# Roche MagNA Pure 96 v1.1

## Overview

The Roche MagNA Pure 96 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 96 (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

**Next Steps Configuration**

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-2038f4b6b0f30f4fc1ab2f84756bf12df1918a95%2Froche-96-protocol1-next-step-config.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)
* Step Type = No Outputs

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-7b3ffbe00100ab5f6205c7de3881caaa9739dcef%2Froche-96-protocol1-step1-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Roche MagNA Pure 96</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.::MagNA Pure 96 Sample Type:: == ::Whole blood::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Plasma::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Serum::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Bacteria::) {nextStep = ::Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Swabs::) {nextStep = ::Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Cultured Cells::) {nextStep = ::Cultured Cells (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Fresh-frozen Tissue::) {nextStep = ::Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::FFPE::) {nextStep = ::Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)::} ' \
-log {compoundinputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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 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 | MagNA Pure 96 Sample Type | Text Dropdown  | Required Field | <p>Presets</p><ul><li>Whole blood</li><li>Plasma</li><li>Serum</li><li>Bacteria</li><li>Stool</li><li>Swabs</li><li>Cultured Cells</li><li>Fresh-frozen Tissue</li><li>FFPE</li></ul> |
    | Derived Sample | Sample Name               | Built-in       |                |                                                                                                                                                                                       |

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

* Master Step Name = Lysates (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNA Pure 96 External Lysis Buffer
    * Catalog Number = 06374913001

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-a67365621984b1c7d29c8b6d7645747e93112f4b%2Froche-96-protocol1-step2-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Calculate Lysed Sample (uL)</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 'output.::Lysed Sample (uL):: = output.::Starting Sample Volume (uL):: + output.::External Lysis Buffer (uL)::' \
-log {compoundinputFileLuid0}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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       |             |                                           |

#### Placement = Enabled

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

#### 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 | External Lysis Buffer (uL)  | Numeric          |                                                         | Default = 200                                              |
    | Derived Sample | Lysed Sample (uL)           | Numeric          |                                                         |                                                            |
    | Derived Sample | Sample Name                 | Built-in         |                                                         |                                                            |
    | Derived Sample | Starting Sample Volume (uL) | Numeric Dropdown | <ul><li>Required Field</li><li>Custom Entries</li></ul> | <p>Presets</p><ul><li>50</li><li>100</li><li>200</li></ul> |

### Step 3: Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNA Pure 96 Bacterial Lysis Buffer
    * Catalog Number = 06374921001
  * PBS
  * Proteinase K
    * Catalog Number = 03 115 828 001

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-75fb3a90448747e6775ac5cc1222559a20ecdfe0%2Froche-96-protocol1-step3-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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       |             |                                           |

#### Placement = Enabled

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

#### 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | 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: Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNA Pure 96 Bacterial Lysis Buffer
    * Catalog Number = 06374921001
  * Proteinase K
    * Catalog Number = 03 115 828 001

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-c04bf7c4da5f9c68bf07fb19f9d99d85602b3b05%2Froche-96-protocol1-step4-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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

* 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       |             |                                           |

### Step 5: Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNA Pure 96 Bacterial Lysis Buffer
    * Catalog Number = 06374921001
  * PBS
  * Proteinase K
    * Catalog Number = 03 115 828 001

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-c1e4227b6c5860f2586c403a276ae2451aa6ed91%2Froche-96-protocol1-step5-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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       |             |                                           |

#### Placement = Enabled

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

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                                                                                            |
  | -------------- | -------------- | ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
  | Directions     | Multiline Text |             | Default = Suspend a dry swab in 200 l BLB; add 20 uL Proteinase K. For swabs in transport medium use 100 uL transport medium, add 100 uL BLB and 20 uL Proteinase K. |
* 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: Cultured Cells (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Cultured Cells (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * PBS

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-4c16d681ba2b391710e1633265a63805d264cff4%2Froche-96-protocol1-step6-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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       |             |                                           |

#### Placement = Enabled

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

#### 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | 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: Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)
* Step Type = No Outputs

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-5e7936bf7790955accd56c169248ab2affccab6b%2Froche-96-protocol1-step7-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Fresh-frozen Tissue</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.::Homogenization Protocol:: == ::Proteinase K Digestion::) {nextStep = ::Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)::} else {nextStep = ::Tissue Homogenization using MagNA Lyser Instrument (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 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 | Homogenization Protocol | Text Dropdown  | Required Field | <p>Presets</p><ul><li>Proteinase K Digestion</li><li>MagNA Lyser Instrument</li></ul> |
    | Derived Sample | Sample Name             | Built-in       |                |                                                                                       |

### Step 8: Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNa Pure 96 DNA Tissue Lysis Buffer
    * Catalog Number = 06640702001
  * Proteinase K
    * Catalog Number = 03 115 828 001

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-f8f4591205e1520e83c38a77dd84de89d3917a49%2Froche-96-protocol1-step8-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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 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 9: Tissue Homogenization using MagNA Lyser Instrument (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Tissue Homogenization using MagNA Lyser Instrument (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNA Lyser Green Beads
    * Catalog Number = 03358941001
  * MagNa Pure 96 DNA Tissue Lysis Buffer
    * Catalog Number = 06640702001

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-97e6137c9e402566e0f165b55c60a41c6ad6e8ac%2Froche-96-protocol1-step9-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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 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 10: Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * MagNa Pure 96 DNA Tissue Lysis Buffer
    * Catalog Number = 06640702001
  * Proteinase K
    * Catalog Number = 03 115 828 001
  * Xylol

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-06169edf4b06bf6db9205e63f5ffc86492f6d0aa%2Froche-96-protocol1-step10-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Purification MagNa Pure 96</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 = ::Isolation Procedure (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

> ℹ The version of the step name 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

* 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       |             |                                           |

### Step 11: Isolation Procedure (CDC COVID-19 RT-PCR v1.1)

* Master Step Name = Isolation Procedure (CDC COVID-19 RT-PCR v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-e1bbc257d153ba19540b8695bf4df580afe4123d%2Froche-96-protocol1-step11-automation.png?alt=media" 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
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options**                                             | **Additional Options and Dropdown Items**                                                                                                                                                                                                                                                   |
  | -------------- | -------------- | ------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
  | Protocol Name  | Text Dropdown  | <ul><li>Required Field</li><li>Custom Entries</li></ul> | <p>Presets</p><ul><li>DNA Blood ds SV</li><li>DNA Blood SV</li><li>DNA Blood ext lys SV</li><li>Viral NA Plasma SV</li><li>Viral NA Plasma ext lys SV</li><li>Viral NA Universal SV</li><li>Pathogen Universal 200</li><li>DNA Cells SV</li><li>DNA Tissue SV</li><li>DNA FFPE SV</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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-f23be9105f57242ef96850973aa901fe2fe50b91%2Froche-96-protocol2-next-step-config.png?alt=media" 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b5ae63e86b9d60aa0c195ca842be50b56558adaf%2Froche-96-protocol2-step1-automation.png?alt=media" 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-4e22245bc04d862353928fd1945104677feb4a5c%2Froche-96-protocol2-step2-automation.png?alt=media" 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-472157f909e4a91ebf1140b2e5e2eb48fafd3508%2Froche-96-protocol2-step3-automation.png?alt=media" 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-25044b457333bd4aa8f9900a8f4405121ca6d6cb%2Froche-96-protocol2-step4-automation.png?alt=media" 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-76f8cbb2cb95c65a5039221cfe7d320ba74b7e14%2Froche-96-protocol2-step5-automation.png?alt=media" 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-26d3ff264f77ed117b9e1381a63f54eed31bfa5d%2Froche-96-protocol2-step6-automation.png?alt=media" 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="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-3bb1ab91cc532abc5418728845ec3dac58bcf83e%2Froche-96-protocol2-step7-automation.png?alt=media" 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           |             |                                           |