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
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
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)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Sort Specimens to Extraction v1.1 The Sort Specimens to Extraction 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: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)
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)
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
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
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 'nextStep = ::ADVANCE:: ; submittedSample.::Extraction Protocol:: = input.::Extraction 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 '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 v1.1' \
--STEP 'Sample Concentration (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Extraction Protocol' \
--FIELD_VALUE 'Qiagen EZ1 Advanced XL' \
--WORKFLOW 'Qiagen EZ1 Advanced XL CDC COVID-19 RT-PCR v1.1' \
--STEP 'Sort Sample Type (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Extraction Protocol' \
--FIELD_VALUE 'Roche MagNA Pure LC' \
--WORKFLOW 'Roche MagNA Pure LC CDC COVID-19 RT-PCR v1.1' \
--STEP 'Sort Roche MagNA Pure LC Samples (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Extraction Protocol' \
--FIELD_VALUE 'Roche MagNA Pure Compact' \
--WORKFLOW 'Roche MagNA Pure Compact CDC COVID-19 RT-PCR v1.1' \
--STEP 'Sort Roche MagNA Pure Compact Samples (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Extraction Protocol' \
--FIELD_VALUE 'Roche MagNA Pure 96' \
--WORKFLOW 'Roche MagNA Pure 96 CDC COVID-19 RT-PCR v1.1' \
--STEP 'Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Extraction Protocol' \
--FIELD_VALUE 'bioMérieux NucliSENSE easyMAG Instrument' \
--WORKFLOW 'bioMerieux NucliSENS easyMAG Instrument CDC COVID-19 RT-PCR v1.1' \
--STEP 'Nucleic Acid Extraction (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Extraction Protocol' \
--FIELD_VALUE 'bioMérieux EMAG Instrument' \
--WORKFLOW 'bioMerieux EMAG Instrument CDC COVID-19 RT-PCR v1.1' \
--STEP 'Custom Protocol CDC Flu V1 (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS'" Additional Options and Dropdown Items
Presets
Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit
bioMérieux NucliSENSE easyMAG Instrument
bioMérieux EMAG Instrument
Roche MagNA Pure LC v1.1 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)
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: External Lysis (CDC COVID-19 RT-PCR v1.1)
Master Step Name = External Lysis (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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
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)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table
Sample Display Default = Collapse
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)
ℹ The version of the step names for nextStep may be different depending on the version of IPP installed.
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}
Reagent Kits
MagNA Pure LC Total Nucleic Acid Isolation Kit
Catalog Number = 03 038 505 001
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Destination Containers
MagNA Pure LC Sample Cartridge
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
MagNA Pure LC Total Nucleic Acid Isolation Kit
Catalog Number = 03 038 505 001
Sample Table (Column Headers)
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
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
Additional Options and Dropdown Items
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.
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 (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}"
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 '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}" Decimal Places Displayed = 2
Additional Options and Dropdown Items
Do Samples Need External Lysis?
Additional Options and Dropdown Items
Lysis/Binding Buffer (uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
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)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Real-Time RT-PCR Prep v1.1 The Real-Time RT-PCR Prep 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: 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)
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
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
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
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
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
Preset
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 upload
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
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 (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
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)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
bioMerieux EMAG Instrument v1.1 The bioMerieux EMAG Instrument 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: bioMérieux EMAG Instrument (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Custom Protocol CDC Flu V1 (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Custom Protocol CDC Flu V1 (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)
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}
Reagent Kits
easyMAG Wash Buffers 1, 2 and 3
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = Add 100 uL of samples to 2000 uL of pre-aliquoted easyMAG lysis buffer (total input sample volume is 2100 uL).
Step File Placeholders
Log - Automatically attached
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
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
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
Roche MagNA Pure Compact v1.1 The Roche MagNA Pure Compact 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.
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
Additional Options and Dropdown Items
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)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
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 Compact (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Step 1: Sort Roche MagNA Pure Compact Samples (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sort Roche MagNA Pure Compact Samples (CDC COVID-19 RT-PCR v1.1)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
ℹ The version of the step names for nextStep may be different depending on the version of IPP installed.
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Step 2: External Lysis Protocol (CDC COVID-19 RT-PCR v1.1)
Master Step Name = External Lysis Protocol (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
MagNA Pure LC DNA Isolation Kit I
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 3: Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
MagNA Pure LC Total Nucleic Acid Isolation Kit
Catalog Number = 03 038 505 001
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 4: Purification Protocol (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification Protocol (CDC COVID-19 RT-PCR v1.1)
Reagent Kits
MagNA Pure LC Total Nucleic Acid Isolation Kit
Catalog Number = 03 038 505 001
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Protocol 2: Real-Time RT-PCR Prep (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
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
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
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
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG
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
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
chevron-right hashtag Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
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
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Promega GoTaq Probe 1- Step RT-qPCR System
Catalog Number = A6120; A6121
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
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
chevron-right hashtag Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Go Script RT Mix for 1-Step RT-qPCR (uL)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
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
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
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
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
chevron-right hashtag Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
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
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Quantabio UltraPlex 1-Step ToughMix (4X)
Catalog Number = 95166-100; 95166-500; 95166-01K
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
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
chevron-right hashtag Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Decimal Places Displayed = 2
Sample Table
Sample Display Default = Expand
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
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Instrument Driver File - Automatically attached
Sample Table
Sample Display Default = Expand
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
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Results File (.csv) - Automatically attached
Sample Table
Sample Display Default = Expand
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.::MagNA Pure Compact Sample Type:: == ::WBCs::) {nextStep = ::External Lysis Protocol (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure Compact Sample Type:: == ::PBMCs::) {nextStep = ::External Lysis Protocol (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure Compact Sample Type:: == ::buffy coat::) {nextStep = ::External Lysis Protocol (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure Compact Sample Type:: == ::Stool::) {nextStep = ::Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure Compact Sample Type:: == ::Biopsies::) {nextStep = ::Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure Compact Sample Type:: == ::Swabs::) {nextStep = ::Purification Protocols from Bacterial-Containing Sources (CDC COVID-19 RT-PCR v1.1)::} ' \
-log {compoundinputFileLuid0}"
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 = ::Purification 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 '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 '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}" Table Columns - Global Fields
Additional Options and Dropdown Items
MagNA Pure Compact Sample Type
Catalog Number = 03 730 964 001
Table Columns - Global Fields
Additional Options and Dropdown Items
Presets
Thermofisher TaqPath 1-Step RT-qPCR
Promega GoTaq Probe 1-Step RT qPCR
Quantabio qScript XLT One-Step RT-qPCR Tough Mix
Catalog Number = A15299; A15300
Table Columns - Global Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Upload Result File - Manually uploaded
Table Columns - Global Fields
Additional Options and Dropdown Items
File Log - Automatically attached
Table Columns - Global Fields
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 2
TaqPath 1-Step RT-qPCR Master Mix (4x) (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
GoTaq Probe qPCR Master Mix with dUTP (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
qScript XLT One-Step RT-qPCR Tough Mix (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Decimal Places Displayed = 2
UltraPlex 1-Step ToughMix (4x) (uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Presets
2019-nCov Dx Panel TaqPath
2019-nCov Dx Panel Quanta
2019-nCov Dx Panel Promega
Additional Options and Dropdown Items
bioMerieux NucliSENS easyMAG Instrument v1.1 The bioMerieux NucliSENS easyMAG Instrument 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: bioMérieux NucliSENS easyMAG Instrument (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Nucleic Acid Extraction (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Nucleic Acid Extraction (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)
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)
Quantabio UltraPlex 1-Step ToughMix (4X)
Naming Convention = {InputItemName}
Reagent Kits
easyMAG Wash Buffers 1, 2 and 3
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
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 100 uL of sample to 1000 uL of pre-aliquoted easyMAG lysis buffer (total input sample volume is 1100 uL)
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 '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
Additional Options and Dropdown Items
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)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Roche MagNA Pure 96 v1.1 The Roche MagNA Pure 96 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 96 (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sort Roche MagNA Pure 96 (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 File Placeholders
Log - Automatically attached
Step 2: Lysates (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Lysates (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log - Automatically attached
Step 3: Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log - Automatically attached
Step 4: Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Stool Samples (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
Sample Table
Sample Display Default = Collapse
Step 5: Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Swabs (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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 6: Cultured Cells (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Cultured Cells (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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log - Automatically attached
Step 7: Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Fresh-frozen Tissue 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 File Placeholders
Log - Automatically attached
Step 8: Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Tissue Homogenization by Proteinase K Digestion (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 File Placeholders
Log - Automatically attached
Step 9: Tissue Homogenization using MagNA Lyser Instrument (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Tissue Homogenization using MagNA Lyser Instrument (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 File Placeholders
Log - Automatically attached
Step 10: Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Deparaffinization of FFPE Tissue Sections (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
Sample Table
Sample Display Default = Collapse
Step 11: Isolation Procedure (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Isolation Procedure (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
Placement = Enabled
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)
Qiagen EZ1 Advanced XL v1.1 The Qiagen EZ1 Advanced XL 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 EZ1 Advanced XL (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sort Sample Type (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sort Sample Type (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: Pretreatment of Urine (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Urine (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
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 3: Pretreatment of Whole Blood (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Whole Blood (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
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 4: Pretreatment of Stool (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Stool (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 = 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 5: Pretreatment of Dried Swabs (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Dried Swabs (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 6: Pretreatment of Viscous Respiratory Samples (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Viscous Respiratory Samples (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 7: Pretreatment of Isolation of gDNA of Gram Positive Bacteria (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Isolation of gDNA of Gram Positive Bacteria (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 File Placeholders
Log - Automatically attached
Step 8: Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification of Viral Nucleic Acids and Bacterial DNA (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)
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)
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
MagNA Pure 96 Sample Type
Naming Convention = {InputItemName}
Reagent Kits
MagNA Pure 96 External Lysis Buffer
Catalog Number = 06374913001
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
External Lysis Buffer (uL)
Naming Convention = {InputItemName}
Reagent Kits
MagNA Pure 96 Bacterial Lysis Buffer
Catalog Number = 06374921001
Proteinase K
Catalog Number = 03 115 828 001
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
MagNA Pure 96 Bacterial Lysis Buffer
Catalog Number = 06374921001
Proteinase K
Catalog Number = 03 115 828 001
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
MagNA Pure 96 Bacterial Lysis Buffer
Catalog Number = 06374921001
Proteinase K
Catalog Number = 03 115 828 001
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
ℹ The version of the step names for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
MagNa Pure 96 DNA Tissue Lysis Buffer
Catalog Number = 06640702001
Proteinase K
Catalog Number = 03 115 828 001
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
MagNA Lyser Green Beads
Catalog Number = 03358941001
MagNa Pure 96 DNA Tissue Lysis Buffer
Catalog Number = 06640702001
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
MagNa Pure 96 DNA Tissue Lysis Buffer
Catalog Number = 06640702001
Proteinase K
Catalog Number = 03 115 828 001
ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Step File Placeholders
Log - Automatically attached
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
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 = Suspend a dry swab in 200 l BLB; add 20 uL Proteinase K. For swabs in transport medium use 100 uL transport medium, add 100 uL BLB and 20 uL Proteinase K.
Additional Options and Dropdown Items
Presets
Viral NA Plasma ext lys SV
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
ℹ The version of the next step names may be different depending on the version of IPP installed.
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 next step name may be different depending on the version of IPP installed.
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 next step name may be different depending on the version of IPP installed.
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 next step name may be different depending on the version of IPP installed.
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 next step name may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Volume of ATL to add to each dried swab (uL)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
ℹ The version of the next step name may be different depending on the version of IPP installed.
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 next step name may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report 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
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
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
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.
Additional Options and Dropdown Items
Default = Transfer 100 uL, 200 uL, or 400 uL of the liquid to a new screw cap tube, depending on the sample volume chosen.
Additional Options and Dropdown Items
Default = Add 1 volume of Sputasol solution to 1 volume of sample and shake well
Additional Options and Dropdown Items
Was Internal Control (IC) Used?
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 (input.::MagNA Pure 96 Sample Type:: == ::Whole blood::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Plasma::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Serum::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Bacteria::) {nextStep = ::Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Swabs::) {nextStep = ::Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Cultured Cells::) {nextStep = ::Cultured Cells (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Fresh-frozen Tissue::) {nextStep = ::Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::FFPE::) {nextStep = ::Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)::} ' \
-log {compoundinputFileLuid0}"
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 'output.::Lysed Sample (uL):: = output.::Starting Sample Volume (uL):: + output.::External Lysis Buffer (uL)::' \
-log {compoundinputFileLuid0}"
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 = ::Isolation Procedure (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 'nextStep = ::Isolation Procedure (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 'nextStep = ::Isolation Procedure (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 'nextStep = ::Isolation Procedure (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 'nextStep = ::Isolation Procedure (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 'if (input.::Homogenization Protocol:: == ::Proteinase K Digestion::) {nextStep = ::Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)::} else {nextStep = ::Tissue Homogenization using MagNA Lyser Instrument (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 'nextStep = ::Isolation Procedure (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 'nextStep = ::Isolation Procedure (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 'nextStep = ::Isolation Procedure (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 '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}"
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.::Extraction Sample Type:: == ::Urine::) {nextStep = ::Pretreatment of Urine (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Whole Blood::) {nextStep = ::Pretreatment of Whole Blood (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Dried Swabs::) {nextStep = ::Pretreatment of Dried Swabs (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Viscous Respiratory Samples::) {nextStep = ::Pretreatment of Viscous Respiratory Samples (CDC COVID-19 RT-PCR v1.1)::} ; \
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 v1.1)::} ' \
-log {compoundinputFileLuid0}"
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 (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}"
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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (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 '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}"
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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (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 'output.::Volume of Buffer ASL (uL):: = 900' \
-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 (output.::Stool (mg):: != 30) {output.::Volume of Buffer ASL (uL):: = output.::Stool (mg):: * 9}' \
-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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (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 'nextStep = ::Purification of Viral Nucleic Acids and Bacterial DNA (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 '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}" Starting Sample Volume (uL)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
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)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Volume of Buffer ASL (uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Presets
Viscous Respiratory Samples
Isolation of gDNA of Gram Positive Bacteria
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
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)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Illumina COVIDSeq v1.6 The Illumina COVIDSeq Workflow workflow includes the following functionality:
Preset Illumina COVIDSeq Workflow protocols that track samples through the quantitative detection of SARS-CoV-2 RNA from nasopharyngeal (NP), oropharyngeal (OP), and nasal swab as well as mid-turbinate specimens collected from individuals who meet COVID-19 clinical or epidemiological criteria.
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.
Sample preparation for use on the NovaSeq 6000 Sequencing System.
Parsing of analysis results into Clarity LIMS.
Protocol 1: RNA Extraction (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Prep Sample (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Prep Sample (Illumina COVIDSeq Workflow v1.6)
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 RNA - Spin (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Spin Purification of RNA (Illumina COVIDSeq Workflow v1.6)
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 = 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 3: Anneal Sample (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Anneal Sample (Illumina COVIDSeq Workflow v1.6)
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)
Protocol 2: cDNA Synthesis (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Synthesize First Strand cDNA (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Synthesize First Strand cDNA (Illumina COVIDSeq Workflow v1.6)
Derived Sample Generation = Fixed, 1
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)
Protocol 3: Target Amplification (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Amplify cDNA (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Amplify cDNA (Illumina COVIDSeq Workflow v1.6)
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 4: Library Prep (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Tagment PCR Amplicons (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Tagment PCR Amplicons (Illumina COVIDSeq Workflow v1.6)
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)
Step 2: Post Tagmentation Clean Up (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Post Tagmentation Clean Up (Illumina COVIDSeq Workflow v1.6)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log File - Automatically attached
Step 3: Amplify Tagmented Amplicons (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Amplify Tagmented Amplicons (Illumina COVIDSeq Workflow v1.6)
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
Label Groups
IDT for Illumina Nextera DNA UD Indexes Set A for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
IDT for Illumina Nextera DNA UD Indexes Set A-D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
Step Data (Master Step Fields)
Step 4: Pool and Clean Up Libraries (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Pool and Clean Up Libraries (Illumina COVIDSeq Workflow v1.6)
Aliquot Generation = Fixed, 1
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
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Placement Pattern = Column
Step Data (Master Step Fields)
Protocol 5: Quantification (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Quantify Libraries (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Quantify Libraries - Qubit (Illumina COVIDSeq Workflow v1.6)
Measurement Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Dilute Libraries (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Dilute Libraries (Illumina COVIDSeq Workflow v1.6)
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 = 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 3: Quantify Libraries (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Quantify Libraries - Qubit (Illumina COVIDSeq Workflow v1.6)
Measurement Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 4: Normalize Libraries (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Normalize Libraries (Illumina COVIDSeq Workflow v1.6)
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 = 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 5: Pool and Dilute Libraries (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Pool and Dilute Libraries (Illumina COVIDSeq Workflow v1.6)
Aliquot Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Protocol 6: NovaSeq 6000 Xp Setup (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Sequencing
Next Steps Configuration
Step 1: NovaSeq Denature & ExAmp (Illumina COVIDSeq Workflow v1.6)
Master Step Name = NovaSeq Denature & ExAmp (Illumina COVIDSeq Workflow v1.6)
Derived Sample Generation = Fixed, 1
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 2: Load to Flowcell (Illumina COVIDSeq Workflow v1.6)
Master Step Name = Load to Flowcell (Illumina COVIDSeq Workflow v1.6)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Placement
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Protocol 7: AUTOMATED - NovaSeq Run (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Sequencing
Next Steps Configuration
Step 1: AUTOMATED - NovaSeq Run (Illumina COVIDSeq Workflow v1.6)
Master Step Name = AUTOMATED - NovaSeq Run (Illumina COVIDSeq Workflow v1.6)
Measurement Generation = Variable
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Protocol 8: Analysis Results (Illumina COVIDSeq Workflow v1.6)
Protocol Type = Data Analysis
Next Steps Configuration
Step 1: Analysis Results (Illumina COVIDSeq Workflow v1.6)
Master Step Name = COVIDSeq Analysis Results (Illumina COVIDSeq Workflow v1.6)
Step Type = Demultiplexing
Measurement Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data
Step Data Heading = WARNING: It might take several minutes to parse the TSV Run Report
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Positive Control HT
Illumina COVIDSeqTest Box 4
Catalog Number = 20043436
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
QIAmp Viral RNA Mini kit
Catalog Number = (50) - 52904; (250) - 52906
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Carrier RNA-Buffer AVE (uL)
Decimal Places Displayed = 0
Elution Incubation End Time
Elution Incubation Start Time
Default =
Enter in No. of Preps before clicking on "Calculate AW1, AW2, AVL Reagent Volumes".
Elute in 30 µl Buffer AVE instead of 60 µl. Incubate elution for at least 1 minute.
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Test Box 5 – 3072 Samples
Catalog Number = 20043648
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default =
Add 8.5 µl EPH3 HT to each well.
Add 8.5 µl eluted sample to each well.
Seal and shake at 1600 rpm for 1 minute.
Centrifuge at 1000 × g for 1 minute.
Thermal Cycler Program Notes
Default = COVIDSeq Anneal
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Test Box 6 – 3072 Samples
Catalog Number = 20043647
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = Add 8 µl First Strand cDNA Master Mix to each well of the CDNA1 plate.
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Test Box 5 – 3072 Samples
Catalog Number = 20043648
Illumina COVIDSEQ Test Box 7 – 3072 Samples
Catalog Number = 20043439
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 0
CPP2 HT for COVIDSeq PCR 2 Master Mix (uL)
Decimal Places Displayed = 0
Default = Add 20 µl COVIDSeq PCR 1 Master Mix to each well of the COV1 plate corresponding to each well of the
CDNA1 plate. Add 5 µl first strand cDNA synthesis from each well of the CDNA1 plate to the corresponding well of the COV1
plate.
Add 20 µl COVIDSeq PCR 2 Master Mix to each well of the COV2 plate corresponding to each well of the
CDNA1 plate. Add 5 µl first strand cDNA synthesis from each well of the CDNA1 plate to the corresponding well of the COV2
plate.
IPM HT for COVIDSeq PCR 1 Master Mix (uL)
Decimal Places Displayed = 0
IPM HT for COVIDSeq PCR 2 Master Mix (uL)
Decimal Places Displayed = 0
Nuclease-free water for COVIDSeq PCR 1 Master Mix (uL)
Decimal Places Displayed = 0
Nuclease-free water for COVIDSeq PCR 2 Master Mix (uL)
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSEQ Test Box 7 – 3072 Samples
Catalog Number = 20043439
Illumina COVIDSeqTest Box 3 – 3072 Samples
Catalog Number = 20043646
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Default = Add 30 µl Tagmentation Master Mix to each well in TAG1 plate.
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Illumina COVIDSeq Test Box 2 – 3072 Samples
Catalog Number = 20043434
Illumina COVIDSeqTest Box 4
Catalog Number = 20043436
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Collapse
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}-{AppliedReagentLabels}
Reagent Kits
Illumina COVIDSeq Test Box 5 – 3072 Samples
Catalog Number = 20043648
Sample Table (Column Headers)
Additional Options and Dropdown Items
IDT for Illumina Nextera DNA UD Indexes Set B for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
IDT for Illumina Nextera DNA UD Indexes Set C for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
IDT for Illumina Nextera DNA UD Indexes Set D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
Illumina DNA-RNA UD Indexes Set A B C D Tagmentation
Illumina DNA-RNA UD Indexes Set A Tagmentation
Illumina DNA-RNA UD Indexes Set B Tagmentation
Illumina DNA-RNA UD Indexes Set C Tagmentation
Illumina DNA-RNA UD Indexes Set D Tagmentation
Default = Add 40 µl PCR Master Mix to each well.
Default = COVIDSeq TAG PCR
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {PoolName}
Reagent Kits
Illumina COVIDSeqTest Box 3 – 3072 Samples
Catalog Number = 20043646
Sample Table (Column Headers)
Additional Options and Dropdown Items
Well Sort Order = Column
Destination Containers
Default =
Enter in Total Pooled ITB Tubes to Calculate ITB (uL) volume.
Transfer 50 µl supernatant from each Pooled ITB tube to a new microcentrifuge tube.
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Criteria 1 - Threshold Value
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
Step File Placeholders
Log - Automatically attached
QC Log File - Automatically attached
QC Result File - Manually uploaded
Upload File - Manually uploaded
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeqTest Box 3 – 3072 Samples
Catalog Number = 20043646
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = Enter Final Volume (uL) then click on "Calculate Sample & RSB Volumes" for dilution volumes.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Criteria 1 - Threshold Value
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
Step File Placeholders
Log - Automatically attached
QC Log File - Automatically attached
QC Result File - Manually uploaded
Upload File - Manually uploaded
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeqTest Box 3 – 3072 Samples
Catalog Number = 20043646
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 = {PoolName}
Reagent Kits
Illumina COVIDSeqTest Box 3 – 3072 Samples
Catalog Number = 20043646
Sample Table (Column Headers)
Additional Options and Dropdown Items
Well Sort Order = Row
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}_WP{OutputItemNumber}
Reagent Kits
DPX1
Catalog Number = 20019916
DPX2
Catalog Number = 20019917
DPX3
Catalog Number = 20019918
Sample Table
Column Headers
Additional Options and Dropdown Items
400 mM Tris-HCl per pool (uL)
400 mM Tris-HCl Prep Date
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Default = Enter the No. of Lanes for your S4 flow cell to calculate DPX 1, DPX2 and DPX 3 volumes.
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Column
Reverse Complement Workflow
UMI - Read 1 Start From Cycle
UMI - Read 2 Start From Cycle
Use Custom Index Read 1 Primer
Step File Placeholders
Sample Sheet - Automatically attached
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = Lane {InputWellLocation}
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Flow Cell Expiration Date
Instrument Control Software Version
Sample Table
Sample Display Default = Collapse
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {InputItemName} (FASTQ reads) {AppliedReagentLabels}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Log - Automatically attached
COVIDSeq TSV_Run Report File - Manually uploaded
COVIDSeq_RunReport PDF - Manually uploaded
Parsing Log - Automatically attached
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Additional Options and Dropdown Items
Default = For each sample, add 140 µl patient sample, dilution 3 CPC HT, or ELB HT (no template control) to a new 1.7 ml microcentrifuge tube.
Additional Options and Dropdown Items
Additional Options and Dropdown Items
COVIDSeq Anneal Program Notes
Default =
Choose the preheat lid option
Set the reaction volume to 17 µl
65°C for 3 minutes
Hold at 4°C
Additional Options and Dropdown Items
COVIDSeq FSS Program Notes
Default =
Choose the preheat lid option
Set the reaction volume to 25 µl
25°C for 5 minutes
50°C for 10 minutes
80°C for 5 minutes
Hold at 4°C
Additional Options and Dropdown Items
Default =
Choose the preheat lid option
Set the reaction volume to 25 µl
98°C for 3 minutes
35 cycles of:
98°C for 15 seconds
65°C for 5 minutes
Hold at 4°C
CPP1 HT for COVIDSeq PCR 1 Master Mix (uL)
Additional Options and Dropdown Items
COVIDSeq TAG Program Notes
Default =
Choose the preheat lid option
Set the reaction volume to 50 µl
55°C for 5 minutes
Hold at 10°C
Additional Options and Dropdown Items
COVIDSeq TAG PCR Program Notes
Default =
Choose the preheat lid option and set to 100°C
Set the reaction volume to 50 µl
72°C for 3 minutes
98°C for 3 minutes
7 cycles of:
98°C for 20 seconds
60°C for 30 seconds
72°C for 1 minute
72°C for 3 minutes
Hold at 10°C
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Default =
For each set of 384 samples, combine 25 µl of each normalized pool containing index adapter set A, B, C, D in a new microcentrifuge tube. Do not combine pools with the same index adapter set. This step produces a final pool of 384 samples for one flow cell lane.
For each flow cell lane, dilute each 384 sample pool with RSB HT as follows. These steps produce 30 µl 0.5 nM pooled library.
Combine 3.75 µl library from the 384-sample pool with 26.25 µl RSB.
Vortex, and then centrifuge briefly. The resulting final loading concentration is 100 pM.
Additional Options and Dropdown Items
Additional Options and Dropdown Items
BaseSpace Sequence Hub Configuration
Presets
Run Monitoring And Storage
Additional Options and Dropdown Items
Decimal Places Displayed = 0
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 \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 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 'if (step.::No. of Preps:: == 50) {step.::AW1 Concentrate (mL):: = 19 ; step.::EtOH for AW1 (mL):: = 25 ; step.::AW2 Concentrate (mL):: = 13 ; step.::EtOH for AW2 (mL):: = 30} else {step.::AW1 Concentrate (mL):: = 98 ; step.::EtOH for AW1 (mL):: = 130 ; step.::AW2 Concentrate (mL):: = 66 ; step.::EtOH for AW2 (mL):: = 160} ; \
step.::Buffer AVL (mL):: = 0.56 * step.::Total Samples:: ; step.::Carrier RNA-Buffer AVE (uL):: = 10 * step.::Buffer AVL (mL):: ' \
-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 '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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::FSA (uL):: = 9 * step.::Total Samples:: ; step.::RVT (uL):: = 1 * step.::Total Samples:: ' -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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::IPM HT for COVIDSeq PCR 1 Master Mix (uL):: = 15 * step.::Total Samples:: ; step.::CPP1 HT for COVIDSeq PCR 1 Master Mix (uL):: = 4.3 * step.::Total Samples:: ; step.::Nuclease-free water for COVIDSeq PCR 1 Master Mix (uL):: = 4.7 * step.::Total Samples:: ; step.::IPM HT for COVIDSeq PCR 2 Master Mix (uL):: = 15 * step.::Total Samples:: ; step.::CPP2 HT for COVIDSeq PCR 2 Master Mix (uL):: = 4.3 * step.::Total Samples:: ; step.::Nuclease-free water for COVIDSeq PCR 2 Master Mix (uL):: = 4.7 * step.::Total Samples::' -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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::TB1 (uL):: = 12 * step.::Total Samples:: ; step.::eBLT (uL):: = 4 * step.::Total Samples:: ; step.::Nuclease-free water (uL):: = 20 * step.::Total Samples::' -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 '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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::EPM HT (uL):: = 24 * step.::Total Samples:: ; step.::Nuclease-free water (uL):: = 24 * step.::Total Samples::' -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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::ITB (uL):: = 0.9 * (55 * step.::Total Pooled ITB Tubes::) ' -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 {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {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 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::SampleVolume (uL):: = 0.1 * step.::Final Volume (uL):: ; output.::RSB (uL):: = step.::Final Volume (uL):: - output.::SampleVolume (uL):: ' -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 {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Starting Molarity (nM):: = (output.::Concentration:: / (660 * 400)) * 1000000 ; output.::Library Pool (uL):: = step.::Final Molarity (nM):: * step.::Final Volume (uL):: / output.::Starting Molarity (nM):: ; output.::RSB (uL):: = step.::Final Volume (uL):: - output.::Library Pool (uL):: ' -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 '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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'step.::DPX1 Volume (ul):: = 315 * step.::No. of Lanes:: ; step.::DPX2 Volume (ul):: = 45 * step.::No. of Lanes:: ; step.::DPX3 Volume (ul):: = 165 * step.::No. of Lanes:: ; output.::Flowcell Type:: = step.::Flowcell Type::; output.::Loading Workflow Type:: = step.::Loading Workflow Type::' -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 script:validate_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -validateSelectedContainer true"
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 \
-exp 'if (input.::Flowcell Type:: == ::SP:: && !output.container.name.matches( ::[A-Z0-9]{5}DR[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S1:: && !output.container.name.matches( ::[A-Z0-9]{5}DR[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S2:: && !output.container.name.matches( ::[A-Z0-9]{5}DM[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S4:: && !output.container.name.matches( ::[A-Z0-9]{5}DS[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' \
-log {compoundOutputFileLuid1}"
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 \
-exp '{udf:Validation Script}' \
-log {compoundOutputFileLuid1} \
-t true \
&& if [ '{udf:Reverse Complement Workflow}' == 'true' ]; then \
templateFilename='NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv'; \
elif [ '{udf:Reverse Complement Workflow}' == 'false' ]; then \
templateFilename='NovaSeq_BCL2FASTQ_Samplesheet.csv'; \
else echo 'UDF Reverse Complement Workflow is empty or undefined.'; exit -1; fi \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {stepURI:v2} -u {username} -p {password} \
script:driver_file_generator \
-t /opt/gls/clarity/extensions/conf/driverfiletemplates/$templateFilename \
-o {compoundOutputFileLuid0}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-l {compoundOutputFileLuid1}"
Copy bash -l -c "sleep 10 && /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 \
-exp 'if (input.::Loading Workflow Type:: == ::NovaSeq Standard::) { output.::name:: = ::Lane :: + step.::Lane Counter::; output.::name:: = output.::name::.split(::\\.::)[0] + :::1::; step.::Lane Counter::++; }' \
-log {compoundOutputFileLuid3} \
-t true \
&& /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 \
-exp 'step.::Lane Counter:: = 1' \
-log {compoundOutputFileLuid3} \
-t true"
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 -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/parseCovidSeqRunReport.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid1} -g {compoundOutputFileLuid3} Website =
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 3
Decimal Places Displayed = 3
Decimal Places Displayed = 3
Decimal Places Displayed = 3
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Cluster Density (K/mm^2) R1
Cluster Density (K/mm^2) R2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Index ID for Control Sample
Index Set for Control Sample
SARS-CoV-2 for Control Sample
Default = 250
8
Decimal Places Displayed = 0
8
Decimal Places Displayed = 0
101
Decimal Places Displayed = 0
101
Decimal Places Displayed = 0
Dual Index
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Respiratory Virus Panel v1.0 The Respiratory Virus Panel workflow includes the following functionality:
Preconfigured protocols that support the preparation of upper and lower respiratory specimens for real-time RT-PCR qualitative detection of nucleic acid from the 2019-nCoV.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
Routing to iSeq, MiniSeq, MiSeq, NextSeq 550, NextSeq 2000.
Protocol 1: Sort Sample Type (Respiratory Virus Panel v1.0)
Protocol Type = Other
Next Steps Configuration
Step 1: Sort Sample Type (Respiratory Virus Panel v1.0)
Master Step Name = Sort Sample Type (Respiratory Virus Panel v1.0)
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)
Protocol 2: QIAamp Viral RNA Mini Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sample Concentration (Respiratory Virus Panel v1.0)
Master Step Name = Sample Concentration (Respiratory Virus Panel v1.0)
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 (Respiratory Virus Panel v1.0)
Master Step Name = Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)
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 (Respiratory Virus Panel v1.0)
Master Step Name = Purification of Viral RNA - Vacuum Protocol (Respiratory Virus Panel v1.0)
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)
Protocol 3: AllPrep PowerViral DNA/RNA Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sort Sample (Respiratory Virus Panel v1.0)
Master Step Name = Sort Sample (Respiratory Virus Panel v1.0)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log File - Automatically attached
Step 2: Prep Samples (Respiratory Virus Panel v1.0)
Master Step Name = Prep Samples (Respiratory Virus Panel v1.0)
Derived Sample Generation = Fixed, 1
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: Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)
Master Step Name = Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)
Derived Sample Generation = Fixed, 1
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)
Protocol 4: Maxima H Minus Double-Stranded cDNA Synthesis Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
Master Step Name = First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
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 Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
Master Step Name = Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
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 Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Removal of RNA (Respiratory Virus Panel v1.0)
Master Step Name = Removal of RNA (Respiratory Virus Panel v1.0)
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 4: Purification of ds cDNA (Respiratory Virus Panel v1.0)
Master Step Name = Purification of ds cDNA (Respiratory Virus Panel v1.0)
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 File Placeholders
Log File - Automatically attached
Protocol 5: NEBNext Ultra II First Strand Synthesis Module (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)
Master Step Name = mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)
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)
Step 2: First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
Master Step Name = First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
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 Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Protocol 6: NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
Master Step Name = Second Strand cDNA Synthesis (Respiratory Virus Panel v1.0)
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 Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Purification of Double-stranded cDNA (Respiratory Virus Panel v1.0)
Master Step Name = Purification of Double-stranded cDNA (Respiratory Virus Panel v1.0)
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 File Placeholders
Log File - Automatically attached
Protocol 7: SuperScript Double-Stranded cDNA Synthesis Kit (Respiratory Virus Panel v1.0)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: First-Strand Synthesis (Respiratory Virus Panel v1.0)
Master Step Name = First-Strand Synthesis (Respiratory Virus Panel v1.0)
Derived Sample Generation = Fixed, 1
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 2: Second-Strand Synthesis (Respiratory Virus Panel v1.0)
Master Step Name = Second-Strand Synthesis (Respiratory Virus Panel v1.0)
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 File Placeholders
Log File - Automatically attached
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.
Sample Table (Column Headers)
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.
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
ℹ The actual version of the workflows and steps in the routing automation 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 File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
QIAvac 24 Plus vacuum manifold
ℹ The actual version of the workflows and steps in the routing automation 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 File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
AllPrep PowerViral DNA/RNA Kit
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AllPrep PowerViral DNA/RNA Kit
Phenol:chloroform:isoamyl alcohol
Supplier = supplied by user
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Maxima H Minus Double-Stranded cDNA Synthesis Kit
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Maxima H Minus Double-Stranded cDNA Synthesis Kit
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Second Strand Enzyme Mix (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
GeneJET PCR Purification Kit
Catalog Number = K0701, K0702
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
NEBNext First Strand Synthesis Reaction Buffer
Catalog Number = E7525S, E7525L
NEBNext Poly(A) mRNA Magnetic Isolation Module
Catalog Number = E7490S, E7490L
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
MM1: NEBNext First Strand Synthesis Reaction Buff (uL)
Decimal Places Displayed = 2
MM1: NEBNext Random Primers (uL)
Decimal Places Displayed = 2
MM1: Nuclease-free Water (uL)
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
ProtoScript II Reverse Transcriptase (uL)
Decimal Places Displayed = 2
Default =
10 minutes at 25°C
50 minutes at 42°C
15 minutes at 70°C
Hold at 4°C
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
Catalog Number = E6111S, E6111L
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
NEBNext Second Strand Synthesis Enzyme Mix (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
Catalog Number = E6111S, E6111L
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
SuperScript Double-Stranded cDNA Synthesis Kit
Catalog Number = 11917-010, 11917-020
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
SuperScript Double-Stranded cDNA Synthesis Kit
Catalog Number = 11917-010, 11917-020
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Default = Please select the Respiratory Virus Extraction Protocol for each sample.
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Default = Please record the volumes for the following fields: Volume of Oligo(dT)18 Used (uL), Volume of Template RNA Used (uL), Nuclease-free Water Used (uL).
Additional Options and Dropdown Items
5x Second Strand Reaction Mix (uL)
Decimal Places Displayed = 2
First Strand cDNA Synthesis (uL)
Additional Options and Dropdown Items
RNase I (uL) to add to each tube
Additional Options and Dropdown Items
Beads MM: Oligo dT Beads d(T)25 (uL)
Decimal Places Displayed = 2
Beads MM: RNA Binding Buffer (2X) (uL)
Additional Options and Dropdown Items
Murine RNase Inhibitor (uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
First-Strand Synthesis Product Volume per Well (uL)
NEBNext Second Strand Reaction Buffer (uL)
Additional Options and Dropdown Items
Default = Please enter ug of starting mRNA or Total RNA and Prep Sample Type in field below.
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::' -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 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'QIAamp Viral Mini Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sample Concentration (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'AllPrep PowerViral DNA/RNA Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sort Sample (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"
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.::Is Bead Beating Required?:: == ::Yes::) {nextStep = ::Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)::} \
else {if (input.::Is Bead Beating Required?:: == ::No::) {nextStep = ::Prep Samples (Respiratory Virus Panel v1.0)::} }' \
-log {compoundOutputFileLuid0}"
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::' -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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
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::' -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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
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.::Is Bead Beating Required?:: == ::Yes::) {nextStep = ::Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)::} \
else {if (input.::Is Bead Beating Required?:: == ::No::) {nextStep = ::Prep Samples (Respiratory Virus Panel v1.0)::} }' \
-log {compoundOutputFileLuid0}"
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::' -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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
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::' -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 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First-Strand Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
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 'output.::4x First Strand Reaction Mix (uL):: = 4 ; output.::First Strand Enzyme Mix (uL):: = 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 '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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Murine RNase Inhibitor (uL):: = step.::Total Samples:: * 0.5 * 1.1 ; \
step.::ProtoScript II Reverse Transcriptase (uL):: = step.::Total Samples:: * 1 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 5 * 1.1 ' \
-log {compoundOutputFileLuid0}"
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 'output.::First Strand cDNA Synthesis (uL):: = 20 ; \
output.::5x Second Strand Reaction Mix (uL):: = 20 ; \
output.::Nuclease-free Water (uL):: = 55 ; \
output.::Second Strand Enzyme Mix (uL):: = 5 ; \
output.::Total Volume (uL):: = 100' \
-log {compoundOutputFileLuid0}"
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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::NEBNext Second Strand Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::NEBNext Second Strand Synthesis Enzyme Mix (uL):: = step.::Total Samples:: * 4 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 48 * 1.1 ' \
-log {compoundOutputFileLuid0}"
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 'output.::Sample Type:: = ::ds cDNA::' \
-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::' -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 'Sample Type' \
--FIELD_VALUE 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
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.::MM1: NEBNext First Strand Synthesis Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::MM1: NEBNext Random Primers (uL):: = step.::Total Samples:: * 2 * 1.1 ; \
step.::MM1: Nuclease-free Water (uL):: = step.::Total Samples:: * 10 * 1.1 ; \
step.::Beads MM: Oligo dT Beads d(T)25 (uL):: = step.::Total Samples:: * 20 * 1.1 ; \
step.::Beads MM: RNA Binding Buffer (2X) (uL):: = step.::Total Samples:: * 100 * 1.1 ' \
-log {compoundOutputFileLuid0}"
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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Murine RNase Inhibitor (uL):: = step.::Total Samples:: * 0.5 * 1.1 ; \
step.::ProtoScript II Reverse Transcriptase (uL):: = step.::Total Samples:: * 1 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 5 * 1.1 ' \
-log {compoundOutputFileLuid0}"
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 'output.::4x First Strand Reaction Mix (uL):: = 4 ; output.::First Strand Enzyme Mix (uL):: = 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.::NEBNext Second Strand Reaction Buffer (uL):: = step.::Total Samples:: * 8 * 1.1 ; \
step.::NEBNext Second Strand Synthesis Enzyme Mix (uL):: = step.::Total Samples:: * 4 * 1.1 ; \
step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 48 * 1.1 ' \
-log {compoundOutputFileLuid0}"
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 'output.::First Strand cDNA Synthesis (uL):: = 20 ; \
output.::5x Second Strand Reaction Mix (uL):: = 20 ; \
output.::Nuclease-free Water (uL):: = 55 ; \
output.::Second Strand Enzyme Mix (uL):: = 5 ; \
output.::Total Volume (uL):: = 100' \
-log {compoundOutputFileLuid0}"
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 'input.::Sample Type:: = ::ds cDNA::' \
-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::' -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 'Sample Type' \
--FIELD_VALUE 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"
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 (!output.hasValue(::Prep Sample Type::)) {fail(::Please enter Prep Sample Type::)} ; \
if (!output.hasValue(::mRNA/Total RNA (ug)::)) {fail(::Please enter mRNA/Total RNA (ug) for each sample::)} ; \
if (output.::mRNA/Total RNA (ug):: <= 1 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ; output.::RNA in DEPC-treated water uL):: = 10 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 1 } ; \
if (output.::mRNA/Total RNA (ug):: == 2 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 9 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 2} ; \
if (output.::mRNA/Total RNA (ug):: == 3 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 8 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 3} ; \
if (output.::mRNA/Total RNA (ug):: == 4 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 7 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 4} ; \
if (output.::mRNA/Total RNA (ug):: == 5 && output.::Prep Sample Type:: == ::mRNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 6 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 5} ; \
if (output.::mRNA/Total RNA (ug):: <= 50 && output.::Prep Sample Type:: == ::Total RNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 9 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 2} ; \
if (output.::mRNA/Total RNA (ug):: <= 50 && output.::Prep Sample Type:: == ::Total RNA::) {output.::Primer (100 pmol/uL):: = 1 ;output.::RNA in DEPC-treated water uL):: = 10 ; output.::5X First-Strand Reaction Buffer (uL):: = 4 ; output.::0.1M DTT (uL):: = 2 ; output.::10 mM dNTP mix (uL):: = 1 ; output.::SuperScript II RT (uL):: = 1} ;' \
-log {compoundOutputFileLuid0}"
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 'output.::Sample Type:: = ::ds cDNA::' \
-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::' -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 'Sample Type' \
--FIELD_VALUE 'ds cDNA' \
--WORKFLOW 'Nextera Flex for Enrichment v1.0' \
--STEP 'Sort Sample (Nextera Flex for Enrichment v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'" Respiratory Virus Extraction Protocol
Presets
AllPrep PowerViral DNA/RNA Kit
Presets
Maxima H Minus Double-Stranded cDNA Synthesis Kit
NEBNext Ultra II First Strand Synthesis Module
SuperScript Double-Stranded cDNA Synthesis Kit
Presets
Maxima H Minus Double-Stranded cDNA Synthesis Kit
NEBNext Ultra II First Strand Synthesis Module
SuperScript Double-Stranded cDNA Synthesis Kit
Presets
Maxima H Minus Double-Stranded cDNA Synthesis Kit
NEBNext Ultra II First Strand Synthesis Module
SuperScript Double-Stranded cDNA Synthesis Kit
Presets
Maxima H Minus Double-Stranded cDNA Synthesis Kit
NEBNext Ultra II First Strand Synthesis Module
SuperScript Double-Stranded cDNA Synthesis Kit
4x First Strand Reaction Mix (uL)
Decimal Places Displayed = 2
First Strand Enzyme Mix (uL)
Decimal Places Displayed = 2
Nuclease-free Water Used (uL)
Decimal Places Displayed = 2
Volume of Oligo(dT)18 Used (uL)
Decimal Places Displayed = 2
Volume of Template RNA Used (uL)
Decimal Places Displayed = 2
5x Second Strand Reaction Mix (uL)
First Strand cDNA Synthesis (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
5X First-Strand Reaction Buffer (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
RNA in DEPC-treated water uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Is Bead Beating Required?
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
