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TruSight Oncology 500 ctDNA v1.1

Overview

TruSight Oncology 500 ctDNA v1.1 includes the following functionality:

Preconfigured TruSight Oncology 500 ctDNA v1.1 protocol that supports the preparation of 48 libraries from cfDNA.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples (when necessary).
Automated assignment of QC Pass/Fail, based on user-selected threshold values. A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: TruSight Oncology 500 ctDNA v1.1

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 2
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 3
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Prepare cfDNA, Perform End Repair and A-Tailing master step name may be different depending on the version of IPP installed.

Automations

Count Samples and 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 'output.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
step.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-log {compoundOutputFileLuid0}"

Calculate Normalization

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.::Sample Volume (uL):: = (step.::Desired Input (ng):: / output.::Concentration:: ) ; \
output.::Buffer Volume (uL):: = step.::Final Volume (uL):: - output.::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
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 = Row
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Desired Input (ng)
Numeric
Required Field
Default = 30
ERA1-A (uL)
Numeric
Decimal Places Displayed = 2
ERA1-B (uL)
Numeric
Decimal Places Displayed = 2
Final Volume (uL)
Numeric
Default = 50
Total Samples
Numeric
Default = 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
  Derived Sample
  Buffer Volume (uL)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (uL)
  Numeric
  Decimal Places Displayed = 2

Step 2: Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 1
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 2
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

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}"

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Add ALB1 (uL) to each well
Numeric
Default = 60
Add LIG3 (uL) to each well
Numeric
Default = 5
Add UMI1 (uL) to each well
Numeric
Default = 10
Note
Multiline Text
Default = Immediately after ligation: add 5ul STL
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 3: Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 3
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Clean Up Ligation 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
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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
80% EtOH Prep Date
Date
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 4: Index PCR (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Index PCR (TruSight Oncology 500 ctDNA v1.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

The version of Index PCR 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
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

Add Labels

Label Groups
- TruSight Oncology 500 ctDNA NovaSeq

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Add EPM (uL) to each well
Numeric
Default = 20
Add UPxx (uL) to each well
Numeric
Default = 5
Thermal Cycler Program
Text
Default = I-PCR
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 5: Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 5
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 6
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 7
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Set Up First Hybridization 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
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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Add OPD2 (uL) to each well
Numeric
Default = 5
Add TCA1 (uL) to each well
Numeric
Default = 10
Add TCB1 (uL) to each well
Numeric
Default = 15
Thermal Cycler Program
Text
Default = HYB1
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 6: Capture Target One (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 5
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 6
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Capture Targets master step name may be different depending on the version of IPP installed.

Automations

Count Samples and 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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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
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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
EE2 (uL)
Numeric
Decimal Places Displayed = 0
HP3 (uL)
Numeric
Decimal Places Displayed = 0
Total Samples
Numeric
Default = 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 7: Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 5
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 6
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 7
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Set Up Second Hybridization 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
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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Add OPD2 (uL) to each well
Numeric
Default = 5
Add TCA1 (uL) to each well
Numeric
Default = 10
Add TCB1 (uL) to each well
Numeric
Default = 15
Thermal Cycler Program
Text
Default = HYB2
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 8: Capture Target Two (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 3
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 5
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com
- TruSight Oncology 500 ctDNA, Box 6
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Capture Targets master step name may be different depending on the version of IPP installed.

Automations

Count Samples and 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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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
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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
EE2 (uL)
Numeric
Decimal Places Displayed = 2
HP3 (uL)
Numeric
Decimal Places Displayed = 2
Total Samples
Numeric
Default = 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 9: Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 6
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Amplified Enriched Libraries 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
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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Add EPM (uL) to each well
Numeric
Default = 20
Add PPC3 (uL) to each well
Numeric
Default = 5
Thermal Cycler Program
Text
Default = EL-PCR
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 10: Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

Master Step Name = Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 ctDNA, Box 3
  - Supplier = Illumina
  - Catalog Number = 20039252; 20039253; 20039254
  - Website = www.illumina.com

The version of Clean Up Amplified Enriched Libraries 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
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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
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