# DNA Library Prep v1.1 ## Protocol 1: DNA Library Prep (AmpliSeq for Illumina Focus Panel v1.1) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Dilute DNA (AmpliSeq for Illumina Focus Panel v1.1) * Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations
Copy Concentration and Set Sample Volume * 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
Calculate Input Amount * 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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \ output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \ output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total Volume (uL):: ' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Advance * 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 '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** | | ----------------------------- | -------------- | ----------- | ----------------------------------------------------------------------- | | Desired Concentration (ng/uL) | Numeric | | | * Step File Placeholders * Log - 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 | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Input Amount (ng) | Numeric | | Decimal Places Displayed = 0 | | Derived Sample | Low TE (uL) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (uL) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Total Volume (uL) | Numeric | | Decimal Places Displayed = 2 | ### Step 2: Qubit (AmpliSeq for Illumina Focus Panel v1.1) * Master Step Name = Qubit (AmpliSeq for Illumina v1.1) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations
Assign QC flags (Qubit 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 {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}" ``` {% endcode %}
Set Next Step and Copy Concentration * 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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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** | | ------------------------------ | -------------- | ----------- | ----------------------------------------- | | Criteria 1 - Operator | Text | | Default = >= | | Criteria 1 - Source Data Field | Text | | Default = Concentration | | Criteria 1 - Threshold Value | Numeric | | | | Criteria 2 - Operator | Text | | Default = <= | | Criteria 2 - Source Data Field | Text | | Default = Concentration | | Criteria 2 - Threshold Value | Numeric | | | * Step File Placeholders * Log - Automatically attached * QC Log File - Automatically attached * QC Result File - Automatically attached * Upload File - Manually uploaded * Sample Table * Enable QC Flags = Yes * Sample Display Default = Expand * Well Sort Order = Row * 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** | | -------------- | -------------- | -------------- | -------------- | ----------------------------------------- | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | ### Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina Focus Panel v1.1) * Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations
Copy Concentration and Set Sample Volume * 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
Calculate Input Amount * 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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \ output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \ output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total 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 = 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** | | ----------------------------- | -------------- | ----------- | ----------------------------------------------------------------------- | | Desired Concentration (ng/uL) | Numeric | | | * Step File Placeholders * Log - 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 | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Input Amount (ng) | Numeric | | Decimal Places Displayed = 0 | | Derived Sample | Low TE (uL) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (uL) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Total Volume (uL) | Numeric | | Decimal Places Displayed = 2 | ### Step 4: Amplify Targets (AmpliSeq for Illumina Focus Panel v1.1) * Master Step Name = Amplify Targets (AmpliSeq for Illumina Focus Panel) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * AmpliSeq Focus Panel for DNA * Supplier = Illumina * Catalog Number = 20019164 * AmpliSeq Library PLUS for Illumina * Supplier = Illumina * Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel/www.illumina.com) #### Automations
Concentration,Total Volume and Input Amount- Focus Panel * 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Total Volume (uL):: = input.::Total Volume (uL):: ; output.::Input Amount (ng):: = input.::Input Amount (ng):: ; output.::5X AmpliSeq HiFi Mix (uL):: = 4.0 ; output.::5x AmpliSeq Focus Panel (uL):: = 4.0'\ -log {compoundOutputFileLuid0}" ``` {% endcode %}
Calculate Prep Input - Focus * 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 false \ -h false \ -exp 'output.::Prep Input Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Concentration:: ; \ if (output.::Prep Input Volume (uL):: < 12) {output.::Nuclease-free water (uL):: = 12 - output.::Prep Input 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 = 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** | | --------------------------- | -------------- | ----------- | --------------------------------------------------------------------------------------------- | | PCR Cycles | Numeric | | Decimal Places Displayed = 0 | | Recommended Prep Input (ng) | Multiline Text | Read Only | Default = This protocol supports 1-1000 ng. The recommended input is 100 ng high-quality DNA. | | Thermal Cycler Program | Text | | Default = AMP | * 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 AmpliSeq Focus Panel (uL) | Numeric | | | | Derived Sample | 5X AmpliSeq HiFi Mix (uL) | Numeric | | | | Derived Sample | Concentration | Numeric | Required Field | | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Input Amount (ng) | Numeric | | | | Derived Sample | Nuclease-free water (uL) | Numeric | | | | Derived Sample | Prep Input Amount (ng) | Numeric | Required Field | | | Derived Sample | Prep Input Volume (uL) | Numeric | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Total Volume (uL) | Numeric | | | | Project | Project Name | Built-in | | | ### Step 5: Partially Digested Amplicons (AmpliSeq for Illumina Focus Panel v1.1) * Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina Focus Panel v1.1) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * AmpliSeq cDNA Synthesis for Illumina * Supplier = Illumina * Catalog Number = 20022654 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel/www.illumina.com) #### 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 %}
Routing cDNA- Focus Panel * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Queue for Plate Transfer' \ --FIELD_VALUE 'Transfer Amplicons' \ --WORKFLOW 'DNA Library Prep AmpliSeq for Illumina Focus Panel v1.1' \ --STEP 'Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Focus Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' " ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
#### 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** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | Thermal Cycler Program | Text | | Default = FUPA | * Step File Placeholders * Log - 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 | | | | Project | Project Name | Built-in | | | ### Step 6: Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Focus Panel v1.1) * Master Step Name = Transfer RNA and DNA Amplicons (AmpliSeq for Illumina) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} #### 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 | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Row * Destination Containers * 96 well plate #### Record Details * Step File Placeholders * Log - 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 7: Ligate Indexes (AmpliSeq for Illumina Focus Panel v1.1) * Master Step Name = Ligate Indexes (AmpliSeq for Illumina v1.1) * Step Type = Add Labels * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * AmpliSeq Library PLUS for Illumina * Supplier = Illumina * Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/ampliseq/focus-panel/www.illumina.com) #### 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 %}
Route AmpliSeq Samples - Focus Panel * 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 {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Focus Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Focus Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Immune Repertoire Panel * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - BRCA * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina BRCA Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina BRCA Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Childhood Cancer Panel * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - CHP v2 * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - CP * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Custom DNA Panel * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Immune Response Panel * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Myeloid Panel * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples -Transcriptome Human GEx Panel * Trigger Location = Not Used {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Standard Workflow' \ --WORKFLOW 'Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'AmpliSeq Workflow' \ --FIELD_VALUE 'Equalizer Workflow' \ --WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \ --STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
#### 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 | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Row * Destination Containers * 96 well plate #### Add Labels * Label Groups * AmpliSeq CD Indexes Set A for Illumina * AmpliSeq CD Indexes Set B for Illumina * AmpliSeq CD Indexes Set C for Illumina * AmpliSeq CD Indexes Set D for Illumina * AmpliSeq UD Indexes for Illumina (24 Indexes) #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | Thermal Cycler Program | Text | | Default = LIGATE | * Step File Placeholders * Log - 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 | AmpliSeq Workflow | Text Dropdown | Required Field |

Preset

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