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

PreviousIllumina COVIDSeq v1.6 NextCompatibility

Last updated 6 months ago

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