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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'"

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
- Log - Automatically attached
- Scan Log - Manually uploaded
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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'"

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
- Scan Log - Manually uploaded
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields