TruSeq Custom Amplicon v1.0
Protocol 1: TruSeq Custom Amplicon (TSCA) v1.0
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Qubit QC (DNA) (TSCA v1.0)
Master Step Name = Qubit QC (DNA) v1.0
Measurement Generation = Fixed, 1
Assign QC flags (Qubit QC)
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step & Copy Concentration
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy Concentration (ng/uL)
Trigger Location = Not Used
Qubit Copy Conc
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Group of Defaults
Concentration Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
TSCA
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
Step 2: Normalize DNA 1 (TSCA v1.0)
Master Step Name = Normalize DNA 1 (TSCA v1.0.10)
Derived Sample Generation = Fixed, 1
Normalize DNA 1 Calculations
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Qubit QC (DNA) (TSCA v1.0)
Master Step Name = Qubit QC (DNA) v1.0
Measurement Generation = Fixed, 1
Assign QC flags (Qubit QC)
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step & Copy Concentration
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy Concentration (ng/uL)
Trigger Location = Not Used
Qubit Copy Conc
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Group of Defaults
Concentration Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
TSCA
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
Step 4: Normalize DNA 2 (TSCA v1.0)
Master Step Name = Normalize DNA 2 (TSCA v1.0.10)
Derived Sample Generation = Fixed, 1
Normalize DNA 2 Calculations
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 5: Hybridize Oligo Pool (TSCA v1.0)
Master Step Name = Hybridize Oligo Pool (TSCA v1.0.10)
Derived Sample Generation = Fixed, 1
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 6: Remove Unbound Oligos (TSCA v1.0)
Master Step Name = Remove Unbound Oligos (TSCA v1.0.10)
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 7: Extend and Ligate Bound Oligos (TSCA v1.0)
Master Step Name = Extend and Ligate Bound Oligos (TSCA v1.0.10)
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 8: Amplify Libraries (TSCA v1.0)
Master Step Name = Amplification with Labels v2.0
Derived Sample Generation = Fixed, 1
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy to Output
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Label Groups
TruSeq Custom Amplicon (TSCA) Low Input
Step Data (Master Step Fields)
Step 9: Clean Up Libraries (TSCA v1.0)
Master Step Name = Clean Up v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 10: Bioanalyzer QC (Library Validation) (TSCA v1.0)
Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Measurement Generation = Fixed, 1
Generate Bioanalyzer Input file
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse Bioanalyzer XML, Copy nM and Assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Output PASS/FAIL
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Parse Bioanalyzer XML and assign QC flags
Trigger Location = Not Used
Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations
Trigger Location = Not Used
Parse Bioanalyzer XML, Calculate nM and assign QC flags
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Group of Defaults
Nextera DNA Flex Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Nextera Mate Pair Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Nextera XT DNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
NRCC Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq ChIP-Seq Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Methyl Capture EPIC Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Rapid Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq RNA Access Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq RNA Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Small RNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Stranded mRNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Stranded Total RNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Targeted RNA Expression Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSight Myeloid Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSight RNA Fusion Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TSCA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Step Data
Group of Defaults = TSCA Library Validation
Step 11: Normalize Libraries (TSCA v1.0)
Master Step Name = Normalize Libraries 3 v2.0.10
Derived Sample Generation = Fixed, 1
Set Next Step - Remove
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Routing script - Normalize Libraries
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Naming Convention = {InputItemName} Qubit
Sample Table
Column Headers
Additional Options and Dropdown Items
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)
Criteria 2 - Threshold Value = 50.00
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Criteria 1 - Threshold Value
Decimal Places Displayed = 2
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
Decimal Places Displayed = 2
Step File Placeholders
Qubit Result File - Manually uploaded
QC Assignment Log File - Automatically attached
QC Assignment Report - Automatically attached
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSeq Custom Amplicon Low Input Kit, Box 2
Catalog Number = FC-134-2002; FC-134-2001
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Target Normalization (ng/ul)
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName} Qubit
Sample Table
Column Headers
Additional Options and Dropdown Items
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)
Criteria 2 - Threshold Value = 50.00
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Criteria 1 - Threshold Value
Decimal Places Displayed = 2
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
Decimal Places Displayed = 2
Step File Placeholders
Qubit Result File - Manually uploaded
QC Assignment Log File - Automatically attached
QC Assignment Report - Automatically attached
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSeq Custom Amplicon Low Input Kit, Box 2
Catalog Number = FC-134-2002; FC-134-2001
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSeq Custom Amplicon Low Input Kit, Box 1
Catalog Number = FC-134-2002; FC-134-2001
TruSeq Custom Amplicon Low Input Kit, Box 2
Catalog Number = FC-134-2002; FC-134-2001
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Row
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSeq Custom Amplicon Low Input Kit, Box 2
Catalog Number = FC-134-2002; FC-134-2001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSeq Custom Amplicon Low Input Kit, Box 1
Catalog Number = FC-134-2002; FC-134-2001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSeq Custom Amplicon Low Input Kit, Box 1
Catalog Number = FC-134-2002; FC-134-2001
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Reagent Kits
TruSeq Custom Amplicon Low Input Kit, Box 1
Catalog Number = FC-134-2002; FC-134-2001
TruSeq Custom Amplicon Low Input Kit, Box 3
Catalog Number = FC-134-2002; FC-134-2001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName} Bioanalyzer
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Column
Destination Containers
BioAnalyzer DNA High Sensitivity Chip
BioAnalyzer DNA 1000 Chip
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,500.00
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00
Criteria 1 - Threshold Value = 350.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 500.00
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 200.00
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00
Criteria 1 - Threshold Value = 160.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 700.00
Criteria 1 - Threshold Value = 300.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Criteria 1 - Threshold Value
Decimal Places Displayed = 2
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
Decimal Places Displayed = 2
Use strict matching for Bioanalyzer results
Step File Placeholders
Bioanalyzer Input File - Automatically attached
Bioanalyzer Input File Generation Log File - Automatically attached
Bioanalyzer XML Result File (required) - Manually uploaded
Result File (optional) - Manually uploaded
PDF Summary File (optional) - Manually uploaded
Bioanalyzer XML Parsing Log File - Automatically attached
QC Assignment Log File - Automatically attached
QC Assignment Report - Automatically attached
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSeq Custom Amplicon Low Input Kit, Box 2
Catalog Number = FC-134-2002; FC-134-2001
TruSeq Custom Amplicon Low Input Kit, Box 3
Catalog Number = FC-134-2002; FC-134-2001
ℹ The field name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
ℹ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Desired Input DNA Amount (ng)
Additional Options and Dropdown Items
ELE Volume (ul) to add to ELB
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"
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:: ; input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -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 'input.::Concentration (ng/ul):: = output.::Concentration::' -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 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ' \
-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 true -h false -exp 'output.::Sample Volume (ul):: = (step.::Target Normalization (ng/ul):: * step.::Final Volume (ul):: ) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul)::' -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 -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"
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:: ; input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -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 'input.::Concentration (ng/ul):: = output.::Concentration::' -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 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ' \
-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 true -h false -exp 'output.::Sample Volume (ul):: = ((step.::Final Volume (ul):: * (step.::Desired Input DNA Amount (ng):: / step.::Final Volume (ul):: )) / input.::Concentration (ng/ul):: ) ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul)::' -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 -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 -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 -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 -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 -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 'output.::RNA Sample Type:: = input.::RNA Sample Type::' -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 -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/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -f {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} -sep COMMA -b ',False,' -h 1 -c LIMSID -pre 'Sample '"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 true -h false -exp 'if (output.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"
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 true -h false -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7} && /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 true -h false -exp 'output.::Concentration:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 true -h false -exp 'output.::Concentration:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"
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 = ::REMOVE::' -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 'Sequencing Instrument' \
--FIELD_VALUE 'MiSeq' \
--WORKFLOW 'MiSeq Sequencing v3.2' \
--STEP 'Library Pooling (MiSeq v3.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq' \
--WORKFLOW 'NextSeq 500/550 Sequencing v1.2' \
--STEP 'Library Pooling (NextSeq 500/550 v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 2.0' \
--WORKFLOW 'NovaSeq 6000 v2.3' \
--STEP 'Define Run Format (NovaSeq 6000 v2.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 3.0' \
--WORKFLOW 'NovaSeq 6000 v3.8' \
--STEP 'Define Run Format (NovaSeq 6000 v3.8)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeqDx' \
--WORKFLOW 'NovaSeqDx v1.2' \
--STEP 'Define Run Format (NovaSeqDx v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000' \
--WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series' \
--WORKFLOW 'NovaSeq X Series v1.1' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \
--WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 1 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 2 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 3 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 4 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 5 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Region 1 Average Size - bp
Region 2 Average Size - bp
Region 3 Average Size - bp
Region 4 Average Size - bp
Region 5 Average Size - bp
Region 1 Average Size - bp
Region 2 Average Size - bp
Region 3 Average Size - bp
Region 4 Average Size - bp
Region 5 Average Size - bp
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Decimal Places Displayed = 2
Additional Options and Dropdown Items
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NextSeq 1000/2000 On-Prem
