GenomeStudio v1.0

Overview

The GenomeStudio workflow includes the following functionality.

• Automatic Generation of a sample sheet for genotyping or methylation. These sample sheets can then be used in GenomeStudio to create a project.

Protocol 1: Infinium Genotyping Analysis (GenomeStudio v1.0)

Protocol Type = Sample Analysis

Next Steps Configuration

Step 1: Create Infinium Genotyping Analysis Sample Sheet (GenomeStudio v1.0)

• Master Step Name = Create Infinium Genotyping Analysis Sample Sheet - GenomeStudio v1.0

• Step Type = No Outputs

Automations

Generate GenomeStudio Genotyping Sample Sheet

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/driverfiletemplates/genomeStudio_Genotyping_SampleSheet_driver_file.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}"

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}"

Queue

• 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	Well	Built-in
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

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	Infinium Kit Name	Text	Read Only
  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
  BeadPool Manifest	Text	Required Field
  Comment	Multiline Text
• Step File Placeholders

  • GenomeStudio Genotyping Sample Sheet - Automatically attached

  • File Generation Log - Automatically attached

  • Log - Automatically attached

• 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

Protocol 2: Infinium Methylation Analysis (GenomeStudio v1.0)

Protocol Type = Data Analysis

Next Steps Configuration

Step 1: Create Infinium Methylation Analysis Sample Sheet (GenomeStudio v1.0)

• Master Step Name = Create Infinium Methylation Analysis Sample Sheet - GenomeStudio v1.0

• Step Type = No Outputs

Automations

Generate GenomeStudio Methylation Sample Sheet

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/driverfiletemplates/genomeStudio_Methylation_SampleSheet_driver_file.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}"

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}"

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	Well	Built-in
  Derived Sample	Infinium Kit Name	Text	Read Only
  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

  • GenomeStudio Methylation Sample Sheet - Automatically attached

  • File Generation Log - Automatically attached

  • Log - Automatically attached

• 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
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    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