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

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