TruSeq Methyl Capture EPIC v2.0

Protocol 1: TruSeq Methyl Capture EPIC v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Fragment DNA (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Fragment DNA (TruSeq Methyl Capture EPIC v2.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {SubmittedSampleName}

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

  • Control Types

    • HCC1187 breast cancer tumor (TruSeq Methyl EPIC v1.0)

      • Supplier = ATCC

      • Catalog Number = CRL2322

    • HCC1187 normal (BL) (TruSeq Methyl EPIC v1.0)

      • Supplier = ATCC

      • Catalog Number = CRL2322-D

      • Conc. = 20

    • Jurkat (TruSeq Methyl EPIC v1.0)

      • Supplier = Biochain

      • Catalog Number = D1255815

    • NA12878 (TruSeq Methyl EPIC v1.0)

      • Supplier = Coriell Institute

      • Catalog Number = NA12878

Automations

Calculate Master Mix
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

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.::RSB (mL):: = step.::Total Samples:: * 5 * 1.1 ; step.::0.5 M EDTA (uL):: = step.::Total Samples:: * 10 * 1.1 ; if (!input.name.contains(::TruSeq Methyl EPIC v1.0::)) {output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::}' -log {compoundOutputFileLuid1}"
Normalize gDNA
  • Trigger Location = Record Details

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (input.name.contains( ::(TruSeq Methyl EPIC v1.0)::) ) { output.::Concentration:: = step.::Control Concentration (ng/ul):: ; output.::Conc. Units:: = ::ng/uL:: ; output.::Sample Volume (ul):: = 500 / step.::Control Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul):: } else {output.::Sample Volume (ul):: = 500 / input.::Concentration:: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul)::}' -log {compoundOutputFileLuid0}"

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

    • 1x8 Strip Tube

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Comment

    Multiline Text

    Control Concentration (ng/ul)

    Numeric

    Required Field

    • Default = 0

    • Decimal Places Displayed = 2

    Control Type

    Text Dropdown

    Custom Entries

    Presets

    • HCC1187 normal (BL) (ATCC, catalog # CRL2323-D)

    • NA12878 (Coriell Institute, catalog # NA12878)

    • HCC1187 breast cancer tumor (ATCC, catalog # CRL2322)

    • HeLa (Biochain, catalog # D1255811)

    • Jurkat (Biochain, catalog # D1255815)

    Cycles/Burst

    Numeric

    • Default = 200

    • Decimal Places Displayed = 0

    Duration (seconds)

    Numeric

    • Default = 280

    • Decimal Places Displayed = 0

    Duty Factor (%)

    Numeric

    • Default = 10

    • Decimal Places Displayed = 0

    Peak/Displayed Power (W)

    Numeric

    • Default = 175

    • Decimal Places Displayed = 0

    RSB (mL)

    Numeric

    • Decimal Places Displayed = 2

    Temperature (C)

    Numeric

    • Default = 7

    • Decimal Places Displayed = 0

    Total Samples

    Numeric

    • Default = 0

    Water Level

    Numeric

    • Default = 12

    • Decimal Places Displayed = 0

    0.5 EDTA (uL)

    Numeric

    • Decimal Places Displayed = 2

  • Step File Placeholders

    • Log File - 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

      Buffer Volume (ul)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Numeric

      Required Field

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (ul)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 2: Bioanalyzer QC (DNA) (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Bioanalyzer QC (DNA) 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

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 '"
Parse Bioanalyzer XML and assign QC flags
  • Trigger Location = Record Details

  • Trigger Style = Manual button

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/defaultBioAnalyzerDNAConfig.groovy' \
      script:assignQC \
        -log {compoundOutputFileLuid6} \
        -qcResult {compoundOutputFileLuid7}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"
Set Next Step - Output PASS/FAIL
  • Trigger Location = Not Used

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}"
Set Next Step and Copy to Input
  • Trigger Location = Not Used

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 'nextStep = ::ADVANCE:: ; input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid7}"

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

    • BioAnalyzer DNA 1000 Chip

Record Details

Group of Defaults

NRCC
  • 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

  • Use strict matching for Bioanalyzer results = No

Peak 2 Size Thresholds
  • 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 = 1,000.00

  • Use strict matching for Bioanalyzer results = No

TruSeq ChIP-Seq
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Region 1 Molarity

  • Criteria 1 - Threshold Value = 5.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Region 1 Molarity

  • Criteria 2 - Threshold Value = 10.00

  • Use strict matching for Bioanalyzer results = No

TruSeq Methyl Capture EPIC
  • 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

TruSeq Rapid Exome
  • 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

  • Use strict matching for Bioanalyzer results = No

  • Step Data

    • Group of Defaults = TruSeq Methyl Capture EPIC

    • 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

      • 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

      Criteria 1 - Threshold Value

      Numeric

      Decimal Places Displayed = 2

      Criteria 2 - Operator

      Text Dropdown

      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

      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 = Expand

    • Well Sort Order = Row

    • File Column Options

      • File Column Display = Hide

      • File Attachment Method = Auto

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Measurement

      A260/280 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

      Sample Comment

      Text

      Project

      Project Name

      Built-in

Step 3: Clean Up Fragmented DNA (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Clean Up Fragmented DNA (TruSeq Methyl Capture EPIC v2.0)

  • Step Type = No Outputs

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"

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 4: Repair Ends (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Repair Ends (TruSeq Methyl Capture EPIC v2.0)

  • Step Type = No Outputs

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"

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

    Thermal Cycler Program

    Text

    Default = ERP

    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 5: Adenylate 3' Ends (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Adenylate 3' Ends v2.0

  • Step Type = No Outputs

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"

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

    Thermal Cycler Program

    Text

    Default = ATAIL70

  • 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 6: Ligate Adapters (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Ligate Adapters v2.0

  • Step Type = Add Labels

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {SubmittedSampleName}

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"
Copy to Output
  • Trigger Location = Not Used

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}"
Set Next Step and Copy to Input
  • Trigger Location = Not Used

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 'nextStep = ::ADVANCE:: ; input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid7}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

  • Sample Table

    • Column Headers

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Waiting

      Built-in

    • Expanded View Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      LIMS ID (Container)

      Built-in

      Project

      Project Name

      Built-in

Add Labels

  • Label Groups

    • TruSeq Methyl Capture EPIC

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Comment

    Multiline Text

    Thermal Cycler Program

    Text

    Default = LIG

    80% EtOH Prep Date

    Date

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Column

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Reagent Name

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 7: Clean Up and Pool Ligated Fragments (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Clean Up and Pool v2.0

  • Step Type = Pooling

  • Aliquot Generation = Fixed, 1

  • Naming Convention = {PoolName}

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"

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

Pooling

  • Label Uniqueness = On

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

Record Details

  • Step File Placeholders

    • Log File - 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 8: Hybridize Probes (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Hybridize v2.0

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 5 - Probes

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"
Library Dilution
  • Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Library Volume (ul):: = 200 / input.::Concentration (ng/ul):: ; output.::RSB Volume (ul):: = 10 - output.::Library Volume (ul)::' -log {compoundOutputFileLuid0}"

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

    • 1x8 Strip Tube

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Comment

    Multiline Text

    Thermal Cycler Program

    Text

    Default = MC HYB1

    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 9: Capture Hybridized Probes (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Capture Hybridized Probes v2.0

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"
Calculate Master Mix
  • Trigger Location = Not Used

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 Number of Samples:: = step.::Total Number of 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.::Enrichment Elution Buffer 1 (ul):: = 28.5 * step.::Total Number of Samples:: ; step.::2N NaOH (ul):: = 1.5 * step.::Total Number of Samples::' -log {compoundOutputFileLuid0}"

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 = 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 10: Perform Second Hybridization (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Perform Second Hybridization v2.0

  • Step Type = No Outputs

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 5 - Probes

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"

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 = 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 11: Perform Second Capture (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Perform Second Capture (TruSeq Methyl Capture EPIC v2.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - IF/ELSE
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (step.::Bisulfite Conversion?:: == ::True:: ) {nextStep = ::Bisulfite Conversion (TruSeq Methyl Capture EPIC v2.0.11):: } else {nextStep = ::Amplify Enriched Library (TruSeq Methyl Capture EPIC v2.0.11):: }'  -log {compoundOutputFileLuid0}"

ℹ The actual TruSeq Methyl Capture EPIC version used in the automation script may vary depending on the version of IPP installed.

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table

    • Column Headers

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      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

    Bisulfite Conversion?

    Text Dropdown

    Required Field

    Presets

    • True

    • False

    Comment

    Multiline Text

  • Step File Placeholders

    • Log File - 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 12: Bisulfite Conversion (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Bisulfite Conversion v1.0

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 1 - Bisulphite Conversion Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"
Copy Placement Information
  • Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Sample_Plate:: = output.container.name' -log {compoundOutputFileLuid0}"

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 = 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: Amplify Enriched Library (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Amplify Enriched Library v2.0

  • Step Type = No Outputs

  • Reagent Kits

    • KAPA HiFi HotStart Uracil+ Ready Mix (2X)

      • Supplier = Kapa

      • Catalog Number = KK2801

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"

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 = 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: Clean Up Amplified Enriched Library (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Clean Up v2.0

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents

    • TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"

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 = 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 15: Bioanalyzer QC (Library Validation) (TruSeq Methyl Capture EPIC v2.0)

  • 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

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 '"
Parse Bioanalyzer XML, Calculate nM and assign QC flags
  • Trigger Location = Record Details

  • Trigger Style = Manual button

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}"
Set Next Step - Output PASS/FAIL
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"
Parse Bioanalyzer XML and assign QC flags
  • Trigger Location = Not Used

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}"
Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations
  • Trigger Location = Not Used

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}"
Parse Bioanalyzer XML, Copy nM and Assign QC flags
  • Trigger Location = Not Used

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}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Placement = Enabled

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

    • Placement Pattern = Column

  • Destination Containers

    • BioAnalyzer DNA High Sensitivity Chip

    • BioAnalyzer DNA 1000 Chip

Record Details

Group of Defaults

Nextera DNA Flex Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Peak 2 Size - bp

  • Criteria 1 - Threshold Value = 150.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Peak 2 Size - bp

  • Criteria 2 - Threshold Value = 1,500.00

Nextera Mate Pair Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Region 1 Average Size - bp

  • Criteria 1 - Threshold Value = 150.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Region 1 Average Size - bp

  • Criteria 2 - Threshold Value = 400.00

Nextera XT DNA Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Peak 2 Size - bp

  • Criteria 1 - Threshold Value = 250.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Peak 2 Size - bp

  • Criteria 2 - Threshold Value = 1,000.00

NRCC Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Peak 2 Size - bp

  • Criteria 1 - Threshold Value = 350.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Peak 2 Size - bp

  • Criteria 2 - Threshold Value = 1,000.00

TruSeq ChIP-Seq Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Region 1 Average Size - bp

  • Criteria 1 - Threshold Value = 150.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Region 1 Average Size - bp

  • Criteria 2 - Threshold Value = 400.00

TruSeq Exome Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Peak 2 Size - bp

  • Criteria 1 - Threshold Value = 150.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Peak 2 Size - bp

  • Criteria 2 - Threshold Value = 1,000.00

TruSeq Methyl Capture EPIC Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Peak 2 Size - bp

  • Criteria 1 - Threshold Value = 200.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Peak 2 Size - bp

  • Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Peak 2 Size - bp

  • Criteria 1 - Threshold Value = 200.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Peak 2 Size - bp

  • Criteria 2 - Threshold Value = 500.00

TruSeq RNA Access Library Validation
  • Criteria 1 - Operator = >=

  • Criteria 1 - Source Data Field = Peak 2 Size - bp

  • Criteria 1 - Threshold Value = 200.00

  • Criteria 2 - Operator = <=

  • Criteria 2 - Source Data Field = Peak 2 Size - bp

  • Criteria 2 - Threshold Value = 500.00

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 = TruSeq Methyl Capture EPIC 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

      Criteria 1 - Threshold Value

      Numeric

      Decimal Places Displayed = 2

      Criteria 2 - Operator

      Text Dropdown

      Custom Entries

      Presets

      • >=

      • <=

      • =

      • !=

      Criteria 2 - Source Data Field

      Text Dropdown

      Presets

      • 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

      Criteria 2 - Threshold Value

      Numeric

      Decimal Places Displayed = 2

      Use strict matching for Bioanalyzer results

      Toggle Switch

      Default = None Set

  • Step File Placeholders

    • Bioanalyzer Input File - Automatically attached

    • Bioanalyzer Input File Generation Log File - Automatically attached

    • Bioanalyzer XML Result File (required) - Manually uploaded

    • Result File (optional) - Manually uploaded

    • PDF Summary File (optional) - Manually uploaded

    • Bioanalyzer XML Parsing Log File - Automatically attached

    • QC Assignment Log File - Automatically attached

    • QC Assignment Report - Automatically attached

  • Sample Table

    • Enable QC Flags = Yes

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • File Column Options

      • File Column Display = Hide

      • File Attachment Method = Auto

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Derived Sample

      Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Measurement

      BA Sample Name

      Text

      Measurement

      Concentration

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Conc. Units

      Text

      Measurement

      Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Number of Peaks found

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Number of Regions found

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 1 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 1 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 1 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 2 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 2 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 2 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 3 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 3 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 3 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 4 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 4 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 4 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 5 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 5 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 5 Size - bp

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 1 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 1 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 1 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 2 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 2 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 2 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 3 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 3 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 3 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 4 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 4 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 4 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 5 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 5 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 5 Molarity

      Numeric

      Decimal Places Displayed = 2

Step 16: Normalize Libraries (TruSeq Methyl Capture EPIC v2.0)

  • Master Step Name = Normalize Libraries 1 v2.0.10

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

The version of Normalized Libraries 1 master step name may be different depending on the version of IPP installed.

Automations

Normalization Calculations - Option 1
  • Trigger Location = Record Details

  • Trigger Style = Manual button

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}"
Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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}"
Routing script - Normalize Libraries
  • Trigger Location = Step

  • Trigger Style = Automatic upon exit

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'"

ℹ The field value and the actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table

    • Column Headers

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      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

    Target Normalization (nM)

    Numeric

    Required Field

    • Default = 2

    • Decimal Places Displayed = 2

  • 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

      Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Buffer Volume (ul)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Normalized Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (ul)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sequencing Instrument

      Text Dropdown

      Required Field

      Presets

      • MiSeq

      • NextSeq

      • NextSeq 1000/2000

      • NextSeq 1000/2000 On-Prem

      • NovaSeq 2.0

      • NovaSeq 3.0

      • NovaSeq X Series

      • NovaSeqDx

      Project

      Project Name

      Built-in

      ℹ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.

Last updated

Was this helpful?