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

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}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Routing Script - GenomeStudio

• Trigger Location = Step

• Trigger Style = Automatic upon exit

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'"

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		Presets GS-GENOTYPING GS-METHYLATION Default = GS-GENOTYPING
    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