> 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/nextera/nextera-mate-pair-v1.0.md).
# Nextera Mate Pair v1.0
## Protocol 1: Nextera Mate Pair v1.0
Protocol Type = Library Prep
**Next Steps Configuration**
Master Mix Calculations
* 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.::Gel Type:: == ::Gel-Free::) {output.::Sample Volume (ul):: = 1000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 76 - output.::Sample Volume (ul)::} ; if (output.::Gel Type:: == ::Gel-Plus::) {output.::Sample Volume (ul):: = 4000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 308 - output.::Sample Volume (ul)::}' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ----------------------------------------------- | ---------------- | -------------- | ---------------------------------------------------------------------------------------------------- |
| Comment | Multiline Text | | |
| Mate Pair Tagment Enzyme Per Sample Volume (ul) | Numeric Dropdown | Custom Entries | Presets
Decimal Places Displayed = 2 Presets
Decimal Places Displayed = 2 Presets
|
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Water Per Sample (ul) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 2: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)
* Master Step Name = Bioanalyzer QC (DNA) v1.0
* Step Type = Standard QC
* Measurement Generation = Fixed, 1
* Naming Convention = {InputItemName}
#### 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 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' 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 %}
Set Next Step & Copy to Input
* 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:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Placement Pattern = Row
* Destination Containers
* BioAnalyzer DNA 7500 and DNA 1200 Chip
Presets
|
| Criteria 1 - Source Data Field | Text Dropdown | | Presets
Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity Presets
|
| Criteria 2 - Source Data Field | Text Dropdown | | Presets
Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | -------------- | --------------------------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Gel Type | Text Dropdown | Required Field | Presets
|
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 4: Purify the DNA (Nextera Mate Pair v1.0)
* Master Step Name = Purify the DNA (Nextera Mate Pair v1.0.10)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* AMPure XP Beads
* Supplier = Beckman Coulter Genomics
* Catalog Number = A63881
* Website =
* Nextera Mate Pair Library Prep Kit - Box 2
* Supplier = Illumina
* Catalog Number = FC-132-1001
> ℹ The version of Purify the DNA master step name may be different depending on the version of IPP installed.
#### Automations
Set Next Step based on Gel Type
* 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 'output.::Gel Type:: = input.::Gel Type:: ; if (step.::Next Step:: == ::Gel-Free::) {nextStep = ::Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Pippin Prep::) {nextStep = ::Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Agarose Gel::) {nextStep = ::Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::}' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------ | -------------- | -------------- | -------------------------------------------------------------------------------------------------- |
| Comment | Multiline Text | | |
| Next Step | Text Dropdown | Required Field | Presets
Gel-Free Gel-Plus Pippin Prep Gel-Plus Agarose Gel
Set Next Step & Copy Gel Type
* 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:: ; output.::Gel Type:: = input.::Gel Type::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* Gel Image - Manually uploaded
* 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: Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)
* Master Step Name = Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* 1 kb plus DNA ladder
* Supplier = Invitrogen
* Catalog Number = 10787-018
* 6X gel loading dye
* Supplier = BioLabs
* Catalog Number = B7021S
* 50X TAE buffer
* Supplier = Bio-Rad
* Catalog Number = 161-0743
* DNA Gel Extraction kit - Zymoclean Large Fragment DNA Recovery Kit
* Supplier = Zymo Research
* Catalog Number = D4045
* Megabase Agarose
* Supplier = Bio-Rad
* Catalog Number = 161-3108
* Nextera Mate Pair Library Prep Kit – Box 2
* Supplier = Illumina
* Catalog Number = FC-132-1001
* SYBR Safe
* Supplier = Invitrogen
* Catalog Number = S33102
> ℹ The version of Agarose Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.
#### Automations
Set Next Step - Advance
* 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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step & Copy Gel Type
* 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:: ; output.::Gel Type:: = input.::Gel Type::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* Gel Image - Manually uploaded
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 7: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)
* Master Step Name = Bioanalyzer QC (DNA) v1.0
* Step Type = Standard QC
* Measurement Generation = Fixed, 1
* Naming Convention = {InputItemName}
> ℹ The version of Bioanalyzer QC (DNA) master step name may be different depending on the version of IPP installed.
#### 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 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' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"
```
{% endcode %}
Set Next Step & Copy to Input
* 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:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Output PASS/FAIL
* 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 true -h false -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Placement Pattern = Row
* Destination Containers
* BioAnalyzer DNA 7500 and DNA 1200 Chip
Presets
|
| Criteria 1 - Source Data Field | Text Dropdown | | Presets
Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity Presets
|
| Criteria 2 - Source Data Field | Text Dropdown | | Presets
Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
Master Mix Calculations
* 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 'input.::Sample Volume (ul):: = input.::DNA Amount (ng):: / input.::Concentration (ng/ul):: ; input.::Water Per Sample (ul):: = 276 - input.::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 | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------- |
| Circularization Buffer 10x Per Sample Volume (ul) | Numeric | | Default = 30 Decimal Places Displayed = 0 Default = 2 Decimal Places Displayed = 0 Presets
|
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Water Per Sample (ul) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 9: Remove Linear DNA (Nextera Mate Pair v1.0)
* Master Step Name = Remove Linear DNA (Nextera Mate Pair v1.0.10)
* Step Type = No Outputs
* Reagent Kits
* Nextera Mate Pair Library Prep Kit - Box 1
* Supplier = Illumina
* Catalog Number = FC-132-1001
> ℹ The version of Remove Linear DNA master step name may be different depending on the version of IPP installed.
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 10: Shear Circularization DNA (Nextera Mate Pair v1.0)
* Master Step Name = Shear Circularization DNA (Nextera Mate Pair v1.0.10)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* Nextera Mate Pair Library Prep Kit - Box 1
* Supplier = Illumina
* Catalog Number = FC-132-1001
> ℹ The version of Shear Circularization DNA master step name may be different depending on the version of IPP installed.
#### Automations
Set Next Step & Copy Gel Type
* 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:: ; output.::Gel Type:: = input.::Gel Type::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------- | ---------------- | -------------- | ------------------------------------------------------------------------------------------ |
| Comment | Multiline Text | | |
| Cycles Per Burst | Numeric Dropdown | Custom Entries | Presets
Decimal Places Displayed = 0 Presets
Decimal Places Displayed = 0 Presets
Decimal Places Displayed = 0 Presets
Decimal Places Displayed = 0 Presets
Decimal Places Displayed = 0 Presets
Decimal Places Displayed = 0
Set Next Step & Copy Gel Type
* 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:: ; output.::Gel Type:: = input.::Gel Type::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Collapse
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 12: End Repair (Nextera Mate Pair v1.0)
* Master Step Name = End Repair (Nextera Mate Pair v1.0.10)
* Step Type = No Outputs
* Reagent Kits
* Nextera Mate Pair Library Prep Kit - Box 2
* Supplier = Illumina
* Catalog Number = FC-132-1001
* TruSeq DNA LT Library Prep Kit - Set A Box
* Supplier = Illumina
* Catalog Number = FC-132-1001
> ℹ The version of End Repair master step name may be different depending on the version of IPP installed.
#### Automations
Master Mix Calculations
* Trigger Location = Record Details
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c " /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::End Repair Mix Volume (ul):: = step.::Total samples:: * 40) ; (step.::Water Volume (ul):: = step.::Total samples:: * 60)' -log {compoundOutputFileLuid1}"
```
{% 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 | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| End Repair Mix Volume (ul) | Numeric | | Decimal Places Displayed = 0 |
| Water Volume (ul) | Numeric | | Decimal Places Displayed = 0 |
* Step File Placeholders
* Log File - Automatically attached
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 13: A-Tailing (Nextera Mate Pair v1.0)
* Master Step Name = A-Tailing (Nextera Mate Pair v1.0.10)
* Step Type = No Outputs
* Reagent Kits
* TruSeq DNA LT Library Prep Kit - Set A Box
* Supplier = Illumina
* Catalog Number = FC-132-1001
> ℹ The version of A-Tailing master step name may be different depending on the version of IPP installed.
#### Automations
Master Mix Calculations
* 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:http} -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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::A-Tailing Mix Volume (ul):: = step.::Total samples:: * 12.5) ; (step.::Water Volume (ul):: = step.::Total samples:: * 17.5)' -log {compoundOutputFileLuid1}"
```
{% 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 | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------- | -------------- | ----------- | ----------------------------------------- |
| A-Tailing Mix Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Comment | Multiline Text | | |
| Water Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
* Step File Placeholders
* Log File - Automatically attached
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 14: Ligate Adapters (Nextera Mate Pair v1.0)
* Master Step Name = Ligate Adapters v2.0
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* Nextera Mate Pair Library Prep Kit - Box 1
* Supplier = Illumina
* Catalog Number = FC-132-1001
* TruSeq DNA LT Library Prep Kit - Set A Box
* Supplier = Illumina
* Catalog Number = FC-132-1001
> ℹ The version of Ligate Adapters master step name may be different depending on the version of IPP installed.
#### 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 %}
Copy to Output
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step & Copy to Input
* 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:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Placement = Enabled
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Placement Pattern = Column
* Destination Containers
* Tube
#### Add Labels
* Label Groups
* Nextera Mate Pair
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------------------------------- | -------------- | ----------- | -------------------------------------------------------------------- |
| A-Tailing Reaction/Bead Mix Per Sample Volume (ul) | Numeric | | Default = 30 Decimal Places Displayed = 0 Default = 2.5 Decimal Places Displayed = 1 Default = 4 Decimal Places Displayed = 0
Master Mix Calculations
* 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 '(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 true -h false -exp '(step.::Enhanced PCR Mix Volume (ul):: = step.::Total samples:: * 20 * 1.1) ; (step.::PCR Primer Cocktail Volume (ul):: = step.::Total samples:: * 5 * 1.1) ; (step.::Water Volume (ul):: = step.::Total samples:: * 25 * 1.1)' -log {compoundOutputFileLuid1}"
```
{% 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 | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------- | ---------------- | -------------- | ---------------------------------------------------------------------------------------------------- |
| Comment | Multiline Text | | |
| Enhanced PCR Mix Volume (ul) | Numeric | | Decimal Places Displayed = 2 Presets
Decimal Places Displayed = 0 Decimal Places Displayed = 2 Decimal Places Displayed = 2
* Nextera Mate Pair Library Prep Kit - Box 2
* Supplier = Illumina
* Catalog Number = FC-132-1001
* TruSeq DNA LT Library Prep Kit - PCR Box
* Supplier = Illumina
* Catalog Number = FC-132-1001
> ℹ The version of Clean Up master step name may be different depending on the version of IPP installed.
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------ | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 17: Bioanalyzer QC (Library Validation) (Nextera Mate Pair v1.0)
* 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 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, 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, 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
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 Mate Pair 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
Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity Presets
|
| Criteria 2 - Source Data Field | Text Dropdown | | Presets
Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
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 field name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
* Sample Table
* Column Headers
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------- | -------------- | -------------- | ------------------------------------------------------------------ |
| Comment | Multiline Text | | |
| Final Volume (ul) | Numeric | Required Field | Decimal Places Displayed = 2 Default = 2 Decimal Places Displayed = 2 Presets
MiSeq NextSeq NextSeq 1000/2000 NextSeq 1000/2000 On-Prem NovaSeq 2.0 NovaSeq 3.0 NovaSeq X Series NovaSeqDx &goal=
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