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'"

ℹ 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'"

ℹ 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 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

      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 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

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

  • 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 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

      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 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

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 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

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'"

ℹ 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'"

ℹ 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 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

      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 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

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 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

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 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

    • TruSight Oncology 500 HT, Box 3

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 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

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 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

    • TruSight Oncology 500 HT, Box 5

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 HT NovaSeq

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 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

    • TruSight Oncology 500 HT, Box 8

    • TruSight Oncology 500 HT, Box 9

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 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

    • TruSight Oncology 500 HT, Box 7

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 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

    • TruSight Oncology 500 HT, Box 8

    • TruSight Oncology 500 HT, Box 9

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 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

    • TruSight Oncology 500 HT, Box 7

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 HT v1.1)

  • Master Step Name = Amplify Enriched Library v2.0

  • Step Type = No Outputs

  • Reagent Kits

    • TruSight Oncology 500 HT, Box 7

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 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

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

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