# RNA Initial QC 5.1.2 ## Overview The initial RNA QC protocol contains steps to track quality control data from commonly used QC instruments. Through data integrations, QC data can be added to Clarity LIMS directly from the instrument outputs. Highlights of this protocol include: * Data integrations for Bioanalyzer 2100, Nanodrop 8000, CaliperGX, and Tapestation 2200, including creation of the input file and parsing of data output. * Assignment of pass/fail QC based on chosen criteria. * Aggregation of data from multiple QC steps. ## Protocol 1: RNA Initial QC 5.1.2 * Protocol Type = QC * Capacity = 50 * QC Filters * Bioanalyzer QC (RNA) 5.1.2 * Did not pass - Bioanalyzer QC (RNA) 5.1.2 * NanoDrop QC (RNA) 5.1.2 * Did not pass - NanoDrop QC (RNA) 5.1.2 * Qubit QC (RNA) 5.1.2 * Did not pass - Qubit QC (RNA) 5.1.2 * PicoGreen QC (RNA) 5.1.2 * Did not pass - PicoGreen QC (RNA) 5.1.2 * CaliperGX QC 5.1.2 * Did not pass - CaliperGX QC 5.1.2 * Tapestation QC (RNA) 5.1.2 * Did not pass - Tapestation QC (RNA) 5.1.2 * Aggregate QC (RNA) 5.1.2 * Passed - Bioanalyzer QC (RNA) 5.1.2 OR * Passed - NanoDrop QC (RNA) 5.1.2 OR * Passed - Qubit QC (RNA) 5.1.2 OR * Passed - PicoGreen QC (RNA) 5.1.2 OR * Passed - CaliperGX QC 5.1.2 OR * Passed - Tapestation QC (RNA) 5.1.2 ### Step: Bioanalyzer QC (RNA) 5.1.2 * Master Step Name = Bioanalyzer QC (RNA) 5.1.2 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} Bioanalyzer #### Automations
Generate Bioanalyzer driver 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 -u {username} -p {password} \ script:driver_file_generator \ -i {processURI:v2} \ -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 -u {username} -p {password} \ script:addBlankLines \ -i {stepURI:v2} \ -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 -u {username} -p {password} -i {processURI:v2} \ script:parseBioAnalyzer \ -inputFile {compoundOutputFileLuid2} \ -log {compoundOutputFileLuid5} \ -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerRNAConfig.groovy' \ script:assignQC \ -log {compoundOutputFileLuid6} \ -qcResult {compoundOutputFileLuid7}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Projects * 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 | | | | Submitted Sample | Sample Type | Text | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Derived Sample | Workflow | Text | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Projects * Well Sort Order = Row * Placement Pattern = Column * Destination Containers * BioAnalyzer RNA Nano Chip
\* BioAnalyzer RNA Pico Chip
#### Record Details * Step Data * Step Data Heading = Begin by uploading the required Bioanalyzer XML result file * Master Step Fields | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------------------- | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Criteria 1 - Operator | Text Dropdown | |

Presets

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

Presets

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

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 Driver File - Automatically attached * Bioanalyzer Driver 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 = Collapse * Well Sort Order = Row * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | 28s/18s ratio | Numeric | | Decimal Places Displayed = 2 | | Measurement | BA Sample Name | Text | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | 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 | | Measurement | RIN | Numeric | | Decimal Places Displayed = 2 | | Measurement | RNA Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Sample Comment | Text | | | | Project | Project Name | Built-in | | | ### Step: NanoDrop QC (RNA) 5.1.2 * Master Step Name = NanoDrop QC (RNA) 5.1.2 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} NanoDrop #### Automations
Generate NanoDrop driver 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 -u {username} -p {password} \ script:driver_file_generator \ -i {processURI:v2} \ -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/nd_driver_file_template.csv \ -o {compoundOutputFileLuid0}.csv \ -l {compoundOutputFileLuid1}" ``` {% endcode %}
Parse NanoDrop NDT 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 -u {username} -p {password} -i {processURI:v2} \ script:parseCSV \ -inputFile {compoundOutputFileLuid2} \ -log {compoundOutputFileLuid3} \ -headerRow '2' \ -separator 'TAB' \ -sampleLocation 'Sample ID' \ -measurementUDFMap 'Concentration::ng/ul' \ -measurementUDFMap 'A260/280 ratio::260/280' \ -measurementUDFMap 'A260/230 ratio::260/230' \ -measurementUDFMap 'A260::260' \ -relaxed 'true' \ script:assignQC \ -log {compoundOutputFileLuid4} \ -qcResult {compoundOutputFileLuid5}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Projects * 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 | | | | Submitted Sample | Sample Type | Text | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Derived Sample | Workflow | Text | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data * Step Data Heading = Begin by uploading the required NanoDrop NDT result file * Master Step Fields | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | ----------- | ---------------------------------------------------------------------------------------------------------------------------- | | Criteria 1 - Operator | Text Dropdown | |

Presets

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

Presets

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

Presets

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

Presets

| | Criteria 2 - Threshold Value | Numeric | | Decimal Places Displayed = 2 | * Step File Placeholders * NanoDrop Driver File - Automatically attached * NanoDrop Driver File Generation Log File - Automatically attached * NanoDrop NDT Result File (required) - Manually uploaded * NanoDrop NDT 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 = Collapse * Well Sort Order = Row * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | A260 | Numeric | | Decimal Places Displayed = 2 | | Measurement | A260/230 ratio | Numeric | | Decimal Places Displayed = 2 | | Measurement | A260/280 ratio | Numeric | | Decimal Places Displayed = 2 | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Project | Project Name | Built-in | | | ### Step: Qubit QC (RNA) 5.1.2 * Master Step Name = Qubit QC (RNA) 5.1.2 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} Qubit #### Automations
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 -u {username} -p {password} \ script:assignQC \ -i {processURI:v2} \ -log {compoundOutputFileLuid1} \ -qcResult {compoundOutputFileLuid2}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Projects * 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 | | | | Submitted Sample | Sample Type | Text | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Derived Sample | Workflow | Text | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data * Step Data Heading = Begin by completing the Sample Details table * Master Step Fields | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | ----------- | ------------------------------------------------------------------ | | Criteria 1 - Operator | Text Dropdown | |

Presets

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

Presets

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

Presets

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

Presets

| | Criteria 2 - Threshold Value | Numeric | | Decimal Places Displayed = 2 | * Step File Placeholders * Qubit Result File - Manually uploaded * QC Assignment Log File - Automatically attached * QC Assignment Report - Automatically attached * Sample Table * Enable QC Flags = Yes * Sample Display Default = Collapse * Well Sort Order = Row * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Project | Project Name | Built-in | | | ### Step: PicoGreen QC (RNA) 5.1.2 * Master Step Name = PicoGreen QC (RNA) 5.1.2 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} PicoGreen #### Automations
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 -u {username} -p {password} \ script:assignQC \ -i {processURI:v2} \ -log {compoundOutputFileLuid1} \ -qcResult {compoundOutputFileLuid2}" ``` {% 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 | | | | Submitted Sample | Sample Type | Text | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Derived Sample | Workflow | Text | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Projects * Well Sort Order = Row * Placement Pattern = Column * Destination Containers * Tube * 96 well plate #### Record Details * Step Data * Step Data Heading = Begin by completing the Sample Details table * Master Step Fields | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | ----------- | ------------------------------------------------------------------ | | Criteria 1 - Operator | Text Dropdown | |

Presets

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

Presets

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

Presets

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

Presets

| | Criteria 2 - Threshold Value | Numeric | | Decimal Places Displayed = 2 | * Step File Placeholders * PicoGreen Result File - Manually uploaded * QC Assignment Log File - Automatically attached * QC Assignment Report - Automatically attached * Sample Table * Enable QC Flags = Yes * Sample Display Default = Collapse * Well Sort Order = Row * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | -------------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Project | Project Name | Built-in | | | ### Step: CaliperGX QC 5.1.2 * Master Step Name = CaliperGX QC 5.1.2 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} CaliperGX #### Automations
Generate Driver 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 -u {username} -p {password} \ script:driver_file_generator \ -i {processURI:v2} \ -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/caliperGX_driver_file_template.csv \ -o {compoundOutputFileLuid0}.csv \ -l {compoundOutputFileLuid1}" ``` {% endcode %}
Parse CaliperGX CSV * 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 -u {username} -p {password} -i {processURI:v2} \ script:parseCSV \ -inputFile {compoundOutputFileLuid2} \ -log {compoundOutputFileLuid3} \ -headerRow '1' \ -separator 'comma' \ -containerName 'Plate Name' \ -wellPosition 'Well Label' \ -measurementUDFMap 'Concentration::Region[100-1000] Conc. (ng/ul)' \ -measurementUDFMap 'Size (bp)::Region[100-1000] Size at Maximum [BP]' \ -relaxed 'true' \ -matchOutput 'true' \ script:assignQC \ -log {compoundOutputFileLuid4} \ -qcResult {compoundOutputFileLuid5}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Projects * 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 Projects * Well Sort Order = Row * Placement Pattern = Column * Destination Containers * 384 well plate * 96 well plate #### Record Details **Group of Defaults**
Caliper Defaults * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Concentration * Criteria 1 - Threshold Value = 0 * Criteria 2 - Operator = >= * Criteria 2 - Source Data Field = Size (bp) * Criteria 2 - Threshold Value = 300
* Step Data * Group of Defaults = Caliper Defaults * 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 | Custom Entries |

Presets

| | Criteria 1 - Threshold Value | Numeric | | Decimal Places Displayed = 0 | | Criteria 2 - Operator | Text Dropdown | Custom Entries |

Presets

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

Presets

| | Criteria 2 - Threshold Value | Numeric | | Decimal Places Displayed = 0 | * Step File Placeholders * Driver File - Automatically attached * Driver File Log - Automatically attached * CaliperGX WellTable (required) - Manually uploaded * CaliperGX 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 = Collapse * Well Sort Order = Row * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Size (bp) | Numeric | | Decimal Places Displayed = 0 | | Project | Project Name | Built-in | | | ### Step: Tapestation QC (RNA) 5.1.2 * Master Step Name = Tapestation QC (RNA) 5.1.2 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} Tapestation #### Automations
Generate Tapestation Input Sampletable CSV * 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 -u {username} -p {password} \ script:driver_file_generator \ -i {processURI:v2} \ -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/tapestation_driver_file_template.csv \ -o {compoundOutputFileLuid0}.csv \ -l {compoundOutputFileLuid1}" ``` {% endcode %}
Parse Tapestation 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/XmlSampleNameParser.jar -u {username} -p {password} \ script:parseXmlBySampleName \ -i {processURI:v2} \ -inputFile {compoundOutputFileLuid2} \ -log {compoundOutputFileLuid3}.html \ -configFile /opt/gls/clarity/extensions/conf/v5/tapestation/defaultTapeStationRNAConfig.groovy \ && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \ script:assignQC \ -i {processURI:v2} \ -log {compoundOutputFileLuid4} \ -qcResult {compoundOutputFileLuid5}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Projects * 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** | | ------------------------------ | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Criteria 1 - Operator | Text Dropdown | | | | Criteria 1 - Source Data Field | Text Dropdown | | | | Criteria 1 - Threshold Value | Numeric | | | | Criteria 2 - Operator | Text Dropdown | | | | Criteria 2 - Source Data Field | Text Dropdown | | | | Criteria 2 - Threshold Value | Numeric | | | * Step File Placeholders * TapeStation Input SampleTable - Automatically attached * Sample Table Generation Log - Automatically attached * Tapestation Output XML (required) - Manually uploaded * Tapestation XML Parsing Log - Automatically attached * QC Assignment Log - Automatically attached * QC Assignment Report - Automatically attached * Sample Table * Enable QC Flags = Yes * Sample Display Default = Collapse * Well Sort Order = Row * File Column Options * File Column Display = Hide * File Attachment Method = Auto * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | 28s/18s ratio | Numeric | | Decimal Places Displayed = 2 | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Measurement | Molarity Units | Text | | | | Measurement | MW Units | Text | | | | Measurement | Peak 1 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 1 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 1 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 2 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 2 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 2 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 3 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 3 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 3 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 4 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 4 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 4 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 5 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 5 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 5 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 1 % of Total | 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 % of Total | 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 % of Total | 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 % of Total | 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 % of Total | 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 | | Measurement | RIN | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step: Aggregate QC (RNA) 5.1.2 * Master Step Name = Aggregate QC (RNA) 5.1.2 * Step Type = No Outputs #### Automations
Aggregate QC Flags and Copy Fields * 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 -u {username} -p {password} \ script:setUDF \ -i {processURI:v2} \ -f 'Progress' \ -t '//input/@uri->//sample/@uri' \ -v 'Initial sample QC complete' \ script:aggregateQC \ -i {stepURI:v2} \ -c 'true' \ -a 'true' \ -log {compoundOutputFileLuid0} \ -aggregatelog {compoundOutputFileLuid1} \ -copylog {compoundOutputFileLuid2}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Projects * Well Sort Order = Row * Sample Table * Column Headers | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Derived Sample | Workflow | Text | | | | Project | Project Name | Built-in | | | * Expanded View Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------ | -------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | #### Record Details **Group of Defaults**
CaliperGX Values * Bioanalzyer QC (RNA) 5.1.2 = Use if available (Priority 5) * CaliperGX QC 5.1.2 = Use if available (Priority 5) * Copy task 1 - Source Field = Concentration * Copy task 1 - Source Step = CaliperGX QC 5.1.2 * Copy task 2 - Source Field = Conc. Units * Copy task 2 - Source Step = CaliperGX QC 5.1.2 * NanoDrop QC (RNA) 5.1.2 = Use if available (Priority 5) * PicoGreen QC (RNA) 5.1.2 = Use if available (Priority 5) * Qubit QC (RNA) 5.1.2 = Use if available (Priority 5) * Tapestation QC (RNA) 5.1.2 = Use if available (Priority 5)
* Step Data * Step Data Heading = Begin by verifying copy tasks and aggregation priorities * Group of Defaults = CaliperGX Values * Master Step Fields | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------------------- | -------------- | -------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Copy task 1 - Source Field | Text Dropdown | |

Presets

| | Copy task 1 - Source Step | Text Dropdown | |

Presets

| | Copy task 2 - Source Field | Text Dropdown | |

Presets

| | Copy task 2 - Source Step | Text Dropdown | |

Presets

| | Copy task 3 - Source Field | Text Dropdown | |

Presets

| | Copy task 3 - Source Step | Text Dropdown | Custom Entries |

Presets

| * Step File Placeholders * Aggregation Script Log - Automatically attached * QC Flag Aggregation Log - Automatically attached * QC UDF Copy Log - Automatically attached * Sample Table * Enable QC Flags = Yes * 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 | Well | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | |