# 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
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/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}"
```
{% endcode %}
Routing Script - Extraction
* Trigger Location = Step
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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'"
```
{% endcode %}
> 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 | | |