Respiratory Virus Panel v1.0

Overview

The Respiratory Virus Panel workflow includes the following functionality:

  • Preconfigured protocols that support the preparation of upper and lower respiratory specimens for real-time RT-PCR qualitative detection of nucleic acid from the 2019-nCoV.

  • Automated calculation of sample and buffer volumes.

  • Automated calculation or display of reagents at every step in the protocol.

  • Automatic step transition when required.

  • Automatic placement of samples when necessary.

  • Automated assignment of QC Pass/Fail, based on user-selected threshold values.

  • Routing to iSeq, MiniSeq, MiSeq, NextSeq 550, NextSeq 2000.

Protocol 1: Sort Sample Type (Respiratory Virus Panel v1.0)

Protocol Type = Other

Next Steps Configuration

Step 1: Sort Sample Type (Respiratory Virus Panel v1.0)

  • Master Step Name = Sort Sample Type (Respiratory Virus Panel v1.0)

  • Step Type = No Outputs

Automations

Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
Routing Script - Extraction
  • 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 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'QIAamp Viral Mini Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sample Concentration (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'AllPrep PowerViral DNA/RNA Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sort Sample (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Instruction

    Multiline Text

    Read Only

    Default = Please select the Respiratory Virus Extraction Protocol for each sample.

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Respiratory Virus Extraction Protocol

      Text Dropdown

      Required Field

      Presets

      • QIAamp Viral Mini Kit

      • AllPrep PowerViral DNA/RNA Kit

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Protocol 2: QIAamp Viral RNA Mini Kit (Respiratory Virus Panel v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sample Concentration (Respiratory Virus Panel v1.0)

  • Master Step Name = Sample Concentration (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Set Next Step - Purification
  • 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 'if (input.::Is Bead Beating Required?:: == ::Yes::) {nextStep = ::Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)::} \
else {if (input.::Is Bead Beating Required?:: == ::No::) {nextStep = ::Prep Samples (Respiratory Virus Panel v1.0)::} }' \
-log {compoundOutputFileLuid0}"

ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Sample Volume (mL)

    Numeric

    Default = 3.5

    Directions

    Multiline Text

    Default = Add up to 3.5 ml of sample to the microconcentrator Centrifuge to a final volume of 140 μl.

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Derived Sample

      Purification Protocol

      Text Dropdown

      Required Field

      Presets

      • Spin

      • Vacuum

      Derived Sample

      Sample Name

      Built-in

Step 2: Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)

  • Master Step Name = Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Buffer AW1

      • Catalog Number = 61904

    • Buffer AW2

      • Catalog Number = 61904

Automations

Calculate Total Samples and 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.::Buffer AVL Volume (ml):: = step.::Total Samples:: * 0.56 ; \
step.::Carrier RNA AVE Volume (uL):: = step.::Buffer AVL Volume (ml):: * 10 ' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
Routing Script - cDNA synthesis
  • 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    96-100% EtOH Prep Date

    Date

    Buffer AVL Volume (ml)

    Numeric

    Decimal Places Displayed = 2

    Carrier RNA AVE Volume (uL)

    Numeric

    Decimal Places Displayed = 2

    Incubation End Time:

    Text

    Incubation Start Time:

    Text

    Total Samples

    Numeric

    Default = 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

      cDNA Synthesis Protocol

      Text Dropdown

      Required Field

      Presets

      • Maxima H Minus Double-Stranded cDNA Synthesis Kit

      • NEBNext Ultra II First Strand Synthesis Module

      • SuperScript Double-Stranded cDNA Synthesis Kit

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 3: Purification of Viral RNA - Vacuum Protocol (Respiratory Virus Panel v1.0)

  • Master Step Name = Purification of Viral RNA - Vacuum Protocol (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Buffer AW1

      • Catalog Number = 61904

    • Buffer AW2

      • Catalog Number = 61904

    • QIAvac 24 Plus vacuum manifold

      • Catalog Number = 19413

Automations

Calculate Total Samples and 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.::Buffer AVL Volume (ml):: = step.::Total Samples:: * 0.56 ; \
step.::Carrier RNA AVE Volume (uL):: = step.::Buffer AVL Volume (ml):: * 10 ' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
Routing Script - cDNA synthesis
  • 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    96-100% EtOH Prep Date

    Date

    Buffer AVL Volume (ml)

    Numeric

    Decimal Places Displayed = 2

    Carrier RNA AVE Volume (uL)

    Numeric

    Decimal Places Displayed = 2

    Incubation End Time:

    Text

    Incubation Start Time:

    Text

    Total Samples

    Numeric

    Default = 0

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      cDNA Synthesis Protocol

      Text Dropdown

      Required Field

      Presets

      • Maxima H Minus Double-Stranded cDNA Synthesis Kit

      • NEBNext Ultra II First Strand Synthesis Module

      • SuperScript Double-Stranded cDNA Synthesis Kit

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Protocol 3: AllPrep PowerViral DNA/RNA Kit (Respiratory Virus Panel v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample (Respiratory Virus Panel v1.0)

  • Master Step Name = Sort Sample (Respiratory Virus Panel v1.0)

  • Step Type = No Outputs

Automations

Set Next Step - Purification
  • 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 'if (input.::Is Bead Beating Required?:: == ::Yes::) {nextStep = ::Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)::} \
else {if (input.::Is Bead Beating Required?:: == ::No::) {nextStep = ::Prep Samples (Respiratory Virus Panel v1.0)::} }' \
-log {compoundOutputFileLuid0}"

ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Is Bead Beating Required?

      Text Dropdown

      Required Field

      Presets

      • Yes

      • No

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 2: Prep Samples (Respiratory Virus Panel v1.0)

  • Master Step Name = Prep Samples (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • AllPrep PowerViral DNA/RNA Kit

    • β-mercaptoethanol

Automations

Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
Routing Script - cDNA synthesis
  • 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    100% EtOH Open Date

    Date

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      cDNA Synthesis Protocol

      Text Dropdown

      Required Field

      Presets

      • Maxima H Minus Double-Stranded cDNA Synthesis Kit

      • NEBNext Ultra II First Strand Synthesis Module

      • SuperScript Double-Stranded cDNA Synthesis Kit

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 3: Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)

  • Master Step Name = Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • AllPrep PowerViral DNA/RNA Kit

    • Phenol:chloroform:isoamyl alcohol

      • Supplier = supplied by user

    • β-mercaptoethanol

Automations

Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
Routing Script - cDNA synthesis
  • 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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    100% EtOH Open Date

    Date

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      cDNA Synthesis Protocol

      Text Dropdown

      Required Field

      Presets

      • Maxima H Minus Double-Stranded cDNA Synthesis Kit

      • NEBNext Ultra II First Strand Synthesis Module

      • SuperScript Double-Stranded cDNA Synthesis Kit

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Protocol 4: Maxima H Minus Double-Stranded cDNA Synthesis Kit (Respiratory Virus Panel v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Master Step Name = First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Maxima H Minus Double-Stranded cDNA Synthesis Kit

      • Supplier = K2561

Automations

Set Master Mix UDFs
  • 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.::4x First Strand Reaction Mix (uL):: = 4 ; output.::First Strand Enzyme Mix (uL):: = 1' \
-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}"
Calculate Total Samples and Master Mix
  • Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp '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.::Murine RNase Inhibitor (uL):: = step.::Total Samples:: * 0.5 * 1.1 ; \
step.::ProtoScript II Reverse Transcriptase (uL):: = step.::Total Samples:: * 1 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 5 * 1.1 ' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Directions

    Multiline Text

    Default = Please record the volumes for the following fields: Volume of Oligo(dT)18 Used (uL), Volume of Template RNA Used (uL), Nuclease-free Water Used (uL).

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      4x First Strand Reaction Mix (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      First Strand Enzyme Mix (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Nuclease-free Water Used (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Volume of Oligo(dT)18 Used (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Volume of Template RNA Used (uL)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 2: Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Master Step Name = Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Step Type = No Outputs

  • Reagent Kits

    • Maxima H Minus Double-Stranded cDNA Synthesis Kit

      • Supplier = K2561

Automations

Set Master Mix UDFs
  • 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.::First Strand cDNA Synthesis (uL):: = 20 ; \
output.::5x Second Strand Reaction Mix (uL):: = 20 ; \
output.::Nuclease-free Water (uL):: = 55 ; \
output.::Second Strand Enzyme Mix (uL):: = 5 ; \
output.::Total Volume (uL):: = 100' \
-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}"
Calculate Total Samples and Master Mix
  • Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp '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.::NEBNext Second Strand Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::NEBNext Second Strand Synthesis Enzyme Mix (uL):: = step.::Total Samples:: * 4 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 48 * 1.1 ' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    5x Second Strand Reaction Mix (uL)

    Numeric

    Decimal Places Displayed = 2

    First Strand cDNA Synthesis (uL)

    Numeric

    Decimal Places Displayed = 2

    Nuclease-free Water (uL)

    Numeric

    Decimal Places Displayed = 2

    Second Strand Enzyme Mix (uL)

    Numeric

    Decimal Places Displayed = 2

    Total Volume (uL)

    Numeric

    Decimal Places Displayed = 2

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      5x Second Strand Reaction Mix (uL)

      Numeric

      Derived Sample

      First Strand cDNA Synthesis (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Nuclease-free water (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Second Strand Enzyme Mix

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Total Volume (uL)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 3: Removal of RNA (Respiratory Virus Panel v1.0)

  • Master Step Name = Removal of RNA (Respiratory Virus Panel v1.0)

  • Step Type = No Outputs

Automations

Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    RNase I (uL) to add to each tube

    Numeric

    Default = 10

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 4: Purification of ds cDNA (Respiratory Virus Panel v1.0)

  • Master Step Name = Purification of ds cDNA (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • GeneJET PCR Purification Kit

      • Catalog Number = K0701, K0702

Automations

Set Sample Type - ds cDNA output
  • 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:: = ::ds 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 Script - Nextera Flex for Enrichment OUTPUTS
  • 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 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

Protocol 5: NEBNext Ultra II First Strand Synthesis Module (Respiratory Virus Panel v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)

  • Master Step Name = mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • NEBNext First Strand Synthesis Reaction Buffer

      • Supplier = NEB

      • Catalog Number = E7525S, E7525L

    • NEBNext Poly(A) mRNA Magnetic Isolation Module

      • Supplier = NEB

      • Catalog Number = E7490S, E7490L

    • NEBNext Random Primers

      • Supplier = NEB

      • Catalog Number = S1330S

Automations

Calculate Total Samples and 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.::MM1: NEBNext First Strand Synthesis Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::MM1: NEBNext Random Primers (uL):: = step.::Total Samples:: * 2 * 1.1 ; \
step.::MM1: Nuclease-free Water (uL):: = step.::Total Samples:: * 10 * 1.1 ; \
step.::Beads MM: Oligo dT Beads d(T)25 (uL):: = step.::Total Samples:: * 20 * 1.1 ; \
step.::Beads MM: RNA Binding Buffer (2X) (uL):: = step.::Total Samples:: * 100 * 1.1 ' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Beads MM: Oligo dT Beads d(T)25 (uL)

    Numeric

    Decimal Places Displayed = 2

    Beads MM: RNA Binding Buffer (2X) (uL)

    Numeric

    Decimal Places Displayed = 2

    MM1: NEBNext First Strand Synthesis Reaction Buff (uL)

    Numeric

    Decimal Places Displayed = 2

    MM1: NEBNext Random Primers (uL)

    Numeric

    Decimal Places Displayed = 2

    MM1: Nuclease-free Water (uL)

    Numeric

    Decimal Places Displayed = 2

    Total Samples

    Numeric

    Default = 0

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 2: First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Master Step Name = First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Calculate Total Samples and 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.::Murine RNase Inhibitor (uL):: = step.::Total Samples:: * 0.5 * 1.1 ; \
step.::ProtoScript II Reverse Transcriptase (uL):: = step.::Total Samples:: * 1 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 5 * 1.1 ' \
-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}"
Set Master Mix UDFs
  • Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::4x First Strand Reaction Mix (uL):: = 4 ; output.::First Strand Enzyme Mix (uL):: = 1' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Murine RNase Inhibitor (uL)

    Numeric

    Decimal Places Displayed = 2

    Nuclease-free Water (uL)

    Numeric

    Decimal Places Displayed = 2

    ProtoScript II Reverse Transcriptase (uL)

    Numeric

    Decimal Places Displayed = 2

    Thermal Cycler Program

    Multiline Text

    Default = 10 minutes at 25°C 50 minutes at 42°C 15 minutes at 70°C Hold at 4°C

    Total Samples

    Numeric

    Default = 0

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Protocol 6: NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (Respiratory Virus Panel v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Master Step Name = Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)

  • Step Type = No Outputs

  • Reagent Kits

    • NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module

      • Supplier = NEB

      • Catalog Number = E6111S, E6111L

Automations

Calculate Total Samples and 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.::NEBNext Second Strand Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::NEBNext Second Strand Synthesis Enzyme Mix (uL):: = step.::Total Samples:: * 4 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 48 * 1.1 ' \
-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}"
Set Master Mix UDFs
  • Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::First Strand cDNA Synthesis (uL):: = 20 ; \
output.::5x Second Strand Reaction Mix (uL):: = 20 ; \
output.::Nuclease-free Water (uL):: = 55 ; \
output.::Second Strand Enzyme Mix (uL):: = 5 ; \
output.::Total Volume (uL):: = 100' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    First-Strand Synthesis Product Volume per Well (uL)

    Numeric

    Default = 20

    NEBNext Second Strand Reaction Buffer (uL)

    Numeric

    Decimal Places Displayed = 2

    NEBNext Second Strand Synthesis Enzyme Mix (uL)

    Numeric

    Decimal Places Displayed = 2

    Nuclease-free Water (uL)

    Numeric

    Decimal Places Displayed = 2

    Total Samples

    Numeric

    Default = 0

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 2: Purification of Double-stranded cDNA (Respiratory Virus Panel v1.0)

  • Master Step Name = Purification of Double-stranded cDNA (Respiratory Virus Panel v1.0)

  • Step Type = No Outputs

  • Reagent Kits

    • NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module

      • Supplier = NEB

      • Catalog Number = E6111S, E6111L

Automations

Set Sample Type - ds cDNA
  • 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 'input.::Sample Type:: = ::ds 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 Script - Nextera Flex for Enrichment INPUTS
  • 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 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Protocol 7: SuperScript Double-Stranded cDNA Synthesis Kit (Respiratory Virus Panel v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: First-Strand Synthesis (Respiratory Virus Panel v1.0)

  • Master Step Name = First-Strand Synthesis (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • SuperScript Double-Stranded cDNA Synthesis Kit

      • Catalog Number = 11917-010, 11917-020

Automations

Calculate Master Mix
  • Trigger Location = Record Details

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'if (!output.hasValue(::Prep Sample Type::)) {fail(::Please enter Prep Sample Type::)} ; \
if (!output.hasValue(::mRNA/Total RNA (ug)::)) {fail(::Please enter mRNA/Total RNA (ug) for each sample::)} ; \
if (output.::mRNA/Total RNA (ug):: <= 1 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ; output.::RNA in DEPC-treated water uL):: = 10 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 1 } ; \
if (output.::mRNA/Total RNA (ug):: == 2 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 9 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 2} ; \
if (output.::mRNA/Total RNA (ug):: == 3 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 8 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 3} ; \
if (output.::mRNA/Total RNA (ug):: == 4 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 7 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 4} ; \
if (output.::mRNA/Total RNA (ug):: == 5 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 6 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 5} ; \
if (output.::mRNA/Total RNA (ug):: <= 50 && output.::Prep Sample Type:: == ::Total RNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 9 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 2} ; \
if (output.::mRNA/Total RNA (ug):: <= 50 && output.::Prep Sample Type:: == ::Total RNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 10 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 1} ;' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Directions

    Multiline Text

    Default = Please enter ug of starting mRNA or Total RNA and Prep Sample Type in field below.

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      5X First-Strand Reaction Buffer (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      0.1M DTT (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      10 mM dNTP mix (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      mRNA/Total RNA (ug)

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Prep Sample Type

      Text Dropdown

      Required Field

      Presets

      • mRNA

      • Total RNA

      Derived Sample

      Primer (100 pmol/uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      RNA in DEPC-treated water uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      SuperScript II RT (uL)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 2: Second-Strand Synthesis (Respiratory Virus Panel v1.0)

  • Master Step Name = Second-Strand Synthesis (Respiratory Virus Panel v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • SuperScript Double-Stranded cDNA Synthesis Kit

      • Catalog Number = 11917-010, 11917-020

Automations

Set Sample Type - ds cDNA output
  • 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:: = ::ds 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 Script - Nextera Flex for Enrichment OUTPUTS
  • 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 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--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 = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

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