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

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}"

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}"

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'"

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