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
- Expanded View Fields

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)
Step File Placeholders
- Log File - Manually uploaded
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

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
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

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Add Labels

Label Groups
- TruSeq Methyl Capture EPIC

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

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
- Expanded View Fields

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

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
- Expanded View Fields

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)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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}"

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Manually uploaded
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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)

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
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

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'"

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.