> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/clarity-lims/library-prep/other-dna-protocols/dna-prep-m-tag-v1.0.md). # Illumina DNA Prep (M) Tagmentation v1.0 ## Overview The Illumina DNA Prep (M) Tagmentation workflow includes the following functionality. * Preset Illumina DNA Prep (M) Tagmentation protocols that support the generation of enriched libraries for dual-indexed, paired-end sequencing. * 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. ## Protocol 1: Prep Sample (Illumina DNA Prep (M) Tagmentation v1.0.9) Protocol Type = Sample Prep **Next Steps Configuration**
### Step 1: Sort Sample Type (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Sort Sample v2.0.8 * Step Type = No Outputs {% hint style="info" %} The version of Sort Sample master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Next Step - Tagmentation * 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 -exp 'if (input.::Prep Sample Type - Tagmentation:: == ::Large Complex Genomes::) {nextStep = ::REMOVE::} ; \ if (input.::Prep Sample Type - Tagmentation:: == ::Small Genomes::) {nextStep = ::DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \ if (input.::Prep Sample Type - Tagmentation:: == ::Saliva::) {nextStep = ::Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \ if (input.::Prep Sample Type - Tagmentation:: == ::Blood::) {nextStep = ::Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ' -log {compoundOutputFileLuid0}" ``` {% endcode %} > ℹ The version of the nextStep step names may be different depending on the version of IPP installed.
Route Samples - Large Complex Genome * 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 'Prep Sample Type - Tagmentation' \ --FIELD_VALUE 'Large Complex Genomes' \ --WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \ --STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \ --INPUTS_OR_OUTPUTS 'INPUTS' " ``` {% endcode %} > ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | * 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 | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 2: DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} {% hint style="info" %} The version of DNA Quantification master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Calculate DNA Amount & 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:evaluateDynamicExpression -t true -h false -exp 'output.::DNA Amount (ng):: = output.::Concentration (ng/ul):: * output.::Sample Volume (ul)::' -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 (output.::DNA Amount (ng):: >= 0.33 && output.::DNA Amount (ng):: <= 100) { output.QC = true } else { output.QC = false } ; input.::DNA Amount (ng):: = output.::DNA Amount (ng):: ; input.::Concentration (ng/ul):: = output.::Concentration (ng/ul):: ; output.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation::' -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 Samples - Small Genomes * 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 'Prep Sample Type - Tagmentation' \ --FIELD_VALUE 'Small Genomes' \ --WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \ --STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \ --INPUTS_OR_OUTPUTS 'INPUTS' " ``` {% endcode %} > ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | * Step File Placeholders * Log - Automatically attached * Sample Table * Enable QC Flags = Yes * Sample Display Default = Expand * Well Sort Order = Row * File Column Options * File Column Display = Show * 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 | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration (ng/ul) | Numeric | | Decimal Places Displayed = 2 | | Measurement | DNA Amount (ng) | Numeric | | Decimal Places Displayed = 0 | | Measurement | Prep Sample Type - Tagmentation | Text | Read Only | | | Measurement | Sample Volume (ul) | Numeric | Required Field | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 3: Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1 * Supplier = Illumina * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Flex Lysis Reagent Kit * Supplier = Illumina {% hint style="info" %} The version of Blood Lysis master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Count Samples and Calculate Master Mix * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \ step.::BLB (uL):: = step.::Total Samples:: * 7 ; \ step.::PK1 (uL):: = step.::Total Samples:: * 2 ; \ step.::Nuclease-free water (uL):: = step.::Total Samples:: * 31' -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 Samples - Blood * 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 'Prep Sample Type - Tagmentation' \ --FIELD_VALUE 'Blood' \ --WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \ --STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' " ``` {% endcode %} > ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------ | -------------- | ----------- | ----------------------------------------- | | 80% Ethanol Prep Date | Date | | | | BLB (uL) | Numeric | | Decimal Places Displayed = 2 | | Comment | Multiline Text | | | | Nuclease-free water (uL) | Numeric | | Decimal Places Displayed = 2 | | PK1 (uL) | Numeric | | Decimal Places Displayed = 2 | | Thermal Cycler Program | Text | | Default = BLP | | Total Samples | Numeric | | Default = 0 | * 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 | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 4: Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1 * Supplier = Illumina {% hint style="info" %} The version of Saliva Lysis master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Copy Prep Sample Type - Tagmentation * 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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation::' -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** | | --------------------- | -------------- | ----------- | ----------------------------------------- | | 80% Ethanol Prep Date | Date | | | | Comment | Multiline Text | | | * 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 | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ## Protocol 2: Library Prep (Illumina DNA Prep (M) Tagmentation v1.0.9) Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Tagment Genomic DNA v1.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 2 * Supplier = Illumina * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 3 * Supplier = Illumina #### Automations
Copy Prep Sample Type - Tagmentation, DNA Amount & Set Blood and Saliva 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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \ if (input.::Prep Sample Type - Tagmentation:: == ::Blood:: || input.::Prep Sample Type - Tagmentation:: == ::Saliva::) {output.::Sample Volume (ul):: = 30} ; \ if (input.hasValue(::DNA Amount (ng)::)) {output.::DNA Amount (ng):: = input.::DNA Amount (ng)::}' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Calculate DNA Amount for SMALL GENOMES * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (output.::Prep Sample Type - Tagmentation:: == ::Small Genomes:: && !step.hasValue(::Desired DNA Amount (ng)::)) {fail(::Please enter Desired DNA Amount (ng)::)} else {if (output.::Prep Sample Type - Tagmentation:: == ::Small Genomes:: && step.hasValue(::Desired DNA Amount (ng)::)) {output.::Sample Volume (ul):: = step.::Desired DNA Amount (ng):: / input.::Concentration (ng/ul):: ; output.::Nuclease-free water (ul):: = 30 - 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 = 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** | | ----------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Comment | Multiline Text | | | | Desired DNA Amount (ng) | Numeric | | Decimal Places Displayed = 1 | | Directions | Multiline Text | |

Default =
If Sample Type is Small Genome, please enter a Desired DNA Amount (ng) at the top of the screen & press blue button.
If Sample Type is Large Complex Genome please enter Sample Volume (ul).

| | Thermal Cycler Program | Text | | Default = TAG | * 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 | Nuclease-free water (ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 2: Post Tagmentation Clean Up (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Post Tagmentation Clean Up v1.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1 * Supplier = Illumina #### Automations
Copy Prep Sample Type - Tagmentation & DNA Amount * 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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \ if (input.hasValue(::DNA Amount (ng)::)) {output.::DNA Amount (ng):: = input.::DNA Amount (ng)::}' -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** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | Thermal Cycler Program | Text | | Default = PTC | * 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 | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 3: Amplify Tagmented DNA (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Amplify Tagmented DNA v3.0 * Step Type = Add Labels * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 2 * Supplier = Illumina #### Automations
Set Prep Sample Type - Tagmentation & Set PCR Cycles * 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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \ if (input.::Prep Sample Type - Tagmentation:: == ::Small Genomes::) {if (input.::DNA Amount (ng):: >= 1 && input.::DNA Amount (ng):: <= 9) {output.::PCR Cycles:: = 12} ; \ if (input.::DNA Amount (ng):: >=10 && input.::DNA Amount (ng):: <= 24) {output.::PCR Cycles:: = 8} ; \ if (input.::DNA Amount (ng):: >=25 && input.::DNA Amount (ng):: <= 49) {output.::PCR Cycles:: = 6} ; \ if (input.::DNA Amount (ng):: >=50 && input.::DNA Amount (ng):: <= 100) {output.::PCR Cycles:: = 5}} else {output.::PCR Cycles:: = 5}' -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 | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Row * Destination Containers * 96 well plate #### Add Labels * Label Groups * IDT for Illumina DNA-RNA UD Indexes Set A Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set A-D Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set B Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set C Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set D Tagmentation * IDT for Illumina Nextera DNA UD Indexes Set A for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000 * IDT for Illumina Nextera DNA UD Indexes Set A-D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000 * IDT for Illumina Nextera DNA UD Indexes Set B for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000 * IDT for Illumina Nextera DNA UD Indexes Set C for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000 * IDT for Illumina Nextera DNA UD Indexes Set D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000 * Illumina DNA-RNA UD Indexes Set A B C D Tagmentation * Illumina DNA-RNA UD Indexes Set A Tagmentation * Illumina DNA-RNA UD Indexes Set B Tagmentation * Illumina DNA-RNA UD Indexes Set C Tagmentation * Illumina DNA-RNA UD Indexes Set D Tagmentation #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | Comment | Multiline Text | | | | Thermal Cycler Program | Text | | Default = BLT PCR | * 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 | PCR Cycles | Numeric | | Decimal Places Displayed = 0 | | Derived Sample | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 4: Clean Up Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Clean Up Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1 * Supplier = Illumina {% hint style="info" %} The version of Clean Up Libraries master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Set Prep Sample Type - Tagmentation, Count Samples & Calculate Master Mix * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \ step.::SPB (ul):: = step.::Total Samples:: * 45 ; \ step.::Nuclease-free water (ul):: = step.::Total Samples:: * 40' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Optional Pooling * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (output.::Pool Samples?:: == ::YES::) {nextStep = ::Optional Pool Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \ if (output.::Pool Samples?:: == ::NO::) {nextStep = ::Bioanalyzer Library QC (Illumina DNA Prep (M) Tagmentation v1.0.9)::}' -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** | | ------------------------ | -------------- | ----------- | ----------------------------------------- | | 80% EtOH Prep Date | Date | | | | Comment | Multiline Text | | | | Nuclease-free water (ul) | Numeric | | Decimal Places Displayed = 2 | | SPB (ul) | Numeric | | Decimal Places Displayed = 2 | | Total Samples | Numeric | | Default = 0 | * 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 | Pool Samples? | Text Dropdown | Required Field |

Presets

| | Derived Sample | Prep Sample Type - Tagmentation | Text Dropdown | Required Field |

Presets

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 5: Optional Pool Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Pool Libraries v2.0 * Step Type = Pooling * Aliquot Generation = Fixed, 1 * Naming Convention = {PoolName} #### 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 | | | #### Pooling * Label Uniqueness = On * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row #### 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 6: Bioanalyzer Library QC (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Bioanalyzer QC (Library Validation) v2.0 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} Bioanalyzer #### Automations
Generate Bioanalyzer Input file * 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/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -f {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} -sep COMMA -b ',False,' -h 1 -c LIMSID -pre 'Sample '" ``` {% endcode %}
Parse Bioanalyzer XML, Copy nM and Assign QC flags * 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:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (output.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /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 {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}" ``` {% endcode %}
Set Next Step - Output 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 (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations * 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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7} && /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.::Concentration:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}" ``` {% endcode %}
Parse Bioanalyzer XML and assign QC flags * 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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}" ``` {% endcode %}
Parse Bioanalyzer XML, Calculate nM and assign QC flags * 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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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.::Concentration:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -log {compoundOutputFileLuid8} && /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 {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}" ``` {% 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 = Column * Placement Pattern = Column * Destination Containers * BioAnalyzer DNA High Sensitivity Chip
* BioAnalyzer DNA 1000 Chip
#### Record Details **Group of Defaults**
Nextera DNA Flex Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 150.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 1,500.00
Nextera Mate Pair Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 150.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Average Size - bp * Criteria 2 - Threshold Value = 400.00
Nextera XT DNA Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 250.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 1,000.00
NRCC Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 350.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 1,000.00
TruSeq ChIP-Seq Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 150.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Average Size - bp * Criteria 2 - Threshold Value = 400.00
TruSeq Exome Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 150.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 1,000.00
TruSeq Methyl Capture EPIC Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 200.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 300.00
TruSeq Rapid Exome Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 200.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 500.00
TruSeq RNA Access Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 200.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 320.00
TruSeq RNA Exome Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 200.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 320.00
TruSeq Small RNA Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 100.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Average Size - bp * Criteria 2 - Threshold Value = 200.00
TruSeq Stranded mRNA Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 250.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Average Size - bp * Criteria 2 - Threshold Value = 275.00
TruSeq Stranded Total RNA Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 250.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Average Size - bp * Criteria 2 - Threshold Value = 275.00
TruSeq Targeted RNA Expression Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 100.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 300.00
TruSight Myeloid Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 150.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Size - bp * Criteria 2 - Threshold Value = 400.00
TruSight RNA Fusion Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 160.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Size - bp * Criteria 2 - Threshold Value = 700.00
TSCA Library Validation * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Average Size - bp * Criteria 1 - Threshold Value = 300.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Size - bp * Criteria 2 - Threshold Value = 400.00
* Step Data * Group of Defaults = Nextera DNA Flex Library Validation * Master Step Fields | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------------------- | -------------- | -------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Criteria 1 - Operator | Text Dropdown | Custom Entries |

Presets

| | Criteria 1 - Source Data Field | Text Dropdown | |

Presets

| | Criteria 1 - Threshold Value | Numeric | | Decimal Places Displayed = 2 | | Criteria 2 - Operator | Text Dropdown | Custom Entries |

Presets

| | Criteria 2 - Source Data Field | Text Dropdown | |

Presets

| | Criteria 2 - Threshold Value | Numeric | | Decimal Places Displayed = 2 | | Use strict matching for Bioanalyzer results | Toggle Switch | | Default = None Set | * Step File Placeholders * Bioanalyzer Input File - Automatically attached * Bioanalyzer Input File Generation Log File - Automatically attached * Bioanalyzer XML Result File (required) - Manually uploaded * Result File (optional) - Manually uploaded * PDF Summary File (optional) - Manually uploaded * Bioanalyzer XML Parsing Log File - Automatically attached * QC Assignment Log File - Automatically attached * QC Assignment Report - 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** | | -------------- | -------------------------- | -------------- | ----------- | ----------------------------------------- | | Derived Sample | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Measurement | BA Sample Name | Text | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Measurement | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Measurement | Number of Peaks found | Numeric | | Decimal Places Displayed = 0 | | Measurement | Number of Regions found | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 1 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 1 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 1 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 2 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 2 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 2 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 3 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 3 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 3 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 4 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 4 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 4 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 5 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 5 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 5 Size - bp | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 1 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 1 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 1 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 2 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 2 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 2 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 3 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 3 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 3 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 4 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 4 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 4 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 5 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 5 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 5 Molarity | Numeric | | Decimal Places Displayed = 2 | ### Step 7: Normalize Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9) * Master Step Name = Normalize Libraries 1 v2.0.10 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} {% hint style="info" %} The version of Normalize Libraries 1 master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Normalization Calculations - Option 1 * 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.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Final Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = (step.::Target Normalization (nM):: * step.::Final Volume (ul):: ) / input.::Molarity (nM):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Remove * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Routing script - 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 actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------- | -------------- | -------------- | ------------------------------------------------------------------ | | Comment | Multiline Text | | | | Final Volume (ul) | Numeric | Required Field | | | Target Normalization (nM) | Numeric | Required Field | | * Step File Placeholders * Log - 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 | Buffer Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sequencing Instrument | Text Dropdown | Required Field |

Presets

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