# 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**

<figure><img src="/files/ksdMkWKyXQ6ciWNhV9qq" alt=""><figcaption></figcaption></figure>

### 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

<figure><img src="/files/kZQAcYHo1NKxY6FBS8x8" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Copy extraction protocol</summary>

* 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 %}

</details>

<details>

<summary>Routing Script - Extraction</summary>

* 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.

</details>

#### 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 | <p>Presets</p><ul><li>Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit</li><li>Qiagen EZ1 Advanced XL</li><li>Roche MagNA Pure LC</li><li>Roche MagNA Pure Compact</li><li>Roche MagNA Pure 96</li><li>bioMérieux NucliSENSE easyMAG Instrument</li><li>bioMérieux EMAG Instrument</li></ul> |
    | Derived Sample | Sample Name         | Built-in       |                |                                                                                                                                                                                                                                                                                                               |


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