Sort Specimens to Extraction v1.1

PreviousCDC COVID-19 RT-PCR NextQiagen QIAamp DSP Viral RNA Mini Kit v1.1

Last updated 8 days ago

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

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

Routing Script - Extraction

Trigger Location = Step
Trigger Style = Automatic upon exit

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

ℹ The version of the workflow and step name for the routing script may be different depending on the version of IPP installed.

Queue/Ice Bucket

Defaults

Sample Grouping = Group by Containers
Well Sort Order = Row

Sample Table (Column Headers)

Category

Field Name

Field Type

Options

Additional Options and Dropdown Items

Container

Container Name

Built-in

Container

LIMS ID (Container)

Built-in

Container

Well

Built-in

Derived Sample

Sample Name

Built-in

Derived Sample

Waiting

Built-in

Project

Project Name

Built-in

Record Details

Step Data (Master Step Fields)

Field Name

Field Type

Options

Additional Options and Dropdown Items

Comment

Multiline Text

Step File Placeholders

Log - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Extraction Protocol
Text Dropdown
Required Field
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
Derived Sample
Sample Name
Built-in