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

ℹ️ 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

• 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'"

ℹ️ 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 - 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'"

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Type	Text Dropdown	Required Field Custom Entries	Presets DNA RNA
    Project	Project Name	Built-in

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}

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Type	Text Dropdown	Required Field Custom Entries	Presets DNA RNA
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Criteria 1 - Operator	Text Dropdown	Custom Entries	Presets >= <= = != Default = >=
  Criteria 1 - Source Data Field	Text		Default = Concentration (ng/ul)
  Criteria 1 - Threshold Value	Numeric		Default = 4.7 Decimal Places Displayed = 2
  Criteria 2 - Operator	Text Dropdown	Custom Entries	Presets >= <= = != Default = >=
  Criteria 2 - Source Data Field	Text		Default = Concentration (ng/ul)
  Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2

• 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

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}

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Dilution Concentration (ng/ul)	Numeric	Required Field	Range = 4.7 To 10 Decimal Places Displayed = 1
  EPH3 to each well (uL)	Numeric		Default = 8.5
  FSM (uL)	Text
  RVT (uL)	Text
  Thermal Cycler Program	Text Dropdown	Custom Entries	Presets LQ-RNA HQ-RNA
  Total Samples	Numeric		Default = 0

• 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Buffer Volume (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

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

• Master Step Name = First Strand cDNA Synthesis v2.0

• Step Type = No Outputs

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Thermal Cycler Program	Text Dropdown	Custom Entries	Presets Synthesize 1st Strand 1stSS

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Thermal Cycler Program	Text	Read Only	Default = 2ndSS

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

• 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'"

ℹ️ 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 - 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'"

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  BIND1 Plate Barcode	Text
  80% EtOH Prep Date	Date

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Type	Text Dropdown	Required Field Custom Entries	Presets DNA RNA
    Project	Project Name	Built-in

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}

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Type	Text Dropdown	Required Field Custom Entries	Presets DNA RNA
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Criteria 1 - Operator	Text Dropdown		Presets >= <= = != Default = >=
  Criteria 1 - Source Data Field	Text		Default = Concentration (ng/ul)
  Criteria 1 - Threshold Value	Numeric		Default = 3.3 Decimal Places Displayed = 2
  Criteria 2 - Operator	Text Dropdown		Presets >= <= = != Default = >=
  Criteria 2 - Source Data Field	Text		Default = Concentration (ng/ul)
  Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2

• 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Column

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Dilution Concentration (ng/ul)	Numeric	Required Field	Range = 3.3 To 10 Decimal Places Displayed = 0

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Buffer Volume (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  ERA1-A (uL)	Numeric		Decimal Places Displayed = 0
  ERA1-B (uL)	Numeric		Decimal Places Displayed = 0

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Add Labels

• Label Groups

  • TruSight Oncology 500 NextSeq

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  PCR Program	Text	Read Only	Default = I-PCR

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Reagent Name	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  PCR Program	Text		Default = HYB1

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  EE2 (uL)	Numeric		Decimal Places Displayed = 0
  HP3 (uL)	Numeric		Decimal Places Displayed = 0
  Total Samples	Numeric		Default = 0

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  PCR Program	Text	Read Only	Default = HYB2

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  BIND1 Plate Barcode	Text
  Comment	Multiline Text
  EE2 (uL)	Numeric		Decimal Places Displayed = 0
  HP3 (uL)	Numeric		Decimal Places Displayed = 0

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 5: 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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  PCR	Text		Default = EL-PCR

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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

ℹ️ 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

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  80% EtOH Prep Date	Date

• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in