# Roche MagNA Pure LC v1.1

## Overview

The Roche MagNA Pure LC 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: Roche MagNA Pure LC (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

**Next Steps Configuration**

<figure><img src="/files/2GHICj0pwLZIXy38vkYY" alt=""><figcaption></figcaption></figure>

### Step 1: Sort Roche MagNA Pure LC Samples (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Sort Roche MagNA Pure LC Samples (CDC COVID-19 RT-PCR v1.1)
* Step Type = No Outputs

#### Automations

<figure><img src="/files/0XesIh18xaq4TLlWvYOV" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Roche MagNA Pure LC</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.::Do Samples Need External Lysis?:: == ::Yes::) {nextStep = ::External Lysis (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Do Samples Need External Lysis?:: == ::No::) {nextStep = ::Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR v1.1)::}' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step names for nextStep 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 | Do Samples Need External Lysis? | Text Dropdown  | Required Field | <p>Presets</p><ul><li>Yes</li><li>No</li></ul> |
    | Derived Sample | Sample Name                     | Built-in       |                |                                                |

### Step 2: External Lysis (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = External Lysis (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNA Pure LC Total Nucleic Acid Isolation Kit
    * Catalog Number = 03 038 505 001

#### Automations

<figure><img src="/files/4IvQBvmZgPVSVbeso4yg" 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       |             |                                           |

#### Placement = Enabled

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

  * MagNA Pure LC Sample Cartridge

  <figure><img src="/files/jA43KRJ0WmRjVWLnjtq7" alt=""><figcaption></figcaption></figure>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                                                                                       |
  | -------------- | -------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------- |
  | Directions     | Multiline Text |             | Default = Transfer 50 to 200 μl of serum/plasma sample or 50 to 100 μl whole blood sample into a suitable vial, such as reaction tubes or the sample cartridge. |
* 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 | Lysis/Binding Buffer (uL) | Numeric        |             | <ul><li>Default = 300</li><li>Decimal Places Displayed = 2</li></ul> |
    | Derived Sample | Sample Name               | Built-in       |             |                                                                      |
    | Derived Sample | Sample Volume (uL)        | Numeric        |             | <ul><li>Decimal Places Displayed = 2</li></ul>                       |

### Step 3: Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Total Nucleic Acid Isolation Protocol (CDC COVID-19 RT-PCR v1.1)
* Step Type = No Outputs
* Reagent Kits
  * MagNA Pure LC Total Nucleic Acid Isolation Kit
    * Catalog Number = 03 038 505 001

#### Automations

<figure><img src="/files/IA4qKaqX3WuVic9aD2UZ" 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

* Sample Table
  * Sample Display Default = Collapse
  * 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/AXGPvasuz7UzhiGOMfJb" 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/4PpImSe6JML8m6qKePHb" 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/cZYA2hb0M2Mf3xeLSTcQ" 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/Zx1yDwjW7gBTHTMsRtFO" 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/NBNa6zKQcF8kD09NYVT2" 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/xcaxCOt4zmyURAt2j7t8" 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/mYKuzeKeEsqjkSq05pIc" 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/FYxFPk1GUVK2YPH0RGDQ" 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           |             |                                           |


---

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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-roche-lc-v1.1.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
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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.