iScan System v1.0

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'"