Qiagen QIAamp DSP Viral RNA Mini Kit v1.1 The Qiagen QIAamp DSP Viral RNA Mini Kit 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: Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Step 1: Sample Concentration (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sample Concentration (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Purification of Viral RNA - Spin Protocol (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification of Viral RNA - Spin Protocol (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Purification of Viral RNA - Vacuum Protocol (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification of Viral RNA - Vacuum Protocol (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
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)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
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)
Derived Sample Generation = Fixed, 3
chevron-right hashtag Trigger Location = Placement
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
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)
Derived Sample Generation = Fixed, 3
chevron-right hashtag Trigger Location = Placement
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
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)
Derived Sample Generation = Fixed, 3
chevron-right hashtag Trigger Location = Placement
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
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)
Derived Sample Generation = Fixed, 3
chevron-right hashtag Trigger Location = Placement
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
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)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 7: Report Results (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Report Results (CDC COVID-19 RT-PCR v1.1)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
ℹ The version of the workflow and step name for the routing script may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Carrier RNA AVE Volume (uL)
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
QIAvac 24 Plus vacuum manifold
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Carrier RNA AVE Volume (uL)
Decimal Places Displayed = 2
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG
Catalog Number = A15299; A15300
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Decimal Places Displayed = 2
TaqPath 1-Step RT-qPCR Master Mix (4x) (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Promega GoTaq Probe 1- Step RT-qPCR System
Catalog Number = A6120; A6121
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Decimal Places Displayed = 2
GoTaq Probe qPCR Master Mix with dUTP (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
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
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Decimal Places Displayed = 2
qScript XLT One-Step RT-qPCR Tough Mix (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Quantabio UltraPlex 1-Step ToughMix (4X)
Catalog Number = 95166-100; 95166-500; 95166-01K
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Decimal Places Displayed = 2
Decimal Places Displayed = 2
UltraPlex 1-Step ToughMix (4x) (uL)
Decimal Places Displayed = 2
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Sample Table (Column Headers)
Additional Options and Dropdown Items
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
Table Columns - Global Fields
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Results File (.csv) - Automatically attached
File Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Default =
Add up to 3.5 ml of sample to the microconcentrator
Centrifuge to a final volume of 140 μl.
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Go Script RT Mix for 1-Step RT-qPCR (uL)
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Copy 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 v1.1)::} \
else {if (output.::Purification Protocol:: == ::Vacuum::) {nextStep = ::Purification of Viral RNA - Vacuum Protocol (CDC COVID-19 RT-PCR v1.1)::} }' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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}"
Copy 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 v1.1' \
--STEP 'Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy 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}"
Copy 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}"
Copy 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}"
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Copy 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}"
Copy 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}"
Copy 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}"
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Copy 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}"
Copy 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}"
Copy 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}"
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Copy 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}"
Copy 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}"
Copy 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}"
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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}" Additional Options and Dropdown Items
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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)
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