Roche MagNA Pure LC v1.1

Overview

The Roche MagNA Pure LC CDC COVID-19 RT-PCR is part of the CDC COVID-19 RT-PCR protocols that include 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: Roche MagNA Pure LC (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Roche MagNA Pure LC Samples (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Sort Roche MagNA Pure LC Samples (CDC COVID-19 RT-PCR v1.1)

• Step Type = No Outputs

Automations

Set Next Step - Roche MagNA Pure LC

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (input.::Do Samples Need External Lysis?:: == ::Yes::) {nextStep = ::External Lysis (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Do Samples Need External Lysis?:: == ::No::) {nextStep = ::Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR v1.1)::}' \
-log {compoundOutputFileLuid0}"

ℹ️ The version of the step names for nextStep may be different depending on the version of IPP installed.

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Do Samples Need External Lysis?	Text Dropdown	Required Field	Presets Yes No
    Derived Sample	Sample Name	Built-in

Step 2: External Lysis (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = External Lysis (CDC COVID-19 RT-PCR v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • MagNA Pure LC Total Nucleic Acid Isolation Kit

    • Catalog Number = 03 038 505 001

Automations

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • MagNA Pure LC Sample Cartridge

  

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Directions	Multiline Text		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

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Lysis/Binding Buffer (uL)	Numeric		Default = 300 Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (uL)	Numeric		Decimal Places Displayed = 2

Step 3: Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR v1.1)

• Step Type = No Outputs

• Reagent Kits

  • MagNA Pure LC Total Nucleic Acid Isolation Kit

    • Catalog Number = 03 038 505 001

Automations

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Protocol 2: Real-Time RT-PCR Prep (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)

• Step Type = No Outputs

Automations

Set Next Step - RT-qPCR

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (input.::RT-qPCR Assay:: == ::Thermofisher TaqPath 1-Step RT-qPCR::) {nextStep = ::Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)::}  ; 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 v1.1)::} ; 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 v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio UltraPlex 1-Step ToughMix (4X)::) {nextStep = ::Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)::}' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	RT-qPCR Assay	Text Dropdown	Required Field	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)
    Derived Sample	Sample Name	Built-in

Step 2: Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 3

• Naming Convention = {InputItemName}-{LIST:N1,N2,P}

• Reagent Kits

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

    • Supplier = Thermofisher

    • Catalog Number = A15299; A15300

• Control Types

  • HSC

  • nCoVPC

  • NTC

Automations

auto placement for 7500 Covid-19 assay

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Calculate Total Samples and Master Mix

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::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

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 v1.1)::' \
-log {compoundOutputFileLuid0}"

ℹ️ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Combined Primer/Probe Mix (uL)	Numeric		Decimal Places Displayed = 2
  Nuclease-free Water (uL)	Numeric		Decimal Places Displayed = 2
  TaqPath 1-Step RT-qPCR Master Mix (4x) (uL)	Numeric		Decimal Places Displayed = 2
  Total Samples	Numeric		Default = 0
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 3: Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 3

• Naming Convention = {InputItemName}-{LIST:N1,N2,P}

• Reagent Kits

  • Promega GoTaq Probe 1- Step RT-qPCR System

    • Catalog Number = A6120; A6121

• Control Types

  • HSC

  • nCoVPC

  • NTC

Automations

auto placement for 7500 Covid-19 assay

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Calculate Total Samples and Master Mix

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::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

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 v1.1)::' \
-log {compoundOutputFileLuid0}"

ℹ️ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Combined Primer/Probe Mix (uL)	Numeric		Decimal Places Displayed = 2
  Go Script RT Mix for 1-Step RT-qPCR (uL)	Numeric		Decimal Places Displayed = 2
  GoTaq Probe qPCR Master Mix with dUTP (uL)	Numeric		Decimal Places Displayed = 2
  Nuclease-free Water (uL)	Numeric		Decimal Places Displayed = 2
  Total Samples	Numeric		Default = 0
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 4: Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 3

• Naming Convention = {InputItemName}-{LIST:N1,N2,P}

• Reagent Kits

  • Quantabio qScript XLT One-Step RT-qPCR ToughMix

    • Catalog Number = 95132-100; 95132-02K; 95132-500

• Control Types

  • HSC

  • nCoVPC

  • NTC

Automations

auto placement for 7500 Covid-19 assay

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Calculate Total Samples and Master Mix

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::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

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 v1.1)::' \
-log {compoundOutputFileLuid0}"

ℹ️ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Combined Primer/Probe Mix (uL)	Numeric		Decimal Places Displayed = 2
  Nuclease-free Water (uL)	Numeric		Decimal Places Displayed = 2
  qScript XLT One-Step RT-qPCR Tough Mix (uL)	Numeric		Decimal Places Displayed = 2
  Total Samples	Numeric		Default = 0
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 5: Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 3

• Naming Convention = {InputItemName}-{LIST:N1,N2,P}

• Reagent Kits

  • Quantabio UltraPlex 1-Step ToughMix (4X)

    • Catalog Number = 95166-100; 95166-500; 95166-01K

• Control Types

  • HSC

  • nCoVPC

  • NTC

Automations

auto placement for 7500 Covid-19 assay

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Calculate Total Samples and Master Mix

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::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

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 v1.1)::' \
-log {compoundOutputFileLuid0}"

ℹ️ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Combined Primer/Probe Mix (uL)	Numeric		Decimal Places Displayed = 2
  Nuclease-free Water (uL)	Numeric		Decimal Places Displayed = 2
  Total Samples	Numeric		Default = 0
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2
  UltraPlex 1-Step ToughMix (4x) (uL)	Numeric		Decimal Places Displayed = 2

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 6: ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)

• Step Type = No Outputs

Automations

Generate ABI Instrument File

• Trigger Location = Record Details

• Trigger Style = Manual button

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"

PLACEHOLDER - Parse ABI File

• Trigger Location = Record Details

• Trigger Style = Manual button

need parser

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Directions	Multiline Text
  Template File	Text Dropdown	Required Field	Presets 2019-nCov Dx Panel TaqPath 2019-nCov Dx Panel Quanta 2019-nCov Dx Panel Promega

• Step File Placeholders

  • Log - Automatically attached

  • Instrument Driver File - Automatically attached

  • Upload Result File - Manually uploaded

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Ct Value	Text
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 7: Report Results (CDC COVID-19 RT-PCR v1.1)

• Master Step Name = Report Results (CDC COVID-19 RT-PCR v1.1)

• Step Type = No Outputs

Automations

Assign Pos/Neg for Ct Value

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (step.::Criteria - Ct Threshold:: >= input.::Ct Value::.toFloat()) {input.::Result:: = ::Positive::} ; if (step.::Criteria - Ct Threshold:: < input.::Ct Value::.toFloat()) {input.::Result:: = ::Negative::} ; ' -log {compoundOutputFileLuid0}"

Generate Results File

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/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}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Criteria - Ct Threshold	Numeric	Required Field
  Criteria - Operator	Text	Read Only	Default = <=
  Criteria - Source	Text	Read Only	Default = Ct Value
  Result	Text	Read Only	Default = Positive

• Step File Placeholders

  • Log - Automatically attached

  • Results File (.csv) - Automatically attached

  • File Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Ct Value	Text
    Derived Sample	Result	Text
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in
    Submitted Sample	Sample Type	Text
    Submitted Sample	Extraction Protocol	Text