# iLASS Infinium Genotyping with PGx Assay v1.1

## Protocol 1: Target Prep (ILASS Infinium Genotyping Assay with PGx 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-e9f00b40e18b826e540e1843ce736f31f4551fa5%2Filass-genotyping-pgx-v1.1.0-target-prep-next-steps.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Make WGA and PGx (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name: Make WGA and PGx (ILASS Infinium Genotyping Assay v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 2
* Instrument Types
  * Hamilton Star
    * Vendor = Hamilton
* Reagent Kits
  * AAX-Infinium
    * Supplier = Illumina
  * MA1-Infinium
    * Supplier = Illumina
  * MA2-Infinium
    * Supplier = Illumina
  * MSM-Infinium
    * Supplier = Illumina
  * PGM-Infinium
    * Supplier = Illumina
  * PGP-Infinium
    * Supplier = Illumina
  * RPM-Infinium
    * Supplier = Illumina

#### Placement = Enabled

* Sample Grouping = Group by Containers
* Well Sort Order = Column
* Placement Pattern = Same Shape
* Destination Containers
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------- | -------------- | ----------- | ----------------------------------------- |
  | Batch ID            | Text           | Read Only   |                                           |
  | Comment             | Multiline Text |             |                                           |
  | Plate Transfer Plan | Multiline Text | Read Only   |                                           |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded
* Sample Table (Global Step Fields)
  * Container

    | **Field Name**           | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------------------ | -------------- | ----------- | ----------------------------------------- |
    | Related Source Container | Text           |             |                                           |
    | Related PGX Container    | Text           |             |                                           |
    | Related WGA Container    | Text           |             |                                           |
    | Step Run History         | Multiline Text |             |                                           |
    | Experiment Name          | Text           | Read Only   |                                           |
    | Product Type             | Text           | Read Only   |                                           |
    | Last Run Datetime        | Text           | Read Only   |                                           |
    | IsInProgress             | Toggle Switch  | Read Only   | Default = No                              |

### Step 2: Amplify WGA (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Amplify WGA (ILASS Infinium Genotyping Assay 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-d31071c26d6e2645399b92d17a81a73ce6586a66%2Filass-genotyping-automation-set-next-step-adv-v1.0-manual-button.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance v1.0</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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**    | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                    |
  | ----------------- | -------------- | ----------- | -------------------------------------------------------------------------------------------- |
  | Batch ID          | Text           | Read Only   |                                                                                              |
  | Comment           | Multiline Text |             |                                                                                              |
  | Instruction Notes | Multiline Text | Read Only   | Default = Incubate the WGA plate in the Illumina Hybridization Oven for 20–24 hours at 37°C. |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded
* Sample Table (Global Step Fields)
  * Derived Sample

    | **Field Name**           | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------------------ | -------------- | ----------- | ----------------------------------------- |
    | Source DNA Plate Barcode | Text           |             |                                           |

### Step 3: Amplify PGx (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Amplify PGx (ILASS Infinium Genotyping Assay with PGx 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-d31071c26d6e2645399b92d17a81a73ce6586a66%2Filass-genotyping-automation-set-next-step-adv-v1.0-manual-button.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance v1.0</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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**          | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                    |
  | ----------------------- | -------------- | ----------- | -------------------------------------------------------------------------------------------- |
  | Batch ID                | Text           | Read Only   |                                                                                              |
  | Thermocycler Start Time | Text           |             |                                                                                              |
  | Thermocycler End Time   | Text           |             |                                                                                              |
  | Comment                 | Multiline Text |             |                                                                                              |
  | Instruction Notes       | Multiline Text | Read Only   | Default = Incubate the WGA plate in the Illumina Hybridization Oven for 20–24 hours at 37°C. |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded
* Sample Table (Global Step Fields)
  * Derived Sample

    | **Field Name**           | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------------------ | -------------- | ----------- | ----------------------------------------- |
    | Source DNA Plate Barcode | Text           |             |                                           |

### Step 4: Recombine and Fragment DNA (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Recombine and Fragment DNA (ILASS Infinium Genotyping Assay v1.1)
* Step Type = Pooling
* Aliquot Generation = Fixed, 1
* Instrument Types
  * Tecan EVO
    * Vendor = Tecan
* Reagent Kits
  * FMS-Infinium
    * Supplier = Illumina

#### Pooling

* Label Uniqueness = Off
* Sample Grouping = Group by Containers
* Well Sort Order = Row

#### Placement = Enabled

* 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** |
  | ------------------- | -------------- | ----------- | ----------------------------------------- |
  | Batch ID            | Text           | Read Only   |                                           |
  | Comment             | Multiline Text |             |                                           |
  | Plate Transfer Plan | Multiline Text | Read Only   |                                           |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded
* Sample Table (Global Step Fields)
  * Container

    | **Field Name**           | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------------------ | -------------- | ----------- | ----------------------------------------- |
    | Related Input Containers | Text           | Read Only   |                                           |

### Step 5: Precipitate DNA (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Precipitate DNA (ILASS Infinium Genotyping Assay v1.1)
* Step Type = No Outputs
* Instrument Types
  * Tecan EVO
    * Vendor = Tecan
* Reagent Kits
  * PM1-Infinium
    * Supplier = Illumina

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**            | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------------- | -------------- | ----------- | ----------------------------------------- |
  | 100% 2-Propanol Prep Date | Date           |             |                                           |
  | Batch ID                  | Text           | Read Only   |                                           |
  | Comment                   | Multiline Text |             |                                           |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded
* Sample Table (Global Step Fields)
  * Derived Sample

    | **Field Name**           | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------------------ | -------------- | ----------- | ----------------------------------------- |
    | IsRecombined             | Toggle Switch  |             | Default = No                              |
    | Source DNA Plate Barcode | Text           |             |                                           |

### Step 6: Resuspend DNA (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Resuspend DNA (ILASS Infinium Genotyping Assay v1.1)
* Step Type = No Outputs
* Instrument Types
  * Tecan EVO
    * Vendor = Tecan
* Reagent Kits
  * IHX-Infinium
    * Supplier = Illumina
  * RA1-Infinium
    * Supplier = Illumina

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | -------------- | -------------- | ----------- | ----------------------------------------- |
  | Batch ID       | Text           | Read Only   |                                           |
  | Comment        | Multiline Text |             |                                           |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded

## Protocol 2: BeadChip Processing (ILASS Infinium Genotyping Assay with PGx 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-cfb9d7c59e3974257cf6994f8b08141119d80deb%2Filass-genotyping-pgx-v1.1.0-beadchip-processing-next-steps.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Prepare Hyb Chamber (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Prepare Hyb Chamber (ILASS Infinium Genotyping Assay v1.1)
* Step Type = No Outputs
* Reagent Kits
  * PB2-Infinium
    * Supplier = Illumina

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-d31071c26d6e2645399b92d17a81a73ce6586a66%2Filass-genotyping-automation-set-next-step-adv-v1.0-manual-button.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance v1.0</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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**    | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                                      |
  | ----------------- | -------------- | ----------- | -------------------------------------------------------------------------------------------------------------- |
  | Batch ID          | Text           | Read Only   |                                                                                                                |
  | Comment           | Multiline Text |             |                                                                                                                |
  | Instruction Notes | Multiline Text | Read Only   | Default = Add 400 µl PB2 to the top and bottom wells of each beadchip subchamber in the hybridization chamber. |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded

### Step 2: Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Instrument Types
  * Tecan EVO
    * Vendor = Tecan

#### Placement = Enabled

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

  * Infinium Genotyping with PGx Array LCG-8

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-cd0a5146bbb95996a6099d7e7b7d1f0b75b57726%2Filass-genotyping-container-lcg-8.png?alt=media" alt=""><figcaption></figcaption></figure>

  * Infinium Genotyping with PGx Array EX-24

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-f04b9f1542e9f70c130bfbd40b6a612964f90b2c%2Filass-genotyping-container-ex24.png?alt=media" alt=""><figcaption></figcaption></figure>

  * Infinium Genotyping with PGx Array EX-48

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-cf0be3b242947a3251e5a9b5f6a18a8a6c0eaf10%2Filass-genotyping-container-ex48.png?alt=media" alt=""><figcaption></figcaption></figure>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------- | -------------- | ----------- | ----------------------------------------- |
  | Batch ID            | Text           | Read Only   |                                           |
  | Comment             | Multiline Text |             |                                           |
  | Plate Transfer Plan | Multiline Text | Read Only   |                                           |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded

### Step 3: Wash BeadChips (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Wash BeadChips (ILASS Infinium Genotyping Assay v1.1)
* Step Type = No Outputs
* Reagent Kits
  * PB1-Infinium
    * Supplier = Illumina

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-d31071c26d6e2645399b92d17a81a73ce6586a66%2Filass-genotyping-automation-set-next-step-adv-v1.0-manual-button.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance v1.0</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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**    | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                      |
  | ----------------- | -------------- | ----------- | ------------------------------------------------------------------------------ |
  | Batch ID          | Text           | Read Only   |                                                                                |
  | Comment           | Multiline Text |             |                                                                                |
  | Instruction Notes | Multiline Text | Read Only   | Default = Fill two wash dish with 200ml PB1 each and labelled Wash 1 and Wash2 |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded

### Step 4: Extend and Stain BeadChips (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Extend and Stain BeadChips (ILASS Infinium Genotyping Assay v1.1)
* Step Type = No Outputs
* Instrument Types
  * Tecan EVO
    * Vendor = Tecan
* Reagent Kits
  * ATM-Infinium
    * Supplier = Illumina
  * ATX-Infinium
    * Supplier = Illumina
  * EML-Infinium
    * Supplier = Illumina
  * LX1-Infinium
    * Supplier = Illumina
  * LX2-Infinium
    * Supplier = Illumina
  * PB1-Infinium
    * Supplier = Illumina
  * RA1-Infinium
    * Supplier = Illumina
  * SML-Infinium
    * Supplier = Illumina
  * STX-Infinium
    * Supplier = Illumina
  * XC3-Infinium
    * Supplier = Illumina

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | -------------- | -------------- | ----------- | ----------------------------------------- |
  | Batch ID       | Text           | Read Only   |                                           |
  | Comment        | Multiline Text |             |                                           |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded
* Sample Table (Global Step Fields)
  * Derived Sample

    | **Field Name**           | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------------------ | -------------- | ----------- | ----------------------------------------- |
    | IsRecombined             | Toggle Switch  |             | Default = No                              |
    | Source DNA Plate Barcode | Text           |             |                                           |

### Step 5: Wash and Coat BeadChips (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Wash and Coat BeadChips (ILASS Infinium Genotyping Assay v1.1)
* Step Type = No Outputs
* Reagent Kits
  * PB1-Infinium
    * Supplier = Illumina
  * XC4-Infinium
    * Supplier = Illumina

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-d31071c26d6e2645399b92d17a81a73ce6586a66%2Filass-genotyping-automation-set-next-step-adv-v1.0-manual-button.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance v1.0</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 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**    | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                     |
  | ----------------- | -------------- | ----------- | --------------------------------------------------------------------------------------------- |
  | Batch ID          | Text           | Read Only   |                                                                                               |
  | Comment           | Multiline Text |             |                                                                                               |
  | Instruction Notes | Multiline Text | Read Only   | <p>Default = Add 310 ml PB1 to the PB1 wash dish.<br>Add 310 ml XC4 to the XC4 wash dish.</p> |
* Step File Placeholders
  * Log - Automatically attached
  * AssayRunLog - Manually uploaded
* Sample Table (Global Step Fields)
  * Derived Sample

    | **Field Name**   | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ---------------- | -------------- | ----------- | ----------------------------------------- |
    | Array Instrument | Text           |             | Default = iScan                           |

## Protocol 3: Infinium Array Imaging on iScan (ILASS Infinium Genotyping Assay with PGx v1.1)

Protocol Type = Other

**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-6e0e125484f9d3492ca1efe4b6b51850d6421881%2Filass-genotyping-v1.1.0-imaging-analysis-next-step.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.1)
* Step Type = Analysis
* Derived Sample Generation = Fixed, 1
* Instrument Types
  * iScan
    * Vendor = Illumina

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**    | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ----------------- | -------------- | ----------- | ----------------------------------------- |
  | BeadChip Barcode  | Text           | Read Only   |                                           |
  | Instrument Type   | Text           | Read Only   |                                           |
  | Instrument        | Text           | Read Only   |                                           |
  | Instrument Run ID | Text           | Read Only   |                                           |
  | Run Start Time    | Text           | Read Only   |                                           |
  | Run Complete Time | Text           | Read Only   |                                           |
  | Run Status        | Text           | Read Only   |                                           |
  | Failure Reason    | Text           | Read Only   |                                           |
  | Comment           | Multiline Text |             |                                           |
  | Log               | Multiline Text | Read Only   |                                           |
* Step File Placeholders
  * Scan Log - Manually uploaded
  * Run Metrics File - Manually uploaded
* Sample Table (Global Step Fields)
  * Derived Sample

    | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | -------------- | -------------- | ----------- | ----------------------------------------- |
    | BeadChip Name  | Text           | Read Only   |                                           |
    | Sample Section | Text           | Read Only   |                                           |
  * Measurement

    | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | -------------- | -------------- | ----------- | ----------------------------------------- |
    | Imaging Result | Text           | Read Only   |                                           |

## Protocol 4: Infinium Analysis (ILASS Infinium Genotyping Assay with PGx 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-6e0e125484f9d3492ca1efe4b6b51850d6421881%2Filass-genotyping-v1.1.0-imaging-analysis-next-step.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Invoke Infinium Analysis (ILASS Infinium Genotyping Assay with PGx v1.1)

* Master Step Name = Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.1)
* Step Type = Analysis
* Derived Sample Generation = Fixed, 1

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-1741ded4bff38441910a84070c3fac13be9e197c%2Filass-genotyping-automation-start-analysis-v1.0-manual-button.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Start Analysis v1.0</summary>

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

{% code overflow="wrap" %}

```markup
bash -c -l "/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 \
-exp 'if( step.::Analysis Run Name::.length()>255 ){ fail( ::Analysis Run Name exceeds maximum length of 255:: )}; if( !step.::Analysis Run Name::.matches(::^(?![wW][fF][rR]\\..*)(^[0-9a-zA-Z-_\\.]*$)::)) { fail( ::Analysis Run Name must consist of only alphanumeric, underscore, hyphen and period characters and cannot start with wfr.:: ) }; ' \
-log {compoundOutputFileLuid0} \
-t true \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/SIS/SISServices/extensions/automation/iscan-automation.jar \
script:start_process_analysis -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**            | **Field Type** | **Options**    | **Additional Options and Dropdown Items** |
  | ------------------------- | -------------- | -------------- | ----------------------------------------- |
  | Analysis Configuration ID | Text           | Required Field |                                           |
  | Analysis Run Name         | Text           | Required Field |                                           |
  | Analysis Start Time       | Text           | Read Only      |                                           |
  | Analysis Complete Time    | Text           | Read Only      |                                           |
  | Analysis Status           | Text           | Read Only      |                                           |
  | Log                       | Multiline Text | Read Only      |                                           |
* Step File Placeholders
  * Log - Automatically attached
  * Analysis Report - Manually uploaded
* Sample Table (Global Step Fields)
  * Derived Sample

    | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | -------------- | -------------- | ----------- | ----------------------------------------- |
    | BeadChip Name  | Text           | Read Only   |                                           |
    | Sample Section | Text           | Read Only   |                                           |