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 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.::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}" 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
