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Sort Specimens to Extraction v1.1

Overview

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)
Step Type = No Outputs

Automations

Set Next Step - Copy extraction protocol

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Routing Script - Extraction

Trigger Location = Step
Trigger Style = Automatic upon exit

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step Data (Master Step Fields)

Sort Specimens to Extraction v1.1

Overview

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)
Step Type = No Outputs

Automations

Set Next Step - Copy extraction protocol

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Routing Script - Extraction

Trigger Location = Step
Trigger Style = Automatic upon exit

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step Data (Master Step Fields)

Category

Field Name

Field Type

Options

Additional Options and Dropdown Items

Container

Container Name

Built-in

Container

LIMS ID (Container)

Built-in

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/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}"

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'"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/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}"

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'"

Presets

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

Sort Specimens to Extraction v1.1

hashtagOverview

hashtagProtocol 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

hashtagStep 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

Sort Specimens to Extraction v1.1

hashtagOverview

hashtagProtocol 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

hashtagStep 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

Overview

Protocol 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

Step 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

Automations

Queue/Ice Bucket

Record Details

Overview

Protocol 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

Step 1: Sort Specimens to Extraction (CDC COVID-19 RT-PCR v1.1)

Automations

Queue/Ice Bucket

Record Details