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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)

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
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

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)

Record Details

Step Data (Master Step Fields)
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

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)

Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
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

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)

Record Details

Step Data (Master Step Fields)
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