Illumina Preset Protocol - CDC COVID-19 RT-PCR

Overview

The CDC COVID-19 RT-PCR workflow includes the following functionality.

• Preconfigured CDC COVID-19 RT-PCR 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.

Protocol 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR)

Master Step 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR)

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

Extraction Protocol

Text Dropdown

Presets

• Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit
• Qiagen EZ1 Advanced XL
• Roche MagNA Pure LC
• Roche MagNA Pure Compact
• Roche MagNA Pure 96
• bioMérieux NucliSENSE easyMAG Instrument
• bioMérieux EMAG Instrument
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Copy extraction protocol

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:: ; submittedSample.::Extraction Protocol:: = input.::Extraction Protocol::' -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 'Extraction Protocol' \

--FIELD_VALUE 'Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit' \

--WORKFLOW 'Qiagen QIAamp DSP Viral RNA Mini Kit CDC COVID-19 RT-PCR v1.0' \

--STEP 'Sample Concentration (CDC COVID-19 RT-PCR v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' \

\

--FIELD_NAME 'Extraction Protocol' \

--FIELD_VALUE 'Qiagen EZ1 Advanced XL' \

--WORKFLOW 'Qiagen EZ1 Advanced XL CDC COVID-19 RT-PCR v1.0' \

--STEP 'Sort Sample Type (CDC COVID-19 RT-PCR v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' \

\

--FIELD_NAME 'Extraction Protocol' \

--FIELD_VALUE 'Roche MagNA Pure LC' \

--WORKFLOW 'Roche MagNA Pure LC CDC COVID-19 RT-PCR v1.0' \

--STEP 'Sort Roche MagNA Pure LC Samples (CDC COVID-19 RT-PCR v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' \

\

--FIELD_NAME 'Extraction Protocol' \

--FIELD_VALUE 'Roche MagNA Pure Compact' \

--WORKFLOW 'Roche MagNA Pure Compact CDC COVID-19 RT-PCR v1.0' \

--STEP 'Sort Roche MagNA Pure Compact Samples (CDC COVID-19 RT-PCR v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' \

\

--FIELD_NAME 'Extraction Protocol' \

--FIELD_VALUE 'Roche MagNA Pure 96' \

--WORKFLOW 'Roche MagNa Pure 96 CDC COVID-19 RT-PCR v1.0' \

--STEP 'Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' \

\

--FIELD_NAME 'Extraction Protocol' \

--FIELD_VALUE 'bioMérieux NucliSENSE easyMAG Instrument' \

--WORKFLOW 'bioMerieux NucliSENS easyMAG Instrument CDC COVID-19 RT-PCR v1.0' \

--STEP 'Nucleic Acid Extraction (CDC COVID-19 RT-PCR v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS' \

\

--FIELD_NAME 'Extraction Protocol' \

--FIELD_VALUE 'bioMérieux EMAG Instrument' \

--WORKFLOW 'bioMerieux EMAG Instrument CDC COVID-19 RT-PCR v1.0' \

--STEP 'Custom Protocol CDC Flu V1 (CDC COVID-19 RT-PCR v1.0)' \

--INPUTS_OR_OUTPUTS 'INPUTS'"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Protocol 2: Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit (CDC COVID-19 RT-PCR)

Master Step 1: Sample Concentration (CDC COVID-19 RT-PCR)

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

Text Dropdown

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 (CDC COVID-19 RT-PCR v1.0)::} \

else {if (output.::Purification Protocol:: == ::Vacuum::) {nextStep = ::Purification of Viral RNA - Vacuum Protocol (CDC COVID-19 RT-PCR 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 (CDC COVID-19 RT-PCR)

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 Finish 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
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 - Spin

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:: ; output.::Purification Protocol:: = input.::Purification Protocol::' \

-log {compoundOutputFileLuid0}"

Routing Script - Spin

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 'Purification Protocol' \

--FIELD_VALUE 'Spin' \

--WORKFLOW 'Qiagen QIAamp DSP Viral RNA Mini Kit CDC COVID-19 RT-PCR v1.0' \

--STEP 'Assay Set Up Sorting (CDC COVID-19 RT-PCR 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 (CDC COVID-19 RT-PCR)

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 Finish 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
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 - 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 3: Qiagen EZ1 Advanced XL (CDC COVID-19 RT-PCR)

Master Step 1: Sort Sample Type (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Urine, Whole Blood, Stool, Dried Swabs, Viscous Respiratory Samples, Isolation of gDNA of Gram Positive Bacteria

Output = Urine, Whole Blood, Stool, Dried Swabs, Viscous Respiratory Samples, Isolation of gDNA of Gram Positive Bacteria

Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

    

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Extraction Sample Type

Dropdown Text

Presets

• Urine
• Whole Blood
• Stool
• Dried Swabs
• Viscous Respiratory Samples
• Isolation of gDNA of Gram Positive Bacteria
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Qiagen EZ1 Advanced XL

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.::Extraction Sample Type:: == ::Urine::) {nextStep = ::Pretreatment of Urine (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::Extraction Sample Type:: == ::Whole Blood::) {nextStep = ::Pretreatment of Whole Blood (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::Extraction Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::Extraction Sample Type:: == ::Dried Swabs::) {nextStep = ::Pretreatment of Dried Swabs (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::Extraction Sample Type:: == ::Viscous Respiratory Samples::) {nextStep = ::Pretreatment of Viscous Respiratory Samples (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::Extraction Sample Type:: == ::Isolation of gDNA of Gram Positive Bacteria::) {nextStep = ::Pretreatment of Isolation of gDNA of Gram Positive Bacteria (CDC COVID-19 RT-PCR v1.0)::} ' \

-log {compoundinputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Pretreatment of Urine (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Urine

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

ATL

  

939016
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

Final Sample Volume (µl)

Numeric Dropdown

Required

Presets

• 100
• 200
• 400

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Volume of Urine (µl)

Numeric

Calculated
   

Volume of ATL (µl)

Numeric

Calculated
Automation

Automation Name

Setting

Value

Specification

Calculate Volumes

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 false \

-h false \

-exp 'if (step.::Final Sample Volume (uL):: == 100) {output.::Volume of Urine (uL):: = 75 ; output.::Volume of ATL (uL):: = 25} ; \

if (step.::Final Sample Volume (uL):: == 200) {output.::Volume of Urine (uL):: = 150 ; output.::Volume of ATL (uL):: = 50} ; \

if (step.::Final Sample Volume (uL):: == 400) {output.::Volume of Urine (uL):: = 300 ; output.::Volume of ATL (uL):: = 100}' \

-log {compoundOutputFileLuid0}"

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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 3: Pretreatment of Whole Blood (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Whole Blood

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

ATL

  

939016
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

Final Sample Volume (µl)

Numeric

Required

Presets

• 100
• 200
• 400

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Volume of Whole Blood (µl)

Numeric

Calculated
   

Volume of ATL (µl)

Numeric

Calculated
Automation

Automation Name

Setting

Value

Specification

Calculate Volumes

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 false \

-h false \

-exp 'if (step.::Final Sample Volume (uL):: == 100) {output.::Volume of Whole Blood (uL):: = 50 ; output.::Volume of ATL (uL):: = 50} ; \

if (step.::Final Sample Volume (uL):: == 200) {output.::Volume of Whole Blood (uL):: = 100 ; output.::Volume of ATL (uL):: = 100} ; \

if (step.::Final Sample Volume (uL):: == 400) {output.::Volume of Whole Blood (uL):: = 200 ; output.::Volume of ATL (uL):: = 200}' \

-log {compoundOutputFileLuid0}"

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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 4: Pretreatment of Stool (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Stool

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

Buffer ASL

  

19082
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 1 Start Time

Text

  
   

Incubation 1 Finish Time

Text

  
   

Incubation 2 Start Time

Text

  
   

Incubation 2 Finish Time

Text

  
 

Multiline Text Fields

Directions

  

Default

• If the weight of stool is not 100 mg, update the Stool (mg) field with the proper weight and press the Recalculate Buffer button.

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Stool (mg)

Numeric
• Default = 100
• Minimum of 30
   

Volume of Buffer ASL (µl)

Numeric

  
Automation

Automation Name

Setting

Value

Specification

Set Volume - Stool

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.::Volume of Buffer ASL (uL):: = 900' \

-log {compoundOutputFileLuid0}"

Recalculate Buffer Volume

Trigger Location

Record Details

  
 

Trigger Style

Manual 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 false \

-h false \

-exp 'if (output.::Stool (mg):: != 30) {output.::Volume of Buffer ASL (uL):: = output.::Stool (mg):: * 9}' \

-log {compoundOutputFileLuid0}"

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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 5: Pretreatment of Dried Swabs (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Dried Swabs

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

ATL

  

939016
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 Finish Time

Text

  
   

Volume of ATL to add to each dried swab (µl)

Numeric

Default = 600
 

Multiline Text Fields

Directions

  

Default

• Transfer 100 µl, 200 µl, or 400 µl of the liquid to a new screw cap tube, depending on the sample volume chosen.

Step File Placeholders

 

File Name

Log

Auto
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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 6: Pretreatment of Viscous Respiratory Samples (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Viscous Respiratory Samples

Output = Purified viral RNA

Reagent Kits

Kit Name

Supplier

Sputasol

Oxiod Limited
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

• Add 1 volume of Sputasol solution to 1 volume of sample and shake well.

Step File Placeholders

 

File Name

Log

Auto
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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 7: Pretreatment of Isolation of gDNA of Gram Positive Bacteria (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = gDNA of Gram Positive Bacteria

Output = Purified viral RNA

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 Finish Time

Text

  

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Enzyme Solution (µl)

Numeric

Default = 180
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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 8: Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Purified Viral RNA

Reagent Kits

Kit Name

Supplier

Cat. #

EZ1 DSP Virus Kit

 

62724
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

Procedure Type

Text Dropdown

Required

Presets

• EZ1 Advanced
• EZ1 Advanced XL
• BioRobot EZ1 DSP
   

Was Internal Control (IC) Used?

Toggle

 

Step File Placeholders

 

File Name

Log

Auto
     

Report File [optional]
• Manual
• 10 placeholders
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

 

Protocol 4: Roche MagNA Pure LC (CDC COVID-19 RT-PCR)

Step 1: Sort Roche MagNA Pure LC Samples (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Serum, Plasma, Whole Blood

Output = Serum, Plasma, Whole Blood

Placement

Setting

Value

Specification

Placement Screen

None

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

    

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Do Samples Need External Lysis?

  

Required

Presets

• Yes
• No
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Roche MagNA Pure LC

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.::Do Samples Need External Lysis?:: == ::Yes::) {nextStep = ::External Lysis (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::Do Samples Need External Lysis?:: == ::No::) {nextStep = ::Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR v1.0)::}' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: External Lysis (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Serum, Plasma, Whole Blood

Output = Lysed Serum, Plasma or Whole Blood

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure LC Total Nucleic Acid Isolation Kit

 

03 038 505 001
Placement

Setting

Value

Specification

Destination Containers

MagNA Pure LC Sample Cartridge

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Directions

  

Default

• Transfer 50 to 200 μl of serum/plasma sample or 50 to 100 μl whole blood sample into a suitable vial, such as reaction tubes or the sample cartridge.

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Lysis/Binding Buffer (µl)

Numeric

Default = 300
   

Sample Volume (µl)

Numeric

  
Automation

Automation Name

Setting

Value

Specification

Set Next Step

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: Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Lysed Serum, Plasma or Whole Blood

Output = Isolated Nucleic Acid

Placement

Setting

Value

Specification

Placement Screen

None

Configured on master step and step
Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure LC Total Nucleic Acid Isolation Kit

 

03 038 505 001
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Protocol

Text Dropdown

Required

Presets

• Total NA Serum_Plasma_Blood
• Total NA Variable_elution_volume
• Total NA External_lysis

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step

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 5: Roche MagNA Pure Compact (CDC COVID-19 RT-PCR)

Master Step 1: Sort Roche MagNA Pure Compact Samples (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = WBCs, PBMCs, buffy coat, Stool, Biopsies, Swabs

Output = WBCs, PBMCs, buffy coat, Stool, Biopsies, Swabs

Placement

Setting

Value

Specification

Placement Screen

None

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

    

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

MagNA Pure Compact Sample Type

Text Dropdown

Required

Presets

• WBCs
• PBMCs
• Buffy Coat
• Stool
• Biopsies
• Swabs
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Roche MagNA Pure Compact

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.::MagNA Pure Compact Sample Type:: == ::WBCs::) {nextStep = ::External Lysis Protocol (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure Compact Sample Type:: == ::PBMCs::) {nextStep = ::External Lysis Protocol (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure Compact Sample Type:: == ::buffy coat::) {nextStep = ::External Lysis Protocol (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure Compact Sample Type:: == ::Stool::) {nextStep = ::Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure Compact Sample Type:: == ::Biopsies::) {nextStep = ::Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure Compact Sample Type:: == ::Swabs::) {nextStep = ::Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.0)::} ' \

-log {compoundinputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: External Lysis Protocol (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = WBCs, PBMCs, buffy coat

Output = Lysed WBCs, PBMCs, buffy coat

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure LC DNA Isolation Kit I

 

03 730 964 001
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure Compact

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 = ::Purification Protocol (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 3: Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Stool, Biopsies, Swabs

Output = Lysed Stool, Biopsies, Swabs

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure LC Total Nucleic Acid Isolation Kit

 

03 038 505 001
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Setting

Value

Specification

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 Protocol (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Lysed WBCs, PBMCs, buffy coat, Serum, Plasma or Whole Blood

Output = Purified RNA

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure LC Total Nucleic Acid Isolation Kit

 

03 038 505 001
Placement

Setting

Value

Specification

Placement Screen

None

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Protocol

  

Required

Presets

• DNA_Blood_100_400
• DNA_Blood_external_lysis
• Total_NA_Plasma_100_400
• Total_NA_Plasma_ external_lysis
• DNA_Culture_Cells
• DNA_Bacteria

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

 

Protocol 6: Roche MagNA Pure 96 (CDC COVID-19 RT-PCR)

Master Step 1: Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Whole blood, plasma, serum, bacteria, stool, swabs, cultured cells, Fresh-frozen tissue, FFPE

Output = Whole blood, plasma, serum, bacteria, stool, swabs, cultured cells, Fresh-frozen tissue, FFPE

Placement

Setting

Value

Specification

Placement Screen

None

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

    

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

MagNA Pure 96 Sample Type

Text Dropdown

Required

Presets

• Whole blood
• Plasma
• Serum
• Bacteria
• Stool
• Swabs
• Cultured Cells
• Fresh-frozen Tissue
• FFPE
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Roche MagNA Pure 96

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.::MagNA Pure 96 Sample Type:: == ::Whole blood::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::Plasma::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::Serum::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::Bacteria::) {nextStep = ::Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::Swabs::) {nextStep = ::Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::Cultured Cells::) {nextStep = ::Cultured Cells (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::Fresh-frozen Tissue::) {nextStep = ::Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.0)::} ; \

if (input.::MagNA Pure 96 Sample Type:: == ::FFPE::) {nextStep = ::Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.0)::} ' \

-log {compoundinputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Lysates (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Whole blood, plasma or serum

Output = Lysed whole blood, plasma or serum

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure 96 External Lysis Buffer

 

06374913001
Placement

Setting

Value

Specification

Destination Containers
• 96 well plate
• Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Directions

Multiline Text

Default

• Add 50, 100, or 200 µl of whole blood, plasma, or serum to 250 µl MagNA Pure 96 External Lysis Buffer and mix by pipetting.

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Starting Sample Volume (µl)

Numeric Dropdown

User selects value

Presets

• 50
• 100
• 200
   

External Lysis Buffer (µl)

Numeric

Default = 250
   

Lysed Sample (µl)

Numeric

Calculated
Automation

Automation Name

Setting

Value

Specification

Calculate Lysed Sample (µl)

Trigger Location

Record Details

  
 

Trigger Style

Manual 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 false \

-h false \

-exp 'output.::Lysed Sample (uL):: = output.::Starting Sample Volume (uL):: + output.::External Lysis Buffer (uL)::' \

-log {compoundinputFileLuid0}"

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 3: Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = bacteria

Output = Lysed bacteria

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure 96 Bacterial Lysis Buffer

 

06374921001

Proteinase K

  

03 115 828 001
Placement

Setting

Value

Specification

Destination Containers
• 96 well plate
• Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 4: Pretreatment of Stool Samples (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = stool

Output = Lysed stool

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure 96 Bacterial Lysis Buffer

 

06374921001

Proteinase K

  

03 115 828 001

PBS

    
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 5: Pretreatment of Swabs (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = swabs

Output = swab specimen diluted in buffer

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Pure 96 Bacterial Lysis Buffer

 

06374921001

Proteinase K

  

03 115 828 001

PBS

    
Placement

Setting

Value

Specification

Destination Containers
• 96 well plate
• Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Directions

  

Preset = Suspend a dry swab in 200 l BLB; add 20 µl Proteinase K. For swabs in transport medium use 100 µl transport medium, add 100 µl BLB, and 20 µl Proteinase K.

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 6: Cultured Cells (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = cultured cells

Output = diluted cultured cells

Reagent Kits

Kit Name

Supplier

PBS

  
Placement

Setting

Value

Specification

Destination Containers
• 96 well plate
• Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 7: Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR )

Step Type: No output

Input = Fresh-frozen tissue

Output = Fresh-frozen tissue

Reagent Kits

Kit Name

Supplier

PBS

  
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Homogenization Protocol

Text Dropdown

Presets

• Proteinase K Digestion
• MagNA Lyser Instrument
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Fresh-frozen Tissue

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.::Homogenization Protocol:: == ::Proteinase K Digestion::) {nextStep = ::Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.0)::} else {nextStep = ::Tissue Homogenization using MagNA Lyser Instrument (CDC COVID-19 RT-PCR v1.0)::} ' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 8: Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Fresh-frozen tissue

Output = Homogenized fresh-frozen tissue

Reagent Kits

Kit Name

Supplier

Cat. #

MagNa Pure 96 DNA Tissue Lysis Buffer

 

06640702001

Proteinase K

  

03 115 828 001
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 9: Tissue Homogenization using MagNA Lyser Instrument (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Fresh-frozen tissue

Output = Homogenized fresh-frozen tissue

Reagent Kits

Kit Name

Supplier

Cat. #

MagNA Lyser Green Beads

 

03358941001

MagNa Pure 96 DNA Tissue Lysis Buffer

  

06640702001
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 10: Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR)

Step Type: STANDARD

Input = FFPE

Output = Tissue lysate

Reagent Kits

Kit Name

Supplier

Cat. #

Xylol

 

  

MagNa Pure 96 DNA Tissue Lysis Buffer

  

06640702001

Proteinase K

  

03 115 828 001
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 11: Isolation Procedure (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = FFPE

Output = Tissue lysate

Placement

Setting

Value

Specification

Destination Containers

96 well plate

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Protocol Name

Text Dropdown

Presets

• DNA Blood ds SV
• DNA Blood SV
• DNA Blood ext lys SV
• Viral NA Plasma SV
• Viral NA Plasma ext lys SV
• Viral NA Universal SV
• Pathogen Universal 200
• DNA Cells SV
• DNA Tissue SV
• DNA FFPE SV

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

 

Protocol 7: bioMérieux NucliSENS easyMAG Instrument (CDC COVID-19 RT-PCR)

Master Step 1: Nucleic Acid Extraction (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Specimen

Output = Extracted Sample

Reagent Kits

Kit Name

Supplier

Cat. #

easyMAG Lysis Buffer

 

200292

easyMAG Wash Buffers 1, 2, and 3

    
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 Finish Time

Text

  
 

Multiline Text Fields

Directions

Multiline Text

Default

• Add 100 µl of sample to 1000 µl of pre-aliquoted easyMAG lysis buffer (total input sample volume is 1100 µl).

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

 

Protocol 8: bioMérieux EMAG Instrument (CDC COVID-19 RT-PCR)

Master Step 1: Custom Protocol CDC Flu V1 (CDC COVID-19 RT-PCR)

Step Type: Standard

Input = Specimen

Output = Extracted Sample

Reagent Kits

Kit Name

Supplier

Cat. #

easyMAG Lysis Buffer

 

280134

easyMAG Wash Buffers 1, 2 and 3

  

280130, 280131, 280132
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 Finish Time

Text

  
   

Custom Protocol

Text

Default = CDC Flu V1
 

Multiline Text Fields

Directions

Multiline Text

Default

• Add 100 µl of samples to 2000 µl of pre-aliquoted easyMAG lysis buffer (total input sample volume is 2100 µl).

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

 

Protocol 9: Real-Time RT-PCR Prep (CDC COVID-19 RT-PCR)

Master Step 1: Assay Set Up Sorting (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Purified RNA

Output = Purified RNA

Placement

Setting

Value

Specification

Placement Screen

None

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

Multiline Text

  

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

RT-qPCR Assay

Text Dropdown

Required

Presets

• Thermofisher TaqPath 1-Step RT-qPCR
• Promega GoTaq Probe 1-Step RT qPCR
• Quantabio qScript XLT One-Step RT-qPCR Tough Mix
• Quantabio UltraPlex 1-Step ToughMix (4X)
Automation

Automation Name

Setting

Value

Specification

Set Next Step - RT-qPCR

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.::RT-qPCR Assay:: == ::Thermofisher TaqPath 1-Step RT-qPCR::) {nextStep = ::Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.0)::} ; if (input.::RT-qPCR Assay:: == ::Promega GoTaq Probe 1-Step RT qPCR::) {nextStep = ::Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.0)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix::) {nextStep = ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.0)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio UltraPlex 1-Step ToughMix (4X)::) {nextStep = ::Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.0)::}' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 2: Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR)

Step Type: Standard

Derived Sample Generation = Fixed, 3

Input = Purified RNA

Output = {InputItemName}-{LIST:N1,N2,P}

Reagent Kits

Kit Name

Supplier

Cat. #

Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG

 

A15299; A15300
Controls

Sample Name

Supplier

NTC

 

nCoVPC

  

HSC

  
Placement

Setting

Value

Specification

Destination Containers

96 well plate
• Configured on master step and step
• Automatic script to plate samples into the proper placement pattern based on -N1, -N2, -P derived sample suffixes
Controls

Sample Name

Supplier

NTC

 

nCoVPC

  

HSC

  
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Total Samples

Numeric

Preset = 0
   

Nuclease-free Water (µl)

Numeric

Calculated

• 2 decimal
   

Combined Primer/Probe Mix (µl)

Numeric

Calculated

• 2 decimal
   

TaqPath 1-Step RT-qPCR Master Mix (4x) (µl)

Numeric

Calculated

• 2 decimal
   

Total Volume (µl)

Numeric

Calculated

• 2 decimal

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.::Nuclease-free Water (uL):: = step.::Total Samples:: * 8.5 ; \

step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \

step.::TaqPath 1-Step RT-qPCR Master Mix (4x) (uL):: = step.::Total Samples:: * 5 ; \

step.::Total Volume (uL):: = step.::Total Samples:: * 15' \

-log {compoundOutputFileLuid0}"

Set Next Step - RT-qPCR Assay

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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Auto placement for 7500 Covid-19 assay

Trigger Location

Placement Screen

  
 

Trigger Style

Automatic upon entry

  
     

Command line

/usr/bin/python /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

copy PCR Product LIMSID to Sample

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 -i {stepURI:v2} -u {username} -p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 3: Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR)

Step Type: Standard

Derived Sample Generation = Fixed, 3

Input = Purified RNA

Output = {InputItemName}-{LIST:N1,N2,P}

Reagent Kits

Kit Name

Supplier

Cat. #

Promega GoTaq Probe 1- Step RT-qPCR System

 

A6120; A6121
Placement

Setting

Value

Specification

Destination Containers

96 well plate
• Configured on master step and step
• Automatic script to plate the samples into the proper placement pattern based upon -N1, -N2, -P derived sample suffixes
Controls

Sample Name

Supplier

NTC

 

nCoVPC

  

HSC

  
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Total Samples

Numeric

Default = 0
   

Nuclease-free Water (µl)

Numeric

Calculated

• 2 decimal
   

Combined Primer/Probe Mix (µl)

Numeric

Calculated

• 2 decimal
   

GoTaq Probe qPCR Master Mix with dUTP (µl)

Numeric

Calculated

• 2 decimal
   

Go Script RT Mix for 1-Step RT-qPCR (µl)

Numeric

Calculated

• 2 decimal
   

Total Volume (µl)

Numeric

Calculated

• 2 decimal

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.::Nuclease-free Water (uL):: = step.::Total Samples:: * 3.1 ; \

step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \

step.::GoTaq Probe qPCR Master Mix with dUTP (uL):: = step.::Total Samples:: * 10 ; \

step.::Go Script RT Mix for 1-Step RT-qPCR (uL):: = step.::Total Samples:: * 0.4 ; \

step.::Total Volume (uL):: = step.::Total Samples:: * 15' \

-log {compoundOutputFileLuid0}"

Set Next Step - RT-qPCR Assay

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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Auto placement for 7500 Covid-19 assay

Trigger Location

Placement Screen

  
 

Trigger Style

Automatic upon entry

  
     

Command line

/usr/bin/python /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Copy PCR Product LIMSID to Sample

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 -i {stepURI:v2} -u {username} -p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 4: Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR)

Step Type: Standard

Derived Sample Generation = Fixed, 3

Input = Purified RNA

Output = {InputItemName}-{LIST:N1,N2,P}

Reagent Kits

Kit Name

Supplier

Cat. #

Quantabio qScript XLT One-Step RT-qPCR ToughMix

 

95132-100; 95132-02K; 95132-500
Placement

Setting

Value

Specification

Destination Containers

96 well plate
• Configured on master step and step
• Automatic script to plate the samples into the proper placement pattern based upon -N1, -N2, -P derived sample suffixes
Controls

Sample Name

Supplier

NTC

 

nCoVPC

  

HSC

  
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Total Samples

Numeric

Default = 0
   

Nuclease-free Water (µl)

Numeric

Calculated

• 2 decimal
   

Combined Primer/Probe Mix (µl)

Numeric

Calculated

• 2 decimal
   

qScript XLT One-Step RT-qPCR Tough Mix (µl)

Numeric

Calculated

• 2 decimal
   

Total Volume (µl)

Numeric

Calculated

• 2 decimal

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.::Nuclease-free Water (uL):: = step.::Total Samples:: * 3.5 ; \

step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \

step.::qScript XLT One-Step RT-qPCR Tough Mix (uL):: = step.::Total Samples:: * 10 ; \

step.::Total Volume (uL):: = step.::Total Samples:: * 15' \

-log {compoundOutputFileLuid0}"

Set Next Step - RT-qPCR Assay

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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Auto placement for 7500 Covid-19 assay

Trigger Location

Placement Screen

  
 

Trigger Style

Automatic upon entry

  
     

Command line

/usr/bin/python /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Copy PCR Product LIMSID to Sample

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 -i {stepURI:v2} -u {username} -p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 5: Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR)

Step Type: Standard

Derived Sample Generation = Fixed, 3

Input = Purified RNA

Output = {InputItemName}-{LIST:N1,N2,P}

Reagent Kits

Kit Name

Supplier

Cat. #

Quantabio UltraPlex 1-Step ToughMix (4X)

 

95166-100; 95166-500; 95166-01K
Placement

Setting

Value

Specification

Destination Containers

96 well plate
• Configured on master step and step
• Automatic script to plate the samples into the proper placement pattern based upon -N1, -N2, -P derived sample suffixes
Controls

Sample Name

Supplier

NTC

 

nCoVPC

  

HSC

  
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Total Samples

Numeric

Default = 0
   

Nuclease-free Water (µl)

Numeric

Calculated

• 2 decimal
   

Combined Primer/Probe Mix (µl)

Numeric

Calculated

• 2 decimal
   

UltraPlex 1-Step ToughMix (4x) (µl)

Numeric

Calculated

• 2 decimal
   

Total Volume (µl)

Numeric

Calculated

• 2 decimal

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 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.::Nuclease-free Water (uL):: = step.::Total Samples:: * 8.5 ; \

step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \

step.::UltraPlex 1-Step ToughMix (4x) (uL):: = step.::Total Samples:: * 5 ; \

step.::Total Volume (uL):: = step.::Total Samples:: * 15' \

-log {compoundOutputFileLuid0}"

Set Next Step - RT-qPCR Assay

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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.0)::' \

-log {compoundOutputFileLuid0}"

Auto placement for 7500 Covid-19 assay

Trigger Location

Placement Screen

  
 

Trigger Style

Automatic upon entry

  
     

Command line

/usr/bin/python /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Copy PCR Product LIMSID to Sample

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 -i {stepURI:v2} -u {username} -p {password} \

script:evaluateDynamicExpression \

-t false \

-h false \

-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Manual

Safe Stopping Point

 

Master Step 6: ABI 7500 Fast DX (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Purified RNA

Placement

Setting

Value

Specification

Placement Screen

None
• Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Template File

Text Dropdown

Required

Presets

• 2019-nCov Dx Panel TaqPath
• 2019-nCov Dx Panel Quanta
• 2019-nCov Dx Panel Promega
 

Multiline Text Fields

Directions

  

Groups of Defaults

• Thermofisher
a. In Stage 1, Set to 2 min at 25°C; 1 Rep.
b. In Stage 2, Set to 15 min at 50°C; 1 Rep.
c. In Stage 3, Set to 2 min at 95°C, 1 Rep.
d. In Stage 4, Step 1 set to 3 sec at 95°C.
e. In Stage 4, Step 2 set to 30 sec at 55.0°C.
f. In Stage 4, Reps should be set to 45.
g. Under Settings, bottom left-hand box, change volume to 20 µL.
h. Under Settings, Run Mode selection should be Standard 7500.
i. Step 2 of Stage 4 should be highlighted in yellow to indicate data collection.
• Quantbio
a. In Stage 1, Set to 10 min at 50°C; 1 Rep.
b. In Stage 2, Set to 3 min at 95°C, 1 Rep.
c. In Stage 3, Step 1 set to 3 sec at 95°C.
d. In Stage 3, Step 2 set to 30 sec at 55.0°C.
e. In Stage 3, Reps should be set to 45.
f. Under Settings, bottom left-hand box, change volume to 20 µL.
g. Under Settings, Run Mode selection should be Standard 7500.
h. Step 2 of Stage 4 should be highlighted in yellow to indicate data collection.
• Promega
a. In Stage 1, Set to 15 min at 45°C; 1 Rep.
b. In Stage 2, Set to 2 min at 95°C, 1 Rep.
c. In Stage 3, Step 1 set to 3 sec at 95°C.
d. In Stage 3, Step 2 set to 30 sec at 55.0°C.
e. In Stage 3, Reps should be set to 45.
f. Under Settings, bottom left-hand box, change volume to 20 µL.
g. Under Settings, Run Mode selection should be Standard 7500.
h. Step 2 of Stage 4 should be highlighted in yellow to indicate data collection.

Step File Placeholders

 

File Name

Log

Auto
     

Instrument Driver File

Auto
     

Upload Result File

Manual

Sample Table

Table Columns

Ct Value

Text

  
Automation

Automation Name

Setting

Value

Specification

Generate ABI Instrument File

Trigger Location

Record Details

  
 

Trigger Style

Manual

  
     

Command line

bash -l -c "/opt/gls/clarity/bin/java -cp /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar driver_file_generator -i {processURI} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/covid/7900sds_container_setup_template.txt -o {compoundOutputFileLuid1}.txt -l {compoundOutputFileLuid0}.html && /opt/gls/clarity/bin/java -cp /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar addBlankLines -i {stepURI} -u {username} -p {password} -f {compoundOutputFileLuid1}.txt -l {compoundOutputFileLuid0}.html -sep TAB -b '0' -h 7 -c PLACEMENT"

 

Parse ABI File

    

Set Next Step

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 7: Report Results (CDC COVID-19 RT-PCR)

Step Type: No Output

Input = Purified RNA

Placement

Setting

Value

Specification

Placement Screen

None

Configured on master step and step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

Multiline Text

 

Step File Placeholders

 

File Name

Log

Auto
     

Results File (.csv)

Auto
     

File Log

Auto

Sample Table

Table Columns

Ct Values

Text

 
   

Result

Text

Required

Presets

• Positive
• Negative
• Unknown
   

Extraction Protocol

  

Sample field
   

Sample Type

  

Sample field
Automation

Automation Name

Setting

Value

Specification

Generate Results File

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/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/covid/covid_report_results.csv -o {compoundOutputFileLuid1}.csv -l {compoundOutputFileLuid2}"

 
     

Template:

Set Next Step

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