IGA Library Prep Automated v2.1

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} -t false -h false script:evaluateDynamicExpression \
-exp 'if (! submittedSample.hasValue(::Sample Type::)) { \
    fail(::Sample Type must be non-empty. Please update :: + submittedSample.::name::); \
}; \
acceptedSampleTypes = [::Genomic DNA::, ::Saliva::, ::Blood::]; \
if (! acceptedSampleTypes.contains(submittedSample.::Sample Type::)) { \
  fail(::Invalid Sample Type found for :: + submittedSample.::name:: + ::. Must be one of :: + acceptedSampleTypes.join(::, ::)); \
}; \
if (! submittedSample.hasValue(::Submitted Sample Labware Type::)) { \
    fail(::Submitted Sample Labware Type must be non-empty. Please update :: + submittedSample.::name::); \
}; \
acceptedSampleLabwareTypes = [::gDNA::, ::Saliva::, ::Blood1.3::, ::Blood2.7::, ::Blood7.5::, ::Blood10::]; \
if (! acceptedSampleLabwareTypes.contains(submittedSample.::Submitted Sample Labware Type::)) { \
  fail(::Invalid Submitted Sample Labware Type found for :: + submittedSample.::name:: + ::. Must be one of :: + acceptedSampleLabwareTypes.join(::, ::)); \
}; \
if (! submittedSample.hasValue(::Units::)) { \
    fail(::Units must be non-empty. Please update :: + submittedSample.::name::); \
}; \
if (submittedSample.::Sample Type:: == ::Genomic DNA:: && ! submittedSample.hasValue(::Sample Conc.::)) { \
    fail(::Sample Conc. must be non-empty for Genomic DNA samples. Please update :: + submittedSample.::name::); \
};' -log {compoundOutputFileLuid0} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/register_sample.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

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 'submittedSample.::Library Prep Method:: = step.::Library Prep Method::' -log {compoundOutputFileLuid0} && /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 'if (submittedSample.::Sample Type:: == ::Genomic DNA:: && input.container.node.type[0].@name == ::96 well plate::) {nextStep = ::REMOVE::} else nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"

bash -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 'if (submittedSample.::Sample Type:: == ::Genomic DNA::) {if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA PCR-Free:: ) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA PCR-Free::} ; if (input.container.node.type[0].@name == ::96 well plate:: && step.::Library Prep Method:: == ::Illumina DNA with Enrichment::) {input.::Submitted Sample Type:: = submittedSample.::Sample Type:: + ::_Illumina DNA with Enrichment::}}' -log {compoundOutputFileLuid0} && /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 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA PCR-Free' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching PCR-Free (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Submitted Sample Type' \
--FIELD_VALUE 'Genomic DNA_Illumina DNA with Enrichment' \
--WORKFLOW 'Illumina Genomics Architecture - Library Prep Automated v2.1' \
--STEP 'DNA Batching with Enrichment (IGA v2.1)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"