> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.0.md). # 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**
### Step 1: Image Infinium BeadChip (iScan v1.0) * Master Step Name = Image Infinium BeadChip - iScan v1.0 * Step Type = No Outputs #### Automations
Set Array Secondary Analysis * 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 %}
Set Next Step - Advance * 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 %}
Routing Script - GenomeStudio * 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.
#### 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 | | | | 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 | | | --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/clarity-lims/instruments-and-integrations/iscan/iscan-v1.0.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.