# iScan System v1.0

## Overview

The iScan workflow includes the following functionality:

* Preset protocol.
* Ability to attach the scan log to the samples.

## Protocol 1: Infinium Array Imaging (iScan v1.0)

Protocol Type = Other

**Next Steps Configuration**

<figure><img src="/files/LO6sNcFl1QNE65bxw108" alt=""><figcaption></figcaption></figure>

### Step 1: Image Infinium BeadChip (iScan v1.0)

* Master Step Name = Image Infinium BeadChip - iScan v1.0
* Step Type = No Outputs

#### Automations

<figure><img src="/files/kDNaGzckHJvjTSmLf705" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Array Secondary Analysis</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 -exp 'if (input.::Infinium Kit Name:: == ::Infinium MethylationEPIC Kit:: ) { input.::Array Secondary Analysis:: = ::GS-METHYLATION::} ; if (input.::Infinium Kit Name:: != ::Infinium MethylationEPIC Kit:: ) { input.::Array Secondary Analysis:: = ::GS-GENOTYPING::}' -log {compoundOutputFileLuid0}"
```

{% 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>

<details>

<summary>Routing Script - GenomeStudio</summary>

* Trigger Location = Step
* Trigger Style = Automatic upon exit

{% code overflow="wrap" %}

```markup
bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Array Secondary Analysis' \
--FIELD_VALUE 'GS-GENOTYPING' \
--WORKFLOW 'GenomeStudio v1.0' \
--STEP 'Create Infinium Genotyping Analysis Sample Sheet (GenomeStudio v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
--FIELD_NAME 'Array Secondary Analysis' \
--FIELD_VALUE 'GS-METHYLATION' \
--WORKFLOW 'GenomeStudio v1.0' \
--STEP 'Create Infinium Methylation Analysis Sample Sheet (GenomeStudio v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"
```

{% endcode %}

> ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.

</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
  * Scan Log - Manually uploaded
* 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**                                                                              |
    | -------------- | ------------------------ | -------------- | ----------- | ---------------------------------------------------------------------------------------------------------------------- |
    | Derived Sample | Array Secondary Analysis | Text Dropdown  |             | <ul><li><p>Presets</p><ul><li>GS-GENOTYPING</li><li>GS-METHYLATION</li></ul></li><li>Default = GS-GENOTYPING</li></ul> |
    | Derived Sample | BeadChip Barcode         | Text           | Read Only   |                                                                                                                        |
    | Derived Sample | BeadChip Position        | Text           | Read Only   |                                                                                                                        |
    | Derived Sample | DNA Plate Barcode        | Text           | Read Only   |                                                                                                                        |
    | Derived Sample | Infinium Kit Name        | Text           | Read Only   |                                                                                                                        |
    | Derived Sample | Sample Name              | Built-in       |             |                                                                                                                        |
    | Derived Sample | Sample\_Well             | Text           |             |                                                                                                                        |
    | Project        | Project Name             | Built-in       |             |                                                                                                                        |


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