TruSight Oncology 500 HT v1.1

Protocol 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 HT v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 HT v1.1)

Master Step Name = DNA/RNA FFPE Extraction (TSO 500 HT v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 2
Naming Convention = {LIST:{SubmittedSampleName}_DNA,{SubmittedSampleName}_RNA}
Reagent Kits
- QIAGEN AllPrep DNA/RNA FFPE Kit
  - Supplier = Qiagen
  - Catalog Number = 80234

The version of DNA/RNA FFPE Extraction master step name may be different depending on the version of IPP installed.

Automations

Set Sample Type

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 'if (output.name.endsWith(::_RNA::)) {output.::Sample Type:: = ::RNA::}; if (output.name.endsWith(::_DNA::)) {output.::Sample Type:: = ::DNA::}' -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}"

Route DNA/RNA samples - HT

Trigger Location = Step
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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

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

Route DNA/RNA samples

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Protocol 2: RNA QC and cDNA Synthesis (TruSight Oncology 500 HT v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit RNA QC (TruSight Oncology 500 HT v1.1)

Master Step Name = Qubit RNA QC (TSO 500 v1.1)
Step Type = Standard QC
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

The version of Qubit RNA QC master step name may be different depending on the version of IPP installed.

Automations

Assign QC flags - RNA

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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid2} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Qubit Result File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 2: Denature and Anneal RNA (TruSight Oncology 500 HT v1.1)

Master Step Name = Denature and Anneal RNA (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 HT, Box 1
  - Supplier = Illumina
  - Catalog Number = 20007000
  - Website = www.illumina.com

The version of Denature and Anneal RNA 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.::FSM (uL):: = step.::Total Samples:: * (27/3) ; \
step.::RVT (uL):: = step.::Total Samples:: * (3/3) ' \
-log {compoundOutputFileLuid0}"

RNA Sample Dilution

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.::Dilution Concentration (ng/ul):: * 8.5) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 8.5 - 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: First Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)

Master Step Name = First Strand cDNA Synthesis v2.0
Step Type = No Outputs

The version of First Strand cDNA Synthesis 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 4: Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)

Master Step Name = Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500 HT, Box 1
  - Supplier = Illumina
  - Catalog Number = 20007000
  - Website = www.illumina.com

The version of Second Strand cDNA Synthesis 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 5: cDNA Clean Up (TruSight Oncology 500 HT v1.1)

Master Step Name = cDNA Clean Up (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_cDNA
Reagent Kits
- TruSight Oncology 500 HT, Box 4
  - Supplier = Illumina
  - Catalog Number = 20007003
  - Website = www.illumina.com

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

Automations

Assign Sample Type

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 'output.::Sample Type:: = ::cDNA::' -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 cDNA Samples - HT

Trigger Location = Step
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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

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

Routing cDNA Samples

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Protocol 3: DNA QC and Fragmentation (TruSight Oncology 500 HT v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit DNA QC (TruSight Oncology 500 HT v1.1)

Master Step Name = Qubit DNA QC (TruSight Oncology 500 HT v1.1)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

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

Automations

Assign QC flags - DNA

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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid1} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Qubit Result File - Automatically attached
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 2: Fragment DNA (TruSight Oncology 500 HT v1.1)

Master Step Name = Fragment DNA (TruSight Oncology 500 HT v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_DNA
Reagent Kits
- TruSight Oncology 500 HT, Box 4
  - Supplier = Illumina
  - Catalog Number = 20007003
  - Website = www.illumina.com

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

Automations

Dilution Calculation

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.::Dilution Concentration (ng/ul):: * 12) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 12 - 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

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

Protocol 4: Library Prep (TruSight Oncology 500 HT v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)

Master Step Name = End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500 HT, Box 3
  - Supplier = Illumina
  - Catalog Number = 20007002
  - Website = www.illumina.com

The version of 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 'step.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

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

Master Step Name = Ligate Adapters (TruSight Oncology 500 HT v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500 HT, Box 2
  - Supplier = Illumina
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 3
  - Supplier = Illumina
  - Catalog Number = 20007002
  - 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: Clean Up Ligation (TruSight Oncology 500 HT v1.1)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 HT, Box 4
  - Supplier = Illumina
  - Catalog Number = 20007003
  - Website = www.illumina.com

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

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

Master Step Name = Index PCR (TruSight Oncology 500 HT v1.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500 HT, Box 3
  - Supplier = Illumina
  - Catalog Number = 20007002
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 5
  - Supplier = Illumina
  - Website = www.illumina.com

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Add Labels

Label Groups
- TruSight Oncology 500 HT NovaSeq

Record Details

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

Protocol 5: Hybridization (TruSight Oncology 500 HT v1.1)

Protocol Type = Library Prep

Next Steps Configuration

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

Master Step Name = Hybridize v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 HT, Box 7
  - Supplier = Illumina
  - Catalog Number = 20026144
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 8
  - Supplier = Illumina
  - Catalog Number = 20026138
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 9
  - Supplier = Illumina
  - Catalog Number = 20007012
  - Website = www.illumina.com

The version of Hybridize 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}"

Library Dilution

Trigger Location = Not Used

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 2: Capture Targets One (TruSight Oncology 500 HT v1.1)

Master Step Name = Capture Targets One (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500 HT, Box 6
  - Supplier = Illumina
  - Catalog Number = 20026143
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 7
  - Supplier = Illumina
  - Catalog Number = 20026144
  - Website = www.illumina.com

The version of Capture Targets One 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: Set Up Second Hybridization (TruSight Oncology 500 HT v1.1)

Master Step Name = Set Up Second Hybridization (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500 HT, Box 7
  - Supplier = Illumina
  - Catalog Number = 20026144
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 8
  - Supplier = Illumina
  - Catalog Number = 20026138
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 9
  - Supplier = Illumina
  - Catalog Number = 20007012
  - 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 4: Capture Targets Two (TruSight Oncology 500 HT v1.1)

Master Step Name = Capture Targets Two (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500 HT, Box 6
  - Supplier = Illumina
  - Catalog Number = 20026143
  - Website = www.illumina.com
- TruSight Oncology 500 HT, Box 7
  - Supplier = Illumina
  - Catalog Number = 20026144
  - Website = www.illumina.com

The version of Capture Targets Two 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
- Expanded View Fields

Record Details

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

Step 5: Amplify Enriched Library (TruSight Oncology 500 HT v1.1)

Master Step Name = Amplify Enriched Library v2.0
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500 HT, Box 7
  - Supplier = Illumina
  - Catalog Number = 20026144
  - Website = www.illumina.com

The version of Amplify Enriched Library 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 6: Clean Up Amplified Enriched Library (TruSight Oncology 500 HT v1.1)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500 HT, Box 6
  - Supplier = Illumina
  - Catalog Number = 20026143
  - Website = www.illumina.com

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

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

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)

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

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

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)

Record Details

Step Data (Master Step Fields)
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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

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)

Record Details

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

Step 4: 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}

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)

Add Labels

Label Groups
- TruSight Oncology 500 ctDNA NovaSeq

Record Details

Step Data (Master Step Fields)
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

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

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)

Record Details

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

Step 6: 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

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)

Record Details

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

Step 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

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)

Record Details

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

Step 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

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)

Record Details

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

Step 9: 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

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)

Record Details

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

Step 10: 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

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)

Record Details

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

TruSight Tumor 170 v2.0

Overview

TruSight Tumor 170 v2.0 includes the following functionality:

Preconfigured TruSight Tumor 170 v2.0 protocol that supports the preparation of samples for the detection of gene variants across 170 gene targets in nucleic acids extracted from FFPE cancer tissue samples.
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.
Routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0)

Master Step Name = DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 2
Naming Convention = {LIST:{SubmittedSampleName}_DNA,{SubmittedSampleName}_RNA}
Reagent Kits
- QIAGEN AllPrep DNA/RNA FFPE Kit
  - Supplier = Qiagen
  - Catalog Number = 80234

Automations

Set Sample Type

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 'if (output.name.endsWith(::_RNA::)) {output.::Sample Type:: = ::RNA::}; if (output.name.endsWith(::_DNA::)) {output.::Sample Type:: = ::DNA::}' -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}"

Route DNA/RNA samples

Trigger Location = Step
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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'Qubit RNA QC (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'Qubit DNA QC (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Protocol 2: RNA QC and cDNA Synthesis (TruSight Tumor 170 v2.0)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit RNA QC (TruSight Tumor 170 v2.0)

Master Step Name = Qubit RNA QC (TruSight Tumor 170 v2.0.10)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

Assign QC flags - RNA

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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid2} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Qubit Result File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 2: Denature and Anneal RNA (TruSight Tumor 170 v2.0)

Master Step Name = Denature and Anneal RNA (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Tumor 170, Box 1
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

Automations

RNA Sample Dilution

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.::Dilution Concentration (ng/ul):: * 17) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 17 - 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: First Strand cDNA Synthesis (TruSight Tumor 170 v2.0)

Master Step Name = First Strand cDNA Synthesis v2.0
Step Type = No Outputs

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 4: Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0)

Master Step Name = Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0.10)
Step Type = No Outputs
Reagent Kits
- TruSight Tumor 170, Box 1
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 5: cDNA Clean Up (TruSight Tumor 170 v2.0)

Master Step Name = cDNA Clean Up (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_cDNA
Reagent Kits
- TruSight Tumor 170, Box 3
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

Automations

Assign Sample Type

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 'output.::Sample Type:: = ::cDNA::' -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 cDNA samples

Trigger Location = Step
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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'End Repair and A-Tailing (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Protocol 3: DNA QC and Fragmentation (TruSight Tumor 170 v2.0)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit DNA QC (TruSight Tumor 170 v2.0)

Master Step Name = Qubit DNA QC (TruSight Tumor 170 v2.0.10)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

Assign QC flags - DNA

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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid1} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Qubit Result File - Automatically attached
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 2: Fragment DNA (TruSight Tumor 170 v2.0)

Master Step Name = Fragment DNA (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_DNA

Automations

Dilution Calculation

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.::Dilution Concentration (ng/ul):: * step.::Minimum Final Volume (uL)::) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = step.::Minimum 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

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

Protocol 4: Library Prep (TruSight Tumor 170 v2.0)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: End Repair and A-Tailing (TruSight Tumor 170 v2.0)

Master Step Name = End Repair and A-Tailing (TruSight Tumor 170 v2.0.10)
Step Type = No Outputs
Reagent Kits
- TruSight Tumor 170, Box 2
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 2: Ligate Adapters (TruSight Tumor 170 v2.0)

Master Step Name = Ligate Adapters (TruSight Tumor 170 v2.0.10)
Step Type = No Outputs
Reagent Kits
- TruSight Tumor 170, Box 2
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: Clean Up Ligation (TruSight Tumor 170 v2.0)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Tumor 170, Box 3
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 4: Index PCR (TruSight Tumor 170 v2.0)

Master Step Name = Index PCR (TruSight Tumor 170 v2.0.10)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Tumor 170, Box 2
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 4
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 5
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Add Labels

Label Groups
- TruSight Tumor 170 Index List

Record Details

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

Protocol 5: Hybridization (TruSight Tumor 170 v2.0)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Perform First Hybridization (TruSight Tumor 170 v2.0)

Master Step Name = Hybridize v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Tumor 170, Box 6
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 7
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 8
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 9
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Library Dilution

Trigger Location = Not Used

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 2: Perform First Capture (TruSight Tumor 170 v2.0)

Master Step Name = Perform First Capture (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Tumor 170, Box 6
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 7
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: Perform Second Hybridization (TruSight Tumor 170 v2.0)

Master Step Name = Perform Second Hybridization (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Tumor 170, Box 6
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 7
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 8
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 9
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 4: Perform Second Capture (TruSight Tumor 170 v2.0)

Master Step Name = Perform Second Capture (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Tumor 170, Box 6
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 7
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 5: Amplify Enriched Library (TruSight Tumor 170 v2.0)

Master Step Name = Amplify Enriched Library v2.0
Step Type = No Outputs
Reagent Kits
- TruSight Tumor 170, Box 7
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 6: Clean Up Amplified Enriched Library (TruSight Tumor 170 v2.0)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Tumor 170, Box 3
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Protocol 6: Library QC and Normalization (TruSight Tumor 170 v2.0)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Quantify Libraries (TruSight Tumor 170 v2.0)

Master Step Name = Quantify Libraries (TruSight Tumor 170 v2.0.10)
Step Type = Standard QC
Derived Sample Generation = Fixed, 3
Naming Convention = {SubmittedSampleName}
Control Types
- Blank Solution (TruSight Tumor 170 v2.0.10)
- DNA Standard (TruSight Tumor 170 v2.0.10)
  - Conc. = 3 ng/ul

Automations

Average Replicate and Assign QC

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:computeReplicateAverage -src 'Concentration (ng/ul)' -dest 'Concentration (ng/ul)' -exclude 'Exclude' -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 'if(input.::Concentration (ng/ul):: >= 3) { output.QC = true } else { output.QC = false } ; input.QC = output.QC' -log {compoundOutputFileLuid0}"

Set Next Steps - 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 (input.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Manual
- Table Columns - Global Fields

Step 2: Normalize Libraries (TruSight Tumor 170 v2.0)

Master Step Name = Normalize Libraries (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Tumor 170, Box 6
  - Supplier = Illumina
  - Catalog Number = OP-101-1004
- TruSight Tumor 170, Box 7
  - Supplier = Illumina
  - Catalog Number = OP-101-1004

Automations

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'"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

TruSight Oncology 500 v1.1

Protocol 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)

Master Step Name = DNA/RNA FFPE Extraction (TSO 500 HT v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 2
Naming Convention = {LIST:{SubmittedSampleName}_DNA,{SubmittedSampleName}_RNA}
Reagent Kits
- QIAGEN AllPrep DNA/RNA FFPE Kit
  - Supplier = Qiagen
  - Catalog Number = 80234

Automations

Set Sample Type

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 'if (output.name.endsWith(::_RNA::)) {output.::Sample Type:: = ::RNA::}; if (output.name.endsWith(::_DNA::)) {output.::Sample Type:: = ::DNA::}' -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}"

Route DNA/RNA samples

Trigger Location = Step
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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

Route DNA/RNA samples - HT

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Protocol 2: RNA QC and cDNA Synthesis (TruSight Oncology 500 v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit RNA QC (TruSight Oncology 500 v1.1)

Master Step Name = Qubit RNA QC (TSO 500 v1.1)
Step Type = Standard QC
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

Assign QC flags - RNA

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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid2} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Qubit Result File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 2: Denature and Anneal RNA (TruSight Oncology 500 v1.1)

Master Step Name = Denature and Anneal RNA (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

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.::FSM (uL):: = step.::Total Samples:: * (27/3) ; \
step.::RVT (uL):: = step.::Total Samples:: * (3/3) ' \
-log {compoundOutputFileLuid0}"

RNA Sample Dilution

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.::Dilution Concentration (ng/ul):: * 8.5) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 8.5 - 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: First Strand cDNA Synthesis (TruSight Oncology 500 v1.1)

Master Step Name = First Strand cDNA Synthesis v2.0
Step Type = No Outputs

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 4: Second Strand cDNA Synthesis (TruSight Oncology 500 v1.1)

Master Step Name = Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500, Box 1
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 5: cDNA Clean Up (TruSight Oncology 500 v1.1)

Master Step Name = cDNA Clean Up (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_cDNA
Reagent Kits
- TruSight Oncology 500, Box 4
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Assign Sample Type

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 'output.::Sample Type:: = ::cDNA::' -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 cDNA Samples

Trigger Location = Step
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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

Routing cDNA Samples - HT

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Protocol 3: DNA QC and Fragmentation (TruSight Oncology 500 v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit DNA QC (TruSight Oncology 500 v1.1)

Master Step Name = Qubit DNA QC (TruSight Oncology 500 HT v1.1)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

Assign QC flags - DNA

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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid1} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Qubit Result File - Automatically attached
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 2: Fragment DNA (TruSight Oncology 500 v1.1)

Master Step Name = Fragment DNA (TruSight Oncology 500 HT v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_DNA
Reagent Kits
- TruSight Oncology 500, Box 4
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Dilution Calculation

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.::Dilution Concentration (ng/ul):: * 12) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 12 - 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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

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

Protocol 4: Library Prep (TruSight Oncology 500 v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: End Repair and A-Tailing (TruSight Oncology 500 v1.1)

Master Step Name = End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500, Box 3
  - Supplier = Illumina
  - Website = www.illumina.com

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.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

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

Master Step Name = Ligate Adapters (TruSight Oncology 500 HT v1.1)
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500, Box 2
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 3
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: Clean Up Ligation (TruSight Oncology 500 v1.1)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500, Box 4
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

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

Master Step Name = Index PCR (TruSight Oncology 500 HT v1.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500, Box 5
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 4
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Add Labels

Label Groups
- TruSight Oncology 500 NextSeq

Record Details

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

Protocol 5: Hybridization (TruSight Oncology 500 v1.1)

Protocol Type = Library Prep

Next Steps Configuration

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

Master Step Name = Hybridize v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500, Box 6
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 7
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 8
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 9
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Library Dilution

Trigger Location = Not Used

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 2: Capture Targets One (TruSight Oncology 500 v1.1)

Master Step Name = Capture Targets One (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500, Box 6
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 7
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

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 = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 3: Set Up Second Hybridization (TruSight Oncology 500 v1.1)

Master Step Name = Set Up Second Hybridization (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500, Box 6
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 7
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 8
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 9
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 4: Capture Targets Two (TruSight Oncology 500 v1.1)

Master Step Name = Capture Targets Two (TSO 500 v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSight Oncology 500, Box 6
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com
- TruSight Oncology 500, Box 7
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

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
- Expanded View Fields

Record Details

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

Step 5: Amplify Enriched Library (TruSight Oncology 500 v1.1)

Master Step Name = Amplify Enriched Library v2.0
Step Type = No Outputs
Reagent Kits
- TruSight Oncology 500, Box 7
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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

Step 6: Clean Up Amplified Enriched Library (TruSight Oncology 500 v1.1)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSight Oncology 500, Box 6
  - Supplier = Illumina
  - Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Record Details

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