# Qiagen EZ1 Advanced XL v1.1

## Overview

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**

<figure><img src="/files/lpjtRLVK73fIvWe7IDku" alt=""><figcaption></figcaption></figure>

### 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)
* Step Type = No Outputs

#### Automations

<figure><img src="/files/PtgLWO5mHhzO7tRYkiLQ" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Qiagen EZ1 Advanced XL</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 '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}"
```

{% endcode %}

> ℹ The version of the next step names 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 Sample Type | Text Dropdown  | Required Field | <p>Presets</p><ul><li>Urine</li><li>Whole Blood</li><li>Stool</li><li>Dried Swabs</li><li>Viscous Respiratory Samples</li><li>Isolation of gDNA of Gram Positive Bacteria</li></ul> |
    | Derived Sample | Sample Name            | Built-in       |                |                                                                                                                                                                                     |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * ATL
    * Catalog Number = 939016

#### Automations

<figure><img src="/files/H8eL685kyDsLWBeLop4z" alt=""><figcaption></figcaption></figure>

<details>

<summary>Calculate Volumes</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% 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 '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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Purification</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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the next step name 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**                   |
  | ------------------------ | ---------------- | -------------- | ----------------------------------------------------------- |
  | Final Sample Volume (uL) | Numeric Dropdown | Required Field | <p>Presets</p><ul><li>100</li><li>200</li><li>400</li></ul> |
* 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 | Sample Name          | Built-in       |             |                                           |
    | Derived Sample | Volume of ATL (uL)   | Numeric        |             | Decimal Places Displayed = 2              |
    | Derived Sample | Volume of Urine (uL) | Numeric        |             | Decimal Places Displayed = 2              |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}

#### Automations

<figure><img src="/files/ZXsuG3KmQIpxhhu02iGi" alt=""><figcaption></figcaption></figure>

<details>

<summary>Calculate Volumes</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% 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 '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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Purification</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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the next step name 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**                   |
  | ------------------------ | ---------------- | -------------- | ----------------------------------------------------------- |
  | Final Sample Volume (uL) | Numeric Dropdown | Required Field | <p>Presets</p><ul><li>100</li><li>200</li><li>400</li></ul> |
* 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 | Sample Name          | Built-in       |             |                                           |
    | Derived Sample | Volume of ATL (uL)   | Numeric        |             | Decimal Places Displayed = 2              |
    | Derived Sample | Volume of Urine (uL) | Numeric        |             | Decimal Places Displayed = 2              |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * Buffer ASL
    * Catalog Number = 19082

#### Automations

<figure><img src="/files/wVd2elyYjfUck6z6Rma2" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Volume - Stool</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% 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 'output.::Volume of Buffer ASL (uL):: = 900' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

<details>

<summary>Recalculate Buffer Volume</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% 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 'if (output.::Stool (mg):: != 30) {output.::Volume of Buffer ASL (uL):: = output.::Stool (mg):: * 9}' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Purification</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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the next step name 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**                                                                                                   |
  | ------------------------ | -------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------- |
  | Directions               | Multiline Text |             | 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. |
  | Incubation 1 Finish Time | Text           |             |                                                                                                                                             |
  | Incubation 1 Start Time  | Text           |             |                                                                                                                                             |
  | Incubation 2 Finish Time | Text           |             |                                                                                                                                             |
  | Incubation 2 Start Time  | 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 | Sample Name               | Built-in       |             |                                                       |
    | Derived Sample | Stool (mg)                | Numeric        |             | <ul><li>Default = 100</li><li>Range From 30</li></ul> |
    | Derived Sample | Volume of Buffer ASL (uL) | Numeric        |             | <ul><li>Decimal Places Displayed = 2</li></ul>        |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * ATL
    * Catalog Number = 939016

#### Automations

<figure><img src="/files/Ml7jqENm09JQgTioqz1d" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification</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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the next step name 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**                                                                                  |
  | -------------------------------------------- | -------------- | ----------- | -------------------------------------------------------------------------------------------------------------------------- |
  | Directions                                   | Multiline Text |             | Default = Transfer 100 uL, 200 uL, or 400 uL of the liquid to a new screw cap tube, depending on the sample volume chosen. |
  | Incubation Finish Time                       | Text           |             |                                                                                                                            |
  | Incubation Start Time                        | Text           |             |                                                                                                                            |
  | Volume of ATL to add to each dried swab (uL) | Numeric        |             | Default = 600                                                                                                              |
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * Sputasol
    * Supplier = Oxoid Limited
    * Website = [www.oxoid.com](https://help.claritylims.illumina.com/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/www.oxoid.com)

#### Automations

<figure><img src="/files/HLDl1eth2NcAHgKniBsC" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification</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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the next step name 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**                                        |
  | -------------- | -------------- | ----------- | -------------------------------------------------------------------------------- |
  | Directions     | Multiline Text |             | Default = Add 1 volume of Sputasol solution to 1 volume of sample and shake well |
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}

#### Automations

<figure><img src="/files/omVijwtTKxBAmJd1RZcB" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification</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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the next step name 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 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 | Enzyme Solution (uL) | Numeric        |             | <ul><li>Default = 180</li><li>Decimal Places Displayed = 2</li></ul> |
    | Derived Sample | Sample Name          | Built-in       |             |                                                                      |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}

#### Automations

<figure><img src="/files/fnf36Or8eaUI2lqZmX2P" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</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::' \
      -log {compoundOutputFileLuid0}"
```

{% endcode %}

</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**                                                     |
  | ------------------------------- | -------------- | -------------- | --------------------------------------------------------------------------------------------- |
  | Procedure Type                  | Text Dropdown  | Required Field | <p>Presets</p><ul><li>EZ1 Advanced</li><li>EZ1 Advanced XL</li><li>BioRobot EZ1 DSP</li></ul> |
  | Was Internal Control (IC) Used? | Toggle Switch  |                | Default = None Set                                                                            |
* 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
  * Well Sort Order = Row
  * Table Columns - Global Fields

    | **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       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

## Protocol 2: Real-Time RT-PCR Prep (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

**Next Steps Configuration**

<figure><img src="/files/CThIGJKJWrjqtk5jtiJm" alt=""><figcaption></figcaption></figure>

### 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)
* Step Type = No Outputs

#### Automations

<figure><img src="/files/Ok5GxPc3tTzcL9N7Ha0C" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - RT-qPCR</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 '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}"
```

{% endcode %}

</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 | RT-qPCR Assay  | Text Dropdown  | Required Field | <p>Presets</p><ul><li>Thermofisher TaqPath 1-Step RT-qPCR</li><li>Promega GoTaq Probe 1-Step RT qPCR</li><li>Quantabio qScript XLT One-Step RT-qPCR Tough Mix</li><li>Quantabio UltraPlex 1-Step ToughMix (4X)</li></ul> |
    | Derived Sample | Sample Name    | Built-in       |                |                                                                                                                                                                                                                          |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 3
* Naming Convention = {InputItemName}-{LIST:N1,N2,P}
* Reagent Kits
  * Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG
    * Supplier = Thermofisher
    * Catalog Number = A15299; A15300
* Control Types
  * HSC
  * nCoVPC
  * NTC

#### Automations

<figure><img src="/files/hSibcW8M3K6eyjCgdLuV" alt=""><figcaption></figcaption></figure>

<details>

<summary>auto placement for 7500 Covid-19 assay</summary>

* Trigger Location = Placement
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
```

{% endcode %}

</details>

<details>

<summary>Calculate Total Samples and Master Mix</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% 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 '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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - RT-qPCR Assay</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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

</details>

<details>

<summary>copy PCR Product LIMSID to Sample</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 -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</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       |             |                                           |

#### Placement = Enabled

* Defaults
  * Sample Grouping = Group by Containers
  * Well Sort Order = Row
  * Placement Pattern = Row
* Destination Containers
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                              | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Combined Primer/Probe Mix (uL)              | Numeric        |             | Decimal Places Displayed = 2              |
  | Nuclease-free Water (uL)                    | Numeric        |             | Decimal Places Displayed = 2              |
  | TaqPath 1-Step RT-qPCR Master Mix (4x) (uL) | Numeric        |             | Decimal Places Displayed = 2              |
  | Total Samples                               | Numeric        |             | Default = 0                               |
  | Total Volume (uL)                           | Numeric        |             | Decimal Places Displayed = 2              |
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 3
* Naming Convention = {InputItemName}-{LIST:N1,N2,P}
* Reagent Kits
  * Promega GoTaq Probe 1- Step RT-qPCR System
    * Catalog Number = A6120; A6121
* Control Types
  * HSC
  * nCoVPC
  * NTC

#### Automations

<figure><img src="/files/MdSMEit7W6EDanef5oBp" alt=""><figcaption></figcaption></figure>

<details>

<summary>auto placement for 7500 Covid-19 assay</summary>

* Trigger Location = Placement
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
```

{% endcode %}

</details>

<details>

<summary>Calculate Total Samples and Master Mix</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% 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 '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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - RT-qPCR Assay</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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

</details>

<details>

<summary>copy PCR Product LIMSID to Sample</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 -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</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       |             |                                           |

#### Placement = Enabled

* Defaults
  * Sample Grouping = Group by Containers
  * Well Sort Order = Row
  * Placement Pattern = Row
* Destination Containers
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                             | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------------------------------ | -------------- | ----------- | ----------------------------------------- |
  | Combined Primer/Probe Mix (uL)             | Numeric        |             | Decimal Places Displayed = 2              |
  | Go Script RT Mix for 1-Step RT-qPCR (uL)   | Numeric        |             | Decimal Places Displayed = 2              |
  | GoTaq Probe qPCR Master Mix with dUTP (uL) | Numeric        |             | Decimal Places Displayed = 2              |
  | Nuclease-free Water (uL)                   | Numeric        |             | Decimal Places Displayed = 2              |
  | Total Samples                              | Numeric        |             | Default = 0                               |
  | Total Volume (uL)                          | Numeric        |             | Decimal Places Displayed = 2              |
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 3
* 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
* Control Types
  * HSC
  * nCoVPC
  * NTC

#### Automations

<figure><img src="/files/J3eijMMeTNkuHtWgpvUi" alt=""><figcaption></figcaption></figure>

<details>

<summary>auto placement for 7500 Covid-19 assay</summary>

* Trigger Location = Placement
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
```

{% endcode %}

</details>

<details>

<summary>Calculate Total Samples and Master Mix</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% 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 '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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - RT-qPCR Assay</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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

</details>

<details>

<summary>copy PCR Product LIMSID to Sample</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 -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</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       |             |                                           |

#### Placement = Enabled

* Defaults
  * Sample Grouping = Group by Containers
  * Well Sort Order = Row
  * Placement Pattern = Row
* Destination Containers
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                              | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Combined Primer/Probe Mix (uL)              | Numeric        |             | Decimal Places Displayed = 2              |
  | Nuclease-free Water (uL)                    | Numeric        |             | Decimal Places Displayed = 2              |
  | qScript XLT One-Step RT-qPCR Tough Mix (uL) | Numeric        |             | Decimal Places Displayed = 2              |
  | Total Samples                               | Numeric        |             | Default = 0                               |
  | Total Volume (uL)                           | Numeric        |             | Decimal Places Displayed = 2              |
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### 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)
* Step Type = Standard
* Derived Sample Generation = Fixed, 3
* Naming Convention = {InputItemName}-{LIST:N1,N2,P}
* Reagent Kits
  * Quantabio UltraPlex 1-Step ToughMix (4X)
    * Catalog Number = 95166-100; 95166-500; 95166-01K
* Control Types
  * HSC
  * nCoVPC
  * NTC

#### Automations

<figure><img src="/files/Ml7jqENm09JQgTioqz1d" alt=""><figcaption></figcaption></figure>

<details>

<summary>auto placement for 7500 Covid-19 assay</summary>

* Trigger Location = Placement
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
```

{% endcode %}

</details>

<details>

<summary>Calculate Total Samples and Master Mix</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% 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 '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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - RT-qPCR Assay</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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

</details>

<details>

<summary>copy PCR Product LIMSID to Sample</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 -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</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       |             |                                           |

#### Placement = Enabled

* Defaults
  * Sample Grouping = Group by Containers
  * Well Sort Order = Row
  * Placement Pattern = Row
* Destination Containers
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ----------------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Combined Primer/Probe Mix (uL)      | Numeric        |             | Decimal Places Displayed = 2              |
  | Nuclease-free Water (uL)            | Numeric        |             | Decimal Places Displayed = 2              |
  | Total Samples                       | Numeric        |             | Default = 0                               |
  | Total Volume (uL)                   | Numeric        |             | Decimal Places Displayed = 2              |
  | UltraPlex 1-Step ToughMix (4x) (uL) | Numeric        |             | Decimal Places Displayed = 2              |
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### 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)
* Step Type = No Outputs

#### Automations

<figure><img src="/files/awpZlMHkTxhxyjvzyj83" alt=""><figcaption></figcaption></figure>

<details>

<summary>Generate ABI Instrument File</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
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"
```

{% endcode %}

</details>

<details>

<summary>PLACEHOLDER - Parse ABI File</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
need parser
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</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::' \
      -log {compoundOutputFileLuid0}"
```

{% endcode %}

</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**                                                                                       |
  | -------------- | -------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------------- |
  | Directions     | Multiline Text |                |                                                                                                                                 |
  | Template File  | Text Dropdown  | Required Field | <p>Presets</p><ul><li>2019-nCov Dx Panel TaqPath</li><li>2019-nCov Dx Panel Quanta</li><li>2019-nCov Dx Panel Promega</li></ul> |
* Step File Placeholders
  * Log - Automatically attached
  * Instrument Driver File - Automatically attached
  * Upload Result File - Manually uploaded
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Ct Value            | Text           |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 7: Report Results (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Report Results (CDC COVID-19 RT-PCR v1.1)
* Step Type = No Outputs

#### Automations

<figure><img src="/files/ikoK54fKTYIGaGX8RQnd" alt=""><figcaption></figcaption></figure>

<details>

<summary>Assign Pos/Neg for Ct Value</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% 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 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}"
```

{% endcode %}

</details>

<details>

<summary>Generate Results File</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</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::' \
      -log {compoundOutputFileLuid0}"
```

{% endcode %}

</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 |                |                                           |
  | Criteria - Ct Threshold | Numeric        | Required Field |                                           |
  | Criteria - Operator     | Text           | Read Only      | Default = <=                              |
  | Criteria - Source       | Text           | Read Only      | Default = Ct Value                        |
  | Result                  | Text           | Read Only      | Default = Positive                        |
* Step File Placeholders
  * Log - Automatically attached
  * Results File (.csv) - Automatically attached
  * File Log - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * Well Sort Order = Column
  * Table Columns - Global Fields

    | **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   | Ct Value            | Text           |             |                                           |
    | Derived Sample   | Result              | Text           |             |                                           |
    | Derived Sample   | Sample Name         | Built-in       |             |                                           |
    | Project          | Project Name        | Built-in       |             |                                           |
    | Submitted Sample | Sample Type         | Text           |             |                                           |
    | Submitted Sample | Extraction Protocol | Text           |             |                                           |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.claritylims.illumina.com/applications/viral-pathogen-protocols/cdc-covid-19-rt-pcr/covid-qiagen-ez1-v1.1.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.