Illumina Preset Protocol - Respiratory Virus Panel

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)

Master Step 1: Sort Sample Type (Respiratory Virus Panel)

Step Type: No Output

Input = Sample

Output = Sample

Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

    

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Respiratory Virus Extraction Protocol

  

Required

Presets

• QIAamp Viral Mini Kit
• AllPrep PowerViral DNA/RNA Kit
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Remove

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

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

Master Step 1: Sample Concentration (Respiratory Virus Panel)

Step Type: Standard

Input = Plasma, serum, urine, cerebrospinal fluid, bone marrow and other body fluids

Output = Sample at 140 µl

Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Sample Volume (mL)

Numeric

Default

• 3.5
 

Multiline Text Fields

Directions

  

Read Only

Default

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

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Purification Protocol

  

Required

Presets

• Spin
• Vacuum
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp 'if (output.::Purification Protocol:: == ::Spin::) {nextStep = ::Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)::} \

else {if (output.::Purification Protocol:: == ::Vacuum::) {nextStep = ::Purification of Viral RNA - Vacuum Protocol (Respiratory Virus Panel v1.0)::} }' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel)

Step Type: Standard

Input = Concentrated sample

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

Buffer AW1

  

61904

Buffer AW2

  

61904
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Incubation Start Time

Text

  
   

Incubation End Time

Text

  
   

96-100% EtOH Prep Date

Date

  
   

Total Samples

Numeric

Default = 0
   

Buffer AVL Volume (ml)

Numeric

Calculated
   

Carrier RNA AVE Volume (µl)

Numeric

Calculated

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

cDNA Synthesis Protocol

  

Required

Presets

• Maxima H Minus Double-Stranded cDNA Synthesis Kit
• NEBNext Ultra II First Strand Synthesis Module
• SuperScript Double-Stranded cDNA Synthesis Kit
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples and Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

  
     

Command line

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

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 3: Purification of Viral RNA - Vacuum Protocol (Respiratory Virus Panel)

Step Type: Standard

Input = Concentrated sample

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

QIAvac 24 Plus vacuum manifold

  

19413

Buffer AW1

  

61904

Buffer AW2

  

61904
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Incubation Start Time

Text

  
   

Incubation End Time

Text

  
   

96-100% EtOH Prep Date

Date

  
   

Total Samples

Numeric

Default = 0
   

Buffer AVL Volume (ml)

Numeric

Calculated
   

Carrier RNA AVE Volume (µl)

Numeric

Calculated

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

cDNA Synthesis Protocol

  

Required

Presets

• Maxima H Minus Double-Stranded cDNA Synthesis Kit
• NEBNext Ultra II First Strand Synthesis Module
• NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
• SuperScript Double-Stranded cDNA Synthesis Kit
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples and Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

  
     

Command line

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

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

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

Master Step 1: Sort Sample (Respiratory Virus Panel)

Step Type: Standard

Input = Plasma, serum, urine, cerebrospinal fluid, bone marrow and other body fluids

Output = Plasma, serum, urine, cerebrospinal fluid, bone marrow and other body fluids

Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Is Bead Beating Required?

  

Required

Presets

• Yes
• No
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Prep Samples (Respiratory Virus Panel)

Step Type: Standard

Input = Concentrated sample

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

AllPrep PowerViral DNA/RNA Kit

  

28000-50

β-mercaptoethanol

   
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

100% EtOH Open Date

Date

  

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

cDNA Synthesis Protocol

  

Required

Presets

• Maxima H Minus Double-Stranded cDNA Synthesis Kit
• NEBNext Ultra II First Strand Synthesis Module
• SuperScript Double-Stranded cDNA Synthesis Kit
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Remove

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step: Prep Samples - Bead Beating (Respiratory Virus Panel)

Step Type: Standard

Input = Plasma, serum, urine, cerebrospinal fluid, bone marrow and other body fluids

Output = Extracted Sample

Reagent Kits

Kit Name

Supplier

Cat. #

AllPrep PowerViral DNA/RNA Kit

  

28000-50

β-mercaptoethanol

    

Phenol:chloroform:isoamyl alcohol

    
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

100% EtOH Open Date

Date

  

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

cDNA Synthesis Protocol

  

Required

Presets

• Maxima H Minus Double-Stranded cDNA Synthesis Kit
• NEBNext Ultra II First Strand Synthesis Module
• NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
• SuperScript Double-Stranded cDNA Synthesis Kit
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Remove

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

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

Master Step 1: First Strand cDNA Synthesis (Respiratory Virus Panel)

Step Type: Standard

Input = Total RNA or poly(A)+ mRNA

Output = First Stranded Sample

Reagent Kits

Kit Name

Supplier

Cat. #

Maxima H Minus Double-Stranded cDNA Synthesis Kit

  

K2561
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Directions

  

Preset

Please record the volumes for the following fields:

• Volume of Oligo(dT)18 Used (µl)
• Volume of Template RNA Used (µl)
• Nuclease-free Water Used (µl)

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Volume of Oligo(dT)18 Used (µl)

Numeric

2 decimal
   

Volume of Template RNA Used (µl)

Numeric

2 decimal
   

Nuclease-free Water Used (µl)

Numeric

2
   

4x First Strand Reaction Mix (µl)

Numeric

  
   

First Strand Enzyme Mix (µl)

Numeric

  
Automation

Automation Name

Setting

Value

Specification

Set Master Mix UDFs

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Automatic

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Second Strand cDNA Synthesis (Respiratory Virus Panel)

Step Type: No Output

Input = First Stranded Sample

Output = Second Stranded Sample

Reagent Kits

Kit Name

Supplier

Cat. #

Maxima H Minus Double-Stranded cDNA Synthesis Kit

  

K2561
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

First Strand cDNA Synthesis (µl)

Numeric

2 decimal
   

5x Second Strand Reaction Mix (µl)

Numeric

2 decimal
   

Nuclease-free Water (µl)

Numeric

2
   

Second Strand Enzyme Mix (µl)

Numeric

2 decimal
   

Total Volume (µl)

Numeric

2 decimal
Automation

Automation Name

Setting

Value

Specification

Set Master Mix UDFs

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 3: Removal of RNA (Respiratory Virus Panel)

Step Type: No Output

Input = Second Stranded Sample

Output = ds cDNA

Reagent Kits

Kit Name

Supplier

Cat. #

Maxima H Minus Double-Stranded cDNA Synthesis Kit

  

K2561
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

RNase I (µl) to add to each tube

Numeric

Default

• 10

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 4: Purification of ds cDNA (Respiratory Virus Panel)

Step Type: Standard

Input = ds cDNA

Output = purified ds cDNA

Reagent Kits

Kit Name

Supplier

Cat. #

GeneJET PCR Purification Kit

  

K0701, K0702
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Sample Type

Text

  
Automation

Automation Name

Setting

Value

Specification

Set Sample Type - ds CDNA output

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

  
     

Command line

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

Trigger Location

Step

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

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

Master Step 1: mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel)

Step Type: Standard

Input = mRNA

Output = Isolated mRNA

Reagent Kits

Kit Name

Supplier

Cat. #

NEBNext Poly(A) mRNA Magnetic Isolation Module

  

E7490S, E7490L

NEBNext First Strand Synthesis Reaction Buffer

  

E7525S, E7525L

NEBNext Random Primers

  

S1330S
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

MM1: NEBNext First Strand Synthesis Reaction Buffer (µl)

Numeric

2 decimal places

 

 

MM1: NEBNext Random Primers (µl)

Numeric

2 decimal places

 

  

MM1: Nuclease-free Water (µl)

Numeric

2 decimal places
   

Beads MM: Oligo dT Beads d(T)25 (µl)

Numeric

2 decimal places
   

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

Numeric

2 decimal places
   

Total Samples

Numeric

Default

• 0

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples and Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: First Strand cDNA Synthesis (Respiratory Virus Panel)

Step Type: Standard

Input = Total RNA

Output = First Stranded Sample

Reagent Kits

Kit Name

Supplier

Cat. #

NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module

  

E6111S, E6111L
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Murine RNase Inhibitor (µl)

Numeric

2 decimal places

 

 

ProtoScript II Reverse Transcriptase (µl)

Numeric

2 decimal places

 

  

Nuclease-free Water (µl)

Numeric

2 decimal places
   

Total Samples

Numeric

Preset

• 0
 

Multiline Text Fields

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

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples and Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

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

Master Step 1: Second Strand cDNA Synthesis (Respiratory Virus Panel)

Step Type: No Output

Input = First Stranded Sample

Output = ds cDNA

Reagent Kits

Kit Name

Supplier

Cat. #

NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module

  

E6111S, E6111L
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

First-Strand Synthesis Product Volume per Well (µl)

Numeric

Default

• 20

 

 

NEBNext Second Strand Reaction Buffer (µl)

Numeric

2 decimal places

 

  

NEBNext Second Strand Synthesis Enzyme Mix (µl)

Numeric

2 decimal places
   

Nuclease-free Water (µl)

Numeric

2 decimal places
   

Total Samples

Numeric

Default

• 0

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples and Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Purification of Double-stranded cDNA (Respiratory Virus Panel)

Step Type: No Output

Input = ds cDNA

Output = Purified ds cDNA

Reagent Kits

Kit Name

Supplier

Cat. #

NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module

  

E6111S, E6111L
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

80% EtOH Date

Date

  

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Sample Type - ds cDNA

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

  
     

Command line

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

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

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

Master Step 1: First-Strand Synthesis (Respiratory Virus Panel)

Step Type: Standard

Input = Total RNA or mRNA to first-strand cDNA

Output = First-strand cDNA

Reagent Kits

Kit Name

Supplier

Cat. #

SuperScript Double-Stranded cDNA Synthesis Kit

  

11917-010, 11917-020
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Directions

  

Default

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

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Prep Sample Type

Text Dropdown

Presets

• mRNA
• Total RNA
   

mRNA/Total RNA (ug)

Numeric

Required

• 2 decimal places

 

  

Primer (100 pmol/µl)

Numeric

2 decimal places
   

RNA in DEPC-treated water µl)

Numeric

2 decimal places
   

5X First-Strand Reaction Buffer (µl)

Numeric

0 decimal
   

0.1M DTT (µl)

Numeric

  
   

10 mM dNTP mix (µl)

Numeric

  
   

SuperScript II RT (µl)

Numeric

  
Automation

Automation Name

Setting

Value

Specification

Calculate Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Button

  
     

Command line

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

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Second-Strand Synthesis (Respiratory Virus Panel)

Step Type: Standard

Input = First strand cDNA

Output = ds cDNA

Reagent Kits

Kit Name

Supplier

Cat. #

SuperScript Double-Stranded cDNA Synthesis Kit

  

11917-010, 11917-020
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

DEPC-treated water per tube (µl)

Numeric

Default

• 91
   

5X Second-Strand Reaction Buffer per tube (µl)

Numeric

Default

• 30
   

10 mM dNTP mix per tube (µl)

Numeric

Default

• 3
   

E. coli DNA Ligase (10 U/μL) per tube (µl)

Numeric

Default

• 1
   

E. coli DNA Polymerase I (10 U/μL) per tube (µl)

Numeric

Default

• 4
   

E. coli RNase H (2 U/μL) per tube (µl)

Numeric

Default

• 1

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Sample Type

  

Default

• ds cDNA
• Set by script
Automation

Automation Name

Setting

Value

Specification

Set Sample Type - ds cDNA output

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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

  
     

Command line

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

  
     

Command line

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'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point