# 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

| | 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

| | 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

| | 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

| | 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

| | 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 | |

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 | |

Presets

| | Project | Project Name | Built-in | | | --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.claritylims.illumina.com/applications/viral-pathogen-protocols/covid-respiratory-virus-panel-v1.0.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.