# TruSight Tumor 170 v2.0 ## Overview TruSight Tumor 170 v2.0 includes the following functionality: * Preconfigured TruSight Tumor 170 v2.0 protocol that supports the preparation of samples for the detection of gene variants across 170 gene targets in nucleic acids extracted from FFPE cancer tissue samples. * 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 script that allows sequencing of libraries using any Illumina sequencing instrument. ## Protocol 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0) Protocol Type = Sample Prep **Next Steps Configuration**
### Step 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0) * Master Step Name = DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 2 * Naming Convention = {LIST:{SubmittedSampleName}\_DNA,{SubmittedSampleName}\_RNA} * Reagent Kits * QIAGEN AllPrep DNA/RNA FFPE Kit * Supplier = Qiagen * Catalog Number = 80234 {% hint style="info" %} The version of DNA/RNA FFPE Extraction master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Sample Type * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (output.name.endsWith(::_RNA::)) {output.::Sample Type:: = ::RNA::}; if (output.name.endsWith(::_DNA::)) {output.::Sample Type:: = ::DNA::}' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Remove * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Route DNA/RNA samples * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Sample Type' \ --FIELD_VALUE 'RNA' \ --WORKFLOW 'TruSight Tumor 170 v2.0.10' \ --STEP 'Qubit RNA QC (TruSight Tumor 170 v2.0.10)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sample Type' \ --FIELD_VALUE 'DNA' \ --WORKFLOW 'TruSight Tumor 170 v2.0.10' \ --STEP 'Qubit DNA QC (TruSight Tumor 170 v2.0.10)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ------------------------------------------------------- | ----------------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Type | Text Dropdown | |

Presets

| | Project | Project Name | Built-in | | | ## Protocol 2: RNA QC and cDNA Synthesis (TruSight Tumor 170 v2.0) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Qubit RNA QC (TruSight Tumor 170 v2.0) * Master Step Name = Qubit RNA QC (TruSight Tumor 170 v2.0.10) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} {% hint style="info" %} The version of Qubit RNA QC master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Assign QC flags - RNA * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid2} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ------------------------------------------------------- | ----------------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Type | Text Dropdown | |

Presets

| | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | -------------- | --------------------------------------------------------------------------------------------------------- | | Criteria 1 - Operator | Text Dropdown | Custom Entries | | | Criteria 1 - Source Data Field | Text | | | | Criteria 1 - Threshold Value | Numeric | | | | Criteria 2 - Operator | Text Dropdown | Custom Entries | | | Criteria 2 - Source Data Field | Text | | | | Criteria 2 - Threshold Value | Numeric | | | * Step File Placeholders * Log File - Automatically attached * Qubit Result File - Manually uploaded * Sample Table * Enable QC Flags = Yes * Sample Display Default = Expand * Well Sort Order = Column * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 2: Denature and Anneal RNA (TruSight Tumor 170 v2.0) * Master Step Name = Denature and Anneal RNA (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSight Tumor 170, Box 1 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Denature and Anneal RNA master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
RNA Sample Dilution * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Sample Volume (ul):: = (step.::Dilution Concentration (ng/ul):: * 17) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 17 - output.::Sample Volume (ul)::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | -------------- | --------------------------------------------------------------------------------------- | | Comment | Multiline Text | | | | Dilution Concentration (ng/ul) | Numeric | Required Field | | | FSM (ul) | Text Dropdown | Custom Entries | | | RVT (ul) | Text Dropdown | Custom Entries | | | Thermal Cycler Program | Text Dropdown | Custom Entries | | * Step File Placeholders * Calculation Log File - Automatically attached * NextStep Log File - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Buffer Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 3: First Strand cDNA Synthesis (TruSight Tumor 170 v2.0) * Master Step Name = First Strand cDNA Synthesis v2.0 * Step Type = No Outputs {% hint style="info" %} The version of First Strand cDNA Synthesis master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------- | -------------- | -------------- | ------------------------------------------------------------------- | | Comment | Multiline Text | | | | Thermal Cycler Program | Text Dropdown | Custom Entries |

Presets

| * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 4: Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0) * Master Step Name = Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0.10) * Step Type = No Outputs * Reagent Kits * TruSight Tumor 170, Box 1 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Second Strand cDNA Synthesis master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | Thermal Cycler Program | Text | Read Only | Default = 2ndSS | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 5: cDNA Clean Up (TruSight Tumor 170 v2.0) * Master Step Name = cDNA Clean Up (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName}\_cDNA * Reagent Kits * TruSight Tumor 170, Box 3 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of cDNA Clean Up master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Assign Sample Type * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Sample Type:: = ::cDNA::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Remove * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Routing cDNA samples * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Sample Type' \ --FIELD_VALUE 'cDNA' \ --WORKFLOW 'TruSight Tumor 170 v2.0.10' \ --STEP 'End Repair and A-Tailing (TruSight Tumor 170 v2.0.10)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | BIND1 Plate Barcode | Text | | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ------------------------------------------------------- | ----------------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Type | Text Dropdown | |

Presets

| | Project | Project Name | Built-in | | | ## Protocol 3: DNA QC and Fragmentation (TruSight Tumor 170 v2.0) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Qubit DNA QC (TruSight Tumor 170 v2.0) * Master Step Name = Qubit DNA QC (TruSight Tumor 170 v2.0.10) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} {% hint style="info" %} The version of Qubit DNA QC master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Assign QC flags - DNA * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid1} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ------------------------------------------------------- | ----------------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Type | Text Dropdown | |

Presets

| | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | ----------- | --------------------------------------------------------------------------------------------------------- | | Criteria 1 - Operator | Text Dropdown | | | | Criteria 1 - Source Data Field | Text | | | | Criteria 1 - Threshold Value | Numeric | | | | Criteria 2 - Operator | Text Dropdown | | | | Criteria 2 - Source Data Field | Text | | | | Criteria 2 - Threshold Value | Numeric | | | * Step File Placeholders * Log File - Automatically attached * Qubit Result File - Automatically attached * Sample Table * Enable QC Flags = Yes * Sample Display Default = Expand * Well Sort Order = Column * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 2: Fragment DNA (TruSight Tumor 170 v2.0) * Master Step Name = Fragment DNA (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName}\_DNA {% hint style="info" %} The version of Fragment DNA master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Dilution Calculation * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Sample Volume (ul):: = (step.::Dilution Concentration (ng/ul):: * step.::Minimum Final Volume (uL)::) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = step.::Minimum Final Volume (uL):: - output.::Sample Volume (ul)::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Placement Pattern = Column * Destination Containers * 96 well plate #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | -------------- | ------------------------------------------------------------------------ | | Comment | Multiline Text | | | | Dilution Concentration (ng/ul) | Numeric | Required Field | | | Minimum Final Volume (uL) | Numeric | Required Field | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Buffer Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ## Protocol 4: Library Prep (TruSight Tumor 170 v2.0) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: End Repair and A-Tailing (TruSight Tumor 170 v2.0) * Master Step Name = End Repair and A-Tailing (TruSight Tumor 170 v2.0.10) * Step Type = No Outputs * Reagent Kits * TruSight Tumor 170, Box 2 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of End Repair and A-Tailing master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ---------------- | -------------- | ---------------------------------------------------------------------------------------------------------------------------- | | Comment | Multiline Text | | | | ERA1-A (ul) | Numeric Dropdown | Custom Entries | | | ERA1-B (ul) | Numeric Dropdown | Custom Entries | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 2: Ligate Adapters (TruSight Tumor 170 v2.0) * Master Step Name = Ligate Adapters (TruSight Tumor 170 v2.0.10) * Step Type = No Outputs * Reagent Kits * TruSight Tumor 170, Box 2 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Ligate Adapters master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 3: Clean Up Ligation (TruSight Tumor 170 v2.0) * Master Step Name = Clean Up v2.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSight Tumor 170, Box 3 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Clean Up master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 4: Index PCR (TruSight Tumor 170 v2.0) * Master Step Name = Index PCR (TruSight Tumor 170 v2.0.10) * Step Type = Add Labels * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} * Reagent Kits * TruSight Tumor 170, Box 2 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 4 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 5 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Index PCR master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Add Labels * Label Groups * TruSight Tumor 170 Index List #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | PCR Program | Text | Read Only | Default = I-PCR | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Reagent Name | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ## Protocol 5: Hybridization (TruSight Tumor 170 v2.0) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Perform First Hybridization (TruSight Tumor 170 v2.0) * Master Step Name = Hybridize v2.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSight Tumor 170, Box 6 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 7 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 8 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 9 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Hybridize master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
Library Dilution * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Library Volume (ul):: = 200 / input.::Concentration (ng/ul):: ; output.::RSB Volume (ul):: = 10 - output.::Library Volume (ul)::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | PCR Program | Text | | Default = HYB1 | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 2: Perform First Capture (TruSight Tumor 170 v2.0) * Master Step Name = Perform First Capture (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} * Reagent Kits * TruSight Tumor 170, Box 6 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 7 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Perform First Capture master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------ | ---------------- | -------------- | ----------------------------------------------------------------------------------------------------------------------------- | | CAP1 Plate Barcode | Text | | | | Comment | Multiline Text | | | | EE2 (ul) | Numeric Dropdown | Custom Entries | | | HP3 (ul) | Numeric Dropdown | Custom Entries | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 3: Perform Second Hybridization (TruSight Tumor 170 v2.0) * Master Step Name = Perform Second Hybridization (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} * Reagent Kits * TruSight Tumor 170, Box 6 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 7 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 8 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 9 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Perform Second Hybridization master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | PCR Program | Text | Read Only | Default = HYB2 | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 4: Perform Second Capture (TruSight Tumor 170 v2.0) * Master Step Name = Perform Second Capture (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} * Reagent Kits * TruSight Tumor 170, Box 6 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 7 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Perform Second Capture master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------- | ---------------- | -------------- | ----------------------------------------------------------------------------------------------------------------------------- | | BIND1 Plate Barcode | Text | | | | Comment | Multiline Text | | | | EE2 (ul) | Numeric Dropdown | Custom Entries | | | HP3 (ul) | Numeric Dropdown | Custom Entries | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 5: Amplify Enriched Library (TruSight Tumor 170 v2.0) * Master Step Name = Amplify Enriched Library v2.0 * Step Type = No Outputs * Reagent Kits * TruSight Tumor 170, Box 7 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Amplify Enriched Library master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | PCR | Text | | Default = EL-PCR | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 6: Clean Up Amplified Enriched Library (TruSight Tumor 170 v2.0) * Master Step Name = Clean Up v2.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSight Tumor 170, Box 3 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Clean Up master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | BIND3 Plate Barcode | Text | | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ## Protocol 6: Library QC and Normalization (TruSight Tumor 170 v2.0) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Quantify Libraries (TruSight Tumor 170 v2.0) * Master Step Name = Quantify Libraries (TruSight Tumor 170 v2.0.10) * Step Type = Standard QC * Derived Sample Generation = Fixed, 3 * Naming Convention = {SubmittedSampleName} * Control Types * Blank Solution (TruSight Tumor 170 v2.0.10) * DNA Standard (TruSight Tumor 170 v2.0.10) * Conc. = 3 ng/ul {% hint style="info" %} The version of Quantify Libraries master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Average Replicate and Assign QC * 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:computeReplicateAverage -src 'Concentration (ng/ul)' -dest 'Concentration (ng/ul)' -exclude 'Exclude' -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 true -h false -exp 'if(input.::Concentration (ng/ul):: >= 3) { output.QC = true } else { output.QC = false } ; input.QC = output.QC' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Steps - PASS/FAIL * 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 true -h false -excludeControls true -exp 'if (input.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Placement Pattern = Column * Destination Containers * 96 well plate #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | * Step File Placeholders * Log File - Manually uploaded * Sample Table * Enable QC Flags = Yes * Sample Display Default = Expand * Well Sort Order = Column * File Column Options * File Column Display = Hide * File Attachment Method = Manual * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Measurement | Exclude | Toggle Switch | | Default = None Set | | Project | Project Name | Built-in | | | ### Step 2: Normalize Libraries (TruSight Tumor 170 v2.0) * Master Step Name = Normalize Libraries (TruSight Tumor 170 v2.0.10) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} * Reagent Kits * TruSight Tumor 170, Box 6 * Supplier = Illumina * Catalog Number = OP-101-1004 * TruSight Tumor 170, Box 7 * Supplier = Illumina * Catalog Number = OP-101-1004 {% hint style="info" %} The version of Normalize Libraries master step name may be different depending on the version of IPP installed. {% endhint %} #### 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 - Normalize Libraries * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'MiSeq' \ --WORKFLOW 'MiSeq Sequencing v3.2' \ --STEP 'Library Pooling (MiSeq v3.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NextSeq' \ --WORKFLOW 'NextSeq 500/550 Sequencing v1.2' \ --STEP 'Library Pooling (NextSeq 500/550 v1.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeq 2.0' \ --WORKFLOW 'NovaSeq 6000 v2.3' \ --STEP 'Define Run Format (NovaSeq 6000 v2.3)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeq 3.0' \ --WORKFLOW 'NovaSeq 6000 v3.8' \ --STEP 'Define Run Format (NovaSeq 6000 v3.8)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeqDx' \ --WORKFLOW 'NovaSeqDx v1.2' \ --STEP 'Define Run Format (NovaSeqDx v1.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NextSeq 1000/2000' \ --WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \ --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeq X Series' \ --WORKFLOW 'NovaSeq X Series v1.1' \ --STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \ --WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \ --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The field name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | --------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | LIMS ID (Container) | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------------- | ---------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------------- | | BIND4 Plate Barcode | Text | | | | Comment | Multiline Text | | | | HP3 (ul) | Numeric Dropdown | Custom Entries | | | LNA1 (ul) | Numeric Dropdown | Custom Entries | | | LNB1 (ul) | Numeric Dropdown | Custom Entries | | | PCR-grade water (ul) | Numeric Dropdown | Custom Entries | | * 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 | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sequencing Instrument | Text Dropdown | Required Field |

Presets

| | Project | Project Name | Built-in | | | > ℹ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.