Nextera Mate Pair v1.0

Protocol 1: Nextera Mate Pair v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Nextera Mate Pair v1.0)

Master Step Name = Tagment Genomic DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- Zymo Genomic DNA Clean & Concentrator
  - Supplier = Zymo Research
  - Catalog Number = D4010 (25 preps) or D4011 (100 preps)

ℹ The version of Tagment Genomic DNA master step name may be different depending on the version of IPP installed.

Automations

Master Mix Calculations

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 (output.::Gel Type:: == ::Gel-Free::) {output.::Sample Volume (ul):: = 1000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 76 - output.::Sample Volume (ul)::} ; if (output.::Gel Type:: == ::Gel-Plus::) {output.::Sample Volume (ul):: = 4000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 308 - output.::Sample Volume (ul)::}' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Mate Pair Tagment Enzyme Per Sample Volume (ul)
Numeric Dropdown
Custom Entries
Presets
4
12
Decimal Places Displayed = 2
Tagment Buffer Mate Pair Per Sample Volume (ul)
Numeric Dropdown
Custom Entries
Presets
20
80
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
  Gel Type
  Text Dropdown
  Required Field
  Presets
  Gel-Free
  Gel-Plus
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Water Per Sample (ul)
  Numeric
  Decimal Places Displayed = 2
  Project
  Project Name
  Built-in

Step 2: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)

Master Step Name = Bioanalyzer QC (DNA) v1.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 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' 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}"

Set Next Step & 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 false -h false -exp 'nextStep = ::ADVANCE:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -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
- BioAnalyzer DNA 7500 and DNA 1200 Chip
- BioAnalyzer DNA High Sensitivity Chip

Record Details

Step Data (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 Input File - Automatically attached
- Bioanalyzer Input File Generation Log - 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: Strand Displacement (Nextera Mate Pair v1.0)

Master Step Name = Strand Displacement (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Strand Displacement master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Gel Type
  Text Dropdown
  Required Field
  Presets
  Gel-Free
  Gel-Plus
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 4: Purify the DNA (Nextera Mate Pair v1.0)

Master Step Name = Purify the DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- AMPure XP Beads
  - Supplier = Beckman Coulter Genomics
  - Catalog Number = A63881
  - Website = https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Purify the DNA master step name may be different depending on the version of IPP installed.

Automations

Set Next Step based on Gel Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Gel Type:: = input.::Gel Type:: ; if (step.::Next Step:: == ::Gel-Free::) {nextStep = ::Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Pippin Prep::) {nextStep = ::Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Agarose Gel::) {nextStep = ::Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::}' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Next Step
Text Dropdown
Required Field
Presets
Gel-Free
Gel-Plus Pippin Prep
Gel-Plus Agarose Gel
70% EtOH Prep Date
Date
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 5: Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Pippin Prep 0.75% agarose cassette and solutions
  - Catalog Number = CSD7510
- Zymo Genomic DNA Clean & Concentrator
  - Supplier = Zymo Research
  - Catalog Number = D4010 (25 preps) or D4011 (100 preps)

ℹ The version of Pippin Prep Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.

Automations

Set Next Step & Copy Gel Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Step File Placeholders
- Log File - Automatically attached
- Gel Image - Manually uploaded
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 6: Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1 kb plus DNA ladder
  - Supplier = Invitrogen
  - Catalog Number = 10787-018
- 6X gel loading dye
  - Supplier = BioLabs
  - Catalog Number = B7021S
- 50X TAE buffer
  - Supplier = Bio-Rad
  - Catalog Number = 161-0743
- DNA Gel Extraction kit - Zymoclean Large Fragment DNA Recovery Kit
  - Supplier = Zymo Research
  - Catalog Number = D4045
- Megabase Agarose
  - Supplier = Bio-Rad
  - Catalog Number = 161-3108
- Nextera Mate Pair Library Prep Kit – Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- SYBR Safe
  - Supplier = Invitrogen
  - Catalog Number = S33102

ℹ The version of Agarose Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Manual button

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}"

Set Next Step & Copy Gel Type

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:: ; output.::Gel Type:: = input.::Gel Type::' -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
- Gel Image - Manually uploaded
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 7: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)

Master Step Name = Bioanalyzer QC (DNA) v1.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

ℹ The version of Bioanalyzer QC (DNA) master step name may be different depending on the version of IPP installed.

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 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' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Set Next Step & Copy to Input

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:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -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}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- BioAnalyzer DNA 7500 and DNA 1200 Chip
- BioAnalyzer DNA High Sensitivity Chip

Record Details

Step Data (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 Input File - Automatically attached
- Bioanalyzer Input File Generation Log - 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 8: Circularize DNA (Nextera Mate Pair v1.0)

Master Step Name = Circularize DNA (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Circularize DNA master step name may be different depending on the version of IPP installed.

Automations

Master Mix Calculations

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 'input.::Sample Volume (ul):: = input.::DNA Amount (ng):: / input.::Concentration (ng/ul):: ; input.::Water Per Sample (ul):: = 276 - input.::Sample Volume (ul)::' -log {compoundOutputFileLuid0}"

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
Circularization Buffer 10x Per Sample Volume (ul)
Numeric
Default = 30
Decimal Places Displayed = 0
Circularization Ligase Per Sample Volume (ul)
Numeric
Default = 2
Decimal Places Displayed = 0
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
  DNA Amount (ng)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Gel Type
  Text Dropdown
  Required Field
  Presets
  Gel-Free
  Gel-Plus
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Water Per Sample (ul)
  Numeric
  Decimal Places Displayed = 2
  Project
  Project Name
  Built-in

Step 9: Remove Linear DNA (Nextera Mate Pair v1.0)

Master Step Name = Remove Linear DNA (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Remove Linear DNA master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 10: Shear Circularization DNA (Nextera Mate Pair v1.0)

Master Step Name = Shear Circularization DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Shear Circularization DNA master step name may be different depending on the version of IPP installed.

Automations

Set Next Step & Copy Gel Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Cycles Per Burst
Numeric Dropdown
Custom Entries
Presets
200
Decimal Places Displayed = 0
Duty Cycle/Duty Factor (%)
Numeric Dropdown
Custom Entries
Presets
20
Decimal Places Displayed = 0
Intensity
Numeric Dropdown
Custom Entries
Presets
8
Decimal Places Displayed = 0
Peak Power Intensity
Numeric Dropdown
Custom Entries
Presets
240
Decimal Places Displayed = 0
Temperature (C)
Numeric Dropdown
Custom Entries
Presets
6
Decimal Places Displayed = 0
Time (seconds)
Numeric Dropdown
Custom Entries
Presets
40
Decimal Places Displayed = 0
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: Purify Sheared DNA (Nextera Mate Pair v1.0)

Master Step Name = Purify Sheared DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Purify Sheared DNA master step name may be different depending on the version of IPP installed.

Automations

Set Next Step & Copy Gel Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 12: End Repair (Nextera Mate Pair v1.0)

Master Step Name = End Repair (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- TruSeq DNA LT Library Prep Kit - Set A Box
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of End Repair master step name may be different depending on the version of IPP installed.

Automations

Master Mix Calculations

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c " /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::End Repair Mix Volume (ul):: = step.::Total samples:: * 40) ; (step.::Water Volume (ul):: = step.::Total samples:: * 60)' -log {compoundOutputFileLuid1}"

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
End Repair Mix Volume (ul)
Numeric
Decimal Places Displayed = 0
Water Volume (ul)
Numeric
Decimal Places Displayed = 0
Step File Placeholders
- Log File - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 13: A-Tailing (Nextera Mate Pair v1.0)

Master Step Name = A-Tailing (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- TruSeq DNA LT Library Prep Kit - Set A Box
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of A-Tailing master step name may be different depending on the version of IPP installed.

Automations

Master Mix Calculations

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c " /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::A-Tailing Mix Volume (ul):: = step.::Total samples:: * 12.5) ; (step.::Water Volume (ul):: = step.::Total samples:: * 17.5)' -log {compoundOutputFileLuid1}"

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
A-Tailing Mix Volume (ul)
Numeric
Decimal Places Displayed = 2
Comment
Multiline Text
Water Volume (ul)
Numeric
Decimal Places Displayed = 2
Step File Placeholders
- Log File - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 14: Ligate Adapters (Nextera Mate Pair v1.0)

Master Step Name = Ligate Adapters v2.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- TruSeq DNA LT Library Prep Kit - Set A Box
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Ligate Adapters master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 & 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 false -h false -exp 'nextStep = ::ADVANCE:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -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 = Column
Destination Containers
- Tube

Add Labels

Label Groups
- Nextera Mate Pair

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
A-Tailing Reaction/Bead Mix Per Sample Volume (ul)
Numeric
Default = 30
Decimal Places Displayed = 0
Add 1ul of DNA adapter index per sample
Toggle Switch
Default = None Set
Comment
Multiline Text
Ligation Mix Per Sample Volume (ul)
Numeric
Default = 2.5
Decimal Places Displayed = 1
Water Per Sample Volume (ul)
Numeric
Default = 4
Decimal Places Displayed = 0
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
  Reagent Name
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 15: Amplify Libraries (Nextera Mate Pair v1.0)

Master Step Name = Amplify Libraries (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq DNA LT Library Prep Kit - PCR Box
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

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

Automations

Master Mix Calculations

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 '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp '(step.::Enhanced PCR Mix Volume (ul):: = step.::Total samples:: * 20 * 1.1) ; (step.::PCR Primer Cocktail Volume (ul):: = step.::Total samples:: * 5 * 1.1) ; (step.::Water Volume (ul):: = step.::Total samples:: * 25 * 1.1)' -log {compoundOutputFileLuid1}"

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
Enhanced PCR Mix Volume (ul)
Numeric
Decimal Places Displayed = 2
Number of PCR Cycles
Numeric Dropdown
Required Field
Presets
10
15
Decimal Places Displayed = 0
PCR Primer Cocktail Volume (ul)
Numeric
Decimal Places Displayed = 2
Water Volume (ul)
Numeric
Decimal Places Displayed = 2
Step File Placeholders
- Log File - Automatically attached
- Log File - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 16: Clean Up Libraries (Nextera Mate Pair v1.0)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- AMPure XP Beads
  - Supplier = Beckman Coulter Genomics
  - Catalog Number = A63881
  - Website = https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- TruSeq DNA LT Library Prep Kit - PCR Box
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

ℹ The version of Clean Up master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 17: Bioanalyzer QC (Library Validation) (Nextera Mate Pair v1.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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, Copy 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 '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}"

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, Calculate 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 '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}"

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 = 320.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 200.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Targeted RNA Expression Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 700.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

Step Data
- Group of Defaults = Nextera Mate Pair Library Validation
- Master Step Fields
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Criteria 1 - Operator
  Text Dropdown
  Custom Entries
  Presets
  >=
  <=
  =
  !=
  Criteria 1 - Source Data Field
  Text Dropdown
  Presets
  Concentration
  Conc. Units
  Number of Peaks found
  Peak 1 Size - bp
  Peak 1 Conc.
  Peak 1 Molarity
  Peak 2 Size - bp
  Peak 2 Conc.
  Peak 2 Molarity
  Peak 3 Size - bp
  Peak 3 Conc.
  Peak 3 Molarity
  Peak 4 Size - bp
  Peak 4 Conc.
  Peak 4 Molarity
  Peak 5 Size - bp
  Peak 5 Conc.
  Peak 5 Molarity
  Number of Regions found
  Region 1 Average Size - bp
  Region 1 Conc.
  Region 1 Molarity
  Region 2 Average Size - bp
  Region 2 Conc.
  Region 2 Molarity
  Region 3 Average Size - bp
  Region 3 Conc.
  Region 3 Molarity
  Region 4 Average Size - bp
  Region 4 Conc.
  Region 4 Molarity
  Region 5 Average Size - bp
  Region 5 Conc.
  Region 5 Molarity
  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 18: Normalize Libraries (Nextera Mate Pair v1.0)

Master Step Name = Normalize Libraries 1 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

ℹ 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 name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Final Volume (ul)
Numeric
Required Field
Decimal Places Displayed = 2
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
  Buffer Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Molarity (nM)
  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.

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