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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 5 - Probes
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 5 - Probes
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

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.

PreviousTruSeq DNA PCR-Free v2.0 NextTruSeq Nano DNA v1.0

Last updated 6 months ago

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