prep Samples (Respiratory Virus Panel v1.0)::} }' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
> ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.
#### 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 | 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** |
| ------------------ | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------ |
| Sample Volume (mL) | Numeric | | Default = 3.5 |
| Directions | Multiline Text | | Default =
Add up to 3.5 ml of sample to the microconcentrator
Centrifuge to a final volume of 140 μl.
|
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | --------------------- | -------------- | -------------- | --------------------------------------------------- |
| Derived Sample | Purification Protocol | Text Dropdown | Required Field | Presets
|
| Derived Sample | Sample Name | Built-in | | |
### Step 2: Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)
* Master Step Name = Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* Buffer AW1
* Catalog Number = 61904
* Buffer AW2
* Catalog Number = 61904
#### Automations
Calculate Total Samples and 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.::Buffer AVL Volume (ml):: = step.::Total Samples:: * 0.56 ; \
step.::Carrier RNA AVE Volume (uL):: = step.::Buffer AVL Volume (ml):: * 10 ' \
-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 Script - cDNA synthesis
* 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = 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** |
| --------------------------- | -------------- | ----------- | ----------------------------------------- |
| 96-100% EtOH Prep Date | Date | | |
| Buffer AVL Volume (ml) | Numeric | | Decimal Places Displayed = 2 |
| Carrier RNA AVE Volume (uL) | Numeric | | Decimal Places Displayed = 2 |
| Incubation End Time: | Text | | |
| Incubation Start Time: | Text | | |
| Total Samples | Numeric | | Default = 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 | cDNA Synthesis Protocol | Text Dropdown | Required Field | Presets
- Maxima H Minus Double-Stranded cDNA Synthesis Kit
- NEBNext Ultra II First Strand Synthesis Module
- SuperScript Double-Stranded cDNA Synthesis Kit
|
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 3: Purification of Viral RNA - Vacuum Protocol (Respiratory Virus Panel v1.0)
* Master Step Name = Purification of Viral RNA - Vacuum Protocol (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* Buffer AW1
* Catalog Number = 61904
* Buffer AW2
* Catalog Number = 61904
* QIAvac 24 Plus vacuum manifold
* Catalog Number = 19413
#### Automations
Calculate Total Samples and 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.::Buffer AVL Volume (ml):: = step.::Total Samples:: * 0.56 ; \
step.::Carrier RNA AVE Volume (uL):: = step.::Buffer AVL Volume (ml):: * 10 ' \
-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 Script - cDNA synthesis
* 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = 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** |
| --------------------------- | -------------- | ----------- | ----------------------------------------- |
| 96-100% EtOH Prep Date | Date | | |
| Buffer AVL Volume (ml) | Numeric | | Decimal Places Displayed = 2 |
| Carrier RNA AVE Volume (uL) | Numeric | | Decimal Places Displayed = 2 |
| Incubation End Time: | Text | | |
| Incubation Start Time: | Text | | |
| Total Samples | Numeric | | Default = 0 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | cDNA Synthesis Protocol | Text Dropdown | Required Field | Presets
- Maxima H Minus Double-Stranded cDNA Synthesis Kit
- NEBNext Ultra II First Strand Synthesis Module
- SuperScript Double-Stranded cDNA Synthesis Kit
|
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
## Protocol 3: AllPrep PowerViral DNA/RNA Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
### Step 1: Sort Sample (Respiratory Virus Panel v1.0)
* Master Step Name = Sort Sample (Respiratory Virus Panel v1.0)
* Step Type = No Outputs
#### Automations
Set Next Step - Purification
* 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 (input.::Is Bead Beating Required?:: == ::Yes::) {nextStep = ::Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)::} \
else {if (input.::Is Bead Beating Required?:: == ::No::) {nextStep = ::Prep Samples (Respiratory Virus Panel v1.0)::} }' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
> ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.
#### 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 | 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 File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Is Bead Beating Required? | Text Dropdown | Required Field | Presets
|
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 2: Prep Samples (Respiratory Virus Panel v1.0)
* Master Step Name = Prep Samples (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* AllPrep PowerViral DNA/RNA Kit
* β-mercaptoethanol
#### Automations
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 Script - cDNA synthesis
* 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = 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** |
| ------------------- | -------------- | ----------- | ----------------------------------------- |
| 100% EtOH Open Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | cDNA Synthesis Protocol | Text Dropdown | Required Field | Presets
- Maxima H Minus Double-Stranded cDNA Synthesis Kit
- NEBNext Ultra II First Strand Synthesis Module
- SuperScript Double-Stranded cDNA Synthesis Kit
|
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 3: Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)
* Master Step Name = Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* AllPrep PowerViral DNA/RNA Kit
* Phenol:chloroform:isoamyl alcohol
* Supplier = supplied by user
* β-mercaptoethanol
#### Automations
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 Script - cDNA synthesis
* 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = 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** |
| ------------------- | -------------- | ----------- | ----------------------------------------- |
| 100% EtOH Open Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | cDNA Synthesis Protocol | Text Dropdown | Required Field | Presets
- Maxima H Minus Double-Stranded cDNA Synthesis Kit
- NEBNext Ultra II First Strand Synthesis Module
- SuperScript Double-Stranded cDNA Synthesis Kit
|
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
## Protocol 4: Maxima H Minus Double-Stranded cDNA Synthesis Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
### Step 1: First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Master Step Name = First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* Maxima H Minus Double-Stranded cDNA Synthesis Kit
* Supplier = K2561
#### Automations
Set Master Mix UDFs
* 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.::4x First Strand Reaction Mix (uL):: = 4 ; output.::First Strand Enzyme Mix (uL):: = 1' \
-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 %}
Calculate Total Samples and Master Mix
* 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} -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.::Murine RNase Inhibitor (uL):: = step.::Total Samples:: * 0.5 * 1.1 ; \
step.::ProtoScript II Reverse Transcriptase (uL):: = step.::Total Samples:: * 1 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 5 * 1.1 ' \
-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 | 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** |
| -------------- | -------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Directions | Multiline Text | | Default = Please record the volumes for the following fields: Volume of Oligo(dT)18 Used (uL), Volume of Template RNA Used (uL), Nuclease-free Water Used (uL). |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | 4x First Strand Reaction Mix (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | First Strand Enzyme Mix (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Nuclease-free Water Used (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Volume of Oligo(dT)18 Used (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Volume of Template RNA Used (uL) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 2: Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Master Step Name = Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Step Type = No Outputs
* Reagent Kits
* Maxima H Minus Double-Stranded cDNA Synthesis Kit
* Supplier = K2561
#### Automations
Set Master Mix UDFs
* 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.::First Strand cDNA Synthesis (uL):: = 20 ; \
output.::5x Second Strand Reaction Mix (uL):: = 20 ; \
output.::Nuclease-free Water (uL):: = 55 ; \
output.::Second Strand Enzyme Mix (uL):: = 5 ; \
output.::Total Volume (uL):: = 100' \
-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 %}
Calculate Total Samples and Master Mix
* 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} -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.::NEBNext Second Strand Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::NEBNext Second Strand Synthesis Enzyme Mix (uL):: = step.::Total Samples:: * 4 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 48 * 1.1 ' \
-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 | 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** |
| ---------------------------------- | -------------- | ----------- | ----------------------------------------- |
| 5x Second Strand Reaction Mix (uL) | Numeric | | Decimal Places Displayed = 2 |
| First Strand cDNA Synthesis (uL) | Numeric | | Decimal Places Displayed = 2 |
| Nuclease-free Water (uL) | Numeric | | Decimal Places Displayed = 2 |
| Second Strand Enzyme Mix (uL) | Numeric | | Decimal Places Displayed = 2 |
| Total Volume (uL) | Numeric | | Decimal Places Displayed = 2 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | 5x Second Strand Reaction Mix (uL) | Numeric | | |
| Derived Sample | First Strand cDNA Synthesis (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Nuclease-free water (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Second Strand Enzyme Mix | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Total Volume (uL) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 3: Removal of RNA (Respiratory Virus Panel v1.0)
* Master Step Name = Removal of RNA (Respiratory Virus Panel v1.0)
* Step Type = No Outputs
#### 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 = 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** |
| -------------------------------- | -------------- | ----------- | ----------------------------------------- |
| RNase I (uL) to add to each tube | Numeric | | Default = 10 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 4: Purification of ds cDNA (Respiratory Virus Panel v1.0)
* Master Step Name = Purification of ds cDNA (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* GeneJET PCR Purification Kit
* Catalog Number = K0701, K0702
#### Automations
Set Sample Type - ds cDNA output
* 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:: = ::ds 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 Script - Nextera Flex for Enrichment OUTPUTS
* 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 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--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 = 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 File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Sample Name | Built-in | | |
| Derived Sample | Sample Type | Text Dropdown | - Required Field
- Custom Entries
| Presets
|
| Project | Project Name | Built-in | | |
## Protocol 5: NEBNext Ultra II First Strand Synthesis Module (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
### Step 1: mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)
* Master Step Name = mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* NEBNext First Strand Synthesis Reaction Buffer
* Supplier = NEB
* Catalog Number = E7525S, E7525L
* NEBNext Poly(A) mRNA Magnetic Isolation Module
* Supplier = NEB
* Catalog Number = E7490S, E7490L
* NEBNext Random Primers
* Supplier = NEB
* Catalog Number = S1330S
#### Automations
Calculate Total Samples and 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.::MM1: NEBNext First Strand Synthesis Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::MM1: NEBNext Random Primers (uL):: = step.::Total Samples:: * 2 * 1.1 ; \
step.::MM1: Nuclease-free Water (uL):: = step.::Total Samples:: * 10 * 1.1 ; \
step.::Beads MM: Oligo dT Beads d(T)25 (uL):: = step.::Total Samples:: * 20 * 1.1 ; \
step.::Beads MM: RNA Binding Buffer (2X) (uL):: = step.::Total Samples:: * 100 * 1.1 ' \
-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 | 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** |
| ------------------------------------------------------ | -------------- | ----------- | ----------------------------------------- |
| Beads MM: Oligo dT Beads d(T)25 (uL) | Numeric | | Decimal Places Displayed = 2 |
| Beads MM: RNA Binding Buffer (2X) (uL) | Numeric | | Decimal Places Displayed = 2 |
| MM1: NEBNext First Strand Synthesis Reaction Buff (uL) | Numeric | | Decimal Places Displayed = 2 |
| MM1: NEBNext Random Primers (uL) | Numeric | | Decimal Places Displayed = 2 |
| MM1: Nuclease-free Water (uL) | Numeric | | Decimal Places Displayed = 2 |
| Total Samples | Numeric | | Default = 0 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 2: First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Master Step Name = First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
#### Automations
Calculate Total Samples and 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.::Murine RNase Inhibitor (uL):: = step.::Total Samples:: * 0.5 * 1.1 ; \
step.::ProtoScript II Reverse Transcriptase (uL):: = step.::Total Samples:: * 1 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 5 * 1.1 ' \
-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 %}
Set Master Mix UDFs
* 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} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::4x First Strand Reaction Mix (uL):: = 4 ; output.::First Strand Enzyme Mix (uL):: = 1' \
-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 | 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** |
| ----------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------------------- |
| Murine RNase Inhibitor (uL) | Numeric | | Decimal Places Displayed = 2 |
| Nuclease-free Water (uL) | Numeric | | Decimal Places Displayed = 2 |
| ProtoScript II Reverse Transcriptase (uL) | Numeric | | Decimal Places Displayed = 2 |
| Thermal Cycler Program | Multiline Text | | Default =
10 minutes at 25°C
50 minutes at 42°C
15 minutes at 70°C
Hold at 4°C
|
| Total Samples | Numeric | | Default = 0 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
## Protocol 6: NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
### Step 1: Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Master Step Name = Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
* Step Type = No Outputs
* Reagent Kits
* NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
* Supplier = NEB
* Catalog Number = E6111S, E6111L
#### Automations
Calculate Total Samples and 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.::NEBNext Second Strand Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::NEBNext Second Strand Synthesis Enzyme Mix (uL):: = step.::Total Samples:: * 4 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 48 * 1.1 ' \
-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 %}
Set Master Mix UDFs
* 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} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::First Strand cDNA Synthesis (uL):: = 20 ; \
output.::5x Second Strand Reaction Mix (uL):: = 20 ; \
output.::Nuclease-free Water (uL):: = 55 ; \
output.::Second Strand Enzyme Mix (uL):: = 5 ; \
output.::Total Volume (uL):: = 100' \
-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 | 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** |
| --------------------------------------------------- | -------------- | ----------- | ----------------------------------------- |
| First-Strand Synthesis Product Volume per Well (uL) | Numeric | | Default = 20 |
| NEBNext Second Strand Reaction Buffer (uL) | Numeric | | Decimal Places Displayed = 2 |
| NEBNext Second Strand Synthesis Enzyme Mix (uL) | Numeric | | Decimal Places Displayed = 2 |
| Nuclease-free Water (uL) | Numeric | | Decimal Places Displayed = 2 |
| Total Samples | Numeric | | Default = 0 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 2: Purification of Double-stranded cDNA (Respiratory Virus Panel v1.0)
* Master Step Name = Purification of Double-stranded cDNA (Respiratory Virus Panel v1.0)
* Step Type = No Outputs
* Reagent Kits
* NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
* Supplier = NEB
* Catalog Number = E6111S, E6111L
#### Automations
Set Sample Type - ds cDNA
* 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 'input.::Sample Type:: = ::ds 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 Script - Nextera Flex for Enrichment INPUTS
* 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 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"
```
{% 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 = 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 File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
## Protocol 7: SuperScript Double-Stranded cDNA Synthesis Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
**Next Steps Configuration**
### Step 1: First-Strand Synthesis (Respiratory Virus Panel v1.0)
* Master Step Name = First-Strand Synthesis (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* SuperScript Double-Stranded cDNA Synthesis Kit
* Catalog Number = 11917-010, 11917-020
#### Automations
Calculate Master Mix
* 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 'if (!output.hasValue(::Prep Sample Type::)) {fail(::Please enter Prep Sample Type::)} ; \
if (!output.hasValue(::mRNA/Total RNA (ug)::)) {fail(::Please enter mRNA/Total RNA (ug) for each sample::)} ; \
if (output.::mRNA/Total RNA (ug):: <= 1 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ; output.::RNA in DEPC-treated water uL):: = 10 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 1 } ; \
if (output.::mRNA/Total RNA (ug):: == 2 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 9 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 2} ; \
if (output.::mRNA/Total RNA (ug):: == 3 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 8 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 3} ; \
if (output.::mRNA/Total RNA (ug):: == 4 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 7 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 4} ; \
if (output.::mRNA/Total RNA (ug):: == 5 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 6 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 5} ; \
if (output.::mRNA/Total RNA (ug):: <= 50 && output.::Prep Sample Type:: == ::Total RNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 9 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 2} ; \
if (output.::mRNA/Total RNA (ug):: <= 50 && output.::Prep Sample Type:: == ::Total RNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 10 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 1} ;' \
-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 | 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** |
| -------------- | -------------- | ----------- | -------------------------------------------------------------------------------------------- |
| Directions | Multiline Text | | Default = Please enter ug of starting mRNA or Total RNA and Prep Sample Type in field below. |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | 5X First-Strand Reaction Buffer (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | 0.1M DTT (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | 10 mM dNTP mix (uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | mRNA/Total RNA (ug) | Numeric | Required Field | Decimal Places Displayed = 2 |
| Derived Sample | Prep Sample Type | Text Dropdown | Required Field | Presets
|
| Derived Sample | Primer (100 pmol/uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | RNA in DEPC-treated water uL) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | SuperScript II RT (uL) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 2: Second-Strand Synthesis (Respiratory Virus Panel v1.0)
* Master Step Name = Second-Strand Synthesis (Respiratory Virus Panel v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* SuperScript Double-Stranded cDNA Synthesis Kit
* Catalog Number = 11917-010, 11917-020
#### Automations
Set Sample Type - ds cDNA output
* 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:: = ::ds 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 Script - Nextera Flex for Enrichment OUTPUTS
* 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 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--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 = 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 File Placeholders
* Log File - Automatically attached
* Sample Table
* 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 | Sample Name | Built-in | | |
| Derived Sample | Sample Type | Text Dropdown | - Required Field
- Custom Entries
| Presets
|
| Project | Project Name | Built-in | | |