Nextera Mate Pair v1.0
Protocol 1: Nextera Mate Pair v1.0
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Tagment Genomic DNA (Nextera Mate Pair v1.0)
Master Step Name = Tagment Genomic DNA (Nextera Mate Pair v1.0.10)
Derived Sample Generation = Fixed, 1
ℹ The version of Tagment Genomic DNA master step name may be different depending on the version of IPP installed.
Master Mix Calculations
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)
Master Step Name = Bioanalyzer QC (DNA) v1.0
Measurement Generation = Fixed, 1
Generate Bioanalyzer Input file
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse Bioanalyzer XML 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
Set Next Step & Copy to Input
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Strand Displacement (Nextera Mate Pair v1.0)
Master Step Name = Strand Displacement (Nextera Mate Pair v1.0.10)
ℹ The version of Strand Displacement master step name may be different depending on the version of IPP installed.
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 4: Purify the DNA (Nextera Mate Pair v1.0)
Master Step Name = Purify the DNA (Nextera Mate Pair v1.0.10)
Derived Sample Generation = Fixed, 1
ℹ The version of Purify the DNA master step name may be different depending on the version of IPP installed.
Set Next Step based on Gel Type
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: Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)
Master Step Name = Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Derived Sample Generation = Fixed, 1
ℹ The version of Pippin Prep Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.
Set Next Step & Copy Gel Type
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 6: Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)
Master Step Name = Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Derived Sample Generation = Fixed, 1
ℹ The version of Agarose Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step & Copy Gel Type
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: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)
Master Step Name = Bioanalyzer QC (DNA) v1.0
Measurement Generation = Fixed, 1
ℹ The version of Bioanalyzer QC (DNA) master step name may be different depending on the version of IPP installed.
Generate Bioanalyzer Input file
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse Bioanalyzer XML and assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step & Copy to Input
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Set Next Step - Output PASS/FAIL
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 8: Circularize DNA (Nextera Mate Pair v1.0)
Master Step Name = Circularize DNA (Nextera Mate Pair v1.0.10)
ℹ The version of Circularize DNA master step name may be different depending on the version of IPP installed.
Master Mix 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 9: Remove Linear DNA (Nextera Mate Pair v1.0)
Master Step Name = Remove Linear DNA (Nextera Mate Pair v1.0.10)
ℹ The version of Remove Linear DNA master step name may be different depending on the version of IPP installed.
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: Shear Circularization DNA (Nextera Mate Pair v1.0)
Master Step Name = Shear Circularization DNA (Nextera Mate Pair v1.0.10)
Derived Sample Generation = Fixed, 1
ℹ The version of Shear Circularization DNA master step name may be different depending on the version of IPP installed.
Set Next Step & Copy Gel Type
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 11: Purify Sheared DNA (Nextera Mate Pair v1.0)
Master Step Name = Purify Sheared DNA (Nextera Mate Pair v1.0.10)
Derived Sample Generation = Fixed, 1
ℹ The version of Purify Sheared DNA master step name may be different depending on the version of IPP installed.
Set Next Step & Copy Gel Type
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 12: End Repair (Nextera Mate Pair v1.0)
Master Step Name = End Repair (Nextera Mate Pair v1.0.10)
ℹ The version of End Repair master step name may be different depending on the version of IPP installed.
Master Mix Calculations
Trigger Location = Record Details
Trigger Style = Automatic upon entry
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 13: A-Tailing (Nextera Mate Pair v1.0)
Master Step Name = A-Tailing (Nextera Mate Pair v1.0.10)
ℹ The version of A-Tailing master step name may be different depending on the version of IPP installed.
Master Mix Calculations
Trigger Location = Record Details
Trigger Style = Automatic upon entry
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 14: Ligate Adapters (Nextera Mate Pair v1.0)
Master Step Name = Ligate Adapters v2.0
Derived Sample Generation = Fixed, 1
ℹ The version of Ligate Adapters master step name may be different depending on the version of IPP installed.
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy to Output
Trigger Location = Not Used
Set Next Step & Copy to Input
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 15: Amplify Libraries (Nextera Mate Pair v1.0)
Master Step Name = Amplify Libraries (Nextera Mate Pair v1.0.10)
Derived Sample Generation = Fixed, 1
ℹ The version of Amplify Libraries master step name may be different depending on the version of IPP installed.
Master Mix 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 16: Clean Up Libraries (Nextera Mate Pair v1.0)
Master Step Name = Clean Up v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
ℹ The version of Clean Up master step name may be different depending on the version of IPP installed.
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 17: Bioanalyzer QC (Library Validation) (Nextera Mate Pair 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 = Nextera Mate Pair Library Validation
Step 18: Normalize Libraries (Nextera Mate Pair v1.0)
Master Step Name = Normalize Libraries 1 v2.0.10
Derived Sample Generation = Fixed, 1
ℹ The version of Normalized Libraries 1 master step name may be different depending on the version of IPP installed.
Normalization Calculations - Option 1
Trigger Location = Record Details
Trigger Style = Manual button
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 = {SubmittedSampleName}
Reagent Kits
Nextera Mate Pair Library Prep Kit - Box 1
Catalog Number = FC-132-1001
Nextera Mate Pair Library Prep Kit - Box 2
Catalog Number = FC-132-1001
Zymo Genomic DNA Clean & Concentrator
Catalog Number = D4010 (25 preps) or D4011 (100 preps)
Sample Table
Column Headers
Additional Options and Dropdown Items
Tagment Buffer Mate Pair Per Sample Volume (ul)
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Row
Destination Containers
BioAnalyzer DNA 7500 and DNA 1200 Chip
BioAnalyzer DNA High Sensitivity Chip
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 - 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
Nextera Mate Pair Library Prep Kit - Box 1
Catalog Number = FC-132-1001
Nextera Mate Pair Library Prep Kit - Box 2
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
AMPure XP Beads
Supplier = Beckman Coulter Genomics
Nextera Mate Pair Library Prep Kit - Box 2
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
Pippin Prep 0.75% agarose cassette and solutions
Zymo Genomic DNA Clean & Concentrator
Catalog Number = D4010 (25 preps) or D4011 (100 preps)
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Gel Image - Manually uploaded
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
1 kb plus DNA ladder
Catalog Number = 10787-018
50X TAE buffer
Catalog Number = 161-0743
DNA Gel Extraction kit - Zymoclean Large Fragment DNA Recovery Kit
Megabase Agarose
Catalog Number = 161-3108
Nextera Mate Pair Library Prep Kit – Box 2
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Gel Image - Manually uploaded
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Row
Destination Containers
BioAnalyzer DNA 7500 and DNA 1200 Chip
BioAnalyzer DNA High Sensitivity Chip
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 - 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
Nextera Mate Pair Library Prep Kit - Box 1
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Nextera Mate Pair Library Prep Kit - Box 1
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
Nextera Mate Pair Library Prep Kit - Box 1
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Duty Cycle/Duty Factor (%)
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
Nextera Mate Pair Library Prep Kit - Box 2
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Nextera Mate Pair Library Prep Kit - Box 2
Catalog Number = FC-132-1001
TruSeq DNA LT Library Prep Kit - Set A Box
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSeq DNA LT Library Prep Kit - Set A Box
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
Nextera Mate Pair Library Prep Kit - Box 1
Catalog Number = FC-132-1001
TruSeq DNA LT Library Prep Kit - Set A Box
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Column
Ligation Mix Per Sample Volume (ul)
Decimal Places Displayed = 1
Water Per Sample Volume (ul)
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSeq DNA LT Library Prep Kit - PCR Box
Catalog Number = FC-132-1001
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 2
PCR Primer Cocktail Volume (ul)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Log File - Automatically attached
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Reagent Kits
AMPure XP Beads
Supplier = Beckman Coulter Genomics
Nextera Mate Pair Library Prep Kit - Box 2
Catalog Number = FC-132-1001
TruSeq DNA LT Library Prep Kit - PCR Box
Catalog Number = FC-132-1001
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 = {InputItemName}
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
Decimal Places Displayed = 2
Target Normalization (nM)
Decimal Places Displayed = 2
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
Mate Pair Tagment Enzyme Per Sample Volume (ul)
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
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
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Circularization Buffer 10x Per Sample Volume (ul)
Decimal Places Displayed = 0
Circularization Ligase Per Sample Volume (ul)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
End Repair Mix Volume (ul)
Additional Options and Dropdown Items
A-Tailing Mix Volume (ul)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
A-Tailing Reaction/Bead Mix Per Sample Volume (ul)
Decimal Places Displayed = 0
Add 1ul of DNA adapter index per sample
Additional Options and Dropdown Items
Enhanced PCR Mix Volume (ul)
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 {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (output.::Gel Type:: == ::Gel-Free::) {output.::Sample Volume (ul):: = 1000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 76 - output.::Sample Volume (ul)::} ; if (output.::Gel Type:: == ::Gel-Plus::) {output.::Sample Volume (ul):: = 4000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 308 - output.::Sample Volume (ul)::}' -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' 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 {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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.::Gel Type:: = input.::Gel Type:: ; if (step.::Next Step:: == ::Gel-Free::) {nextStep = ::Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Pippin Prep::) {nextStep = ::Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Agarose Gel::) {nextStep = ::Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::}' -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:: ; output.::Gel Type:: = input.::Gel 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/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE:: ; output.::Gel Type:: = input.::Gel Type::' -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' 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 = ::ADVANCE:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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 -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 {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'input.::Sample Volume (ul):: = input.::DNA Amount (ng):: / input.::Concentration (ng/ul):: ; input.::Water Per Sample (ul):: = 276 - input.::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:: ; output.::Gel Type:: = input.::Gel 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:: ; output.::Gel Type:: = input.::Gel 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 '(step.::Total samples:: = step.::Total samples:: + 1)' -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 '(step.::End Repair Mix Volume (ul):: = step.::Total samples:: * 40) ; (step.::Water Volume (ul):: = step.::Total samples:: * 60)' -log {compoundOutputFileLuid1}"
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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /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} script:evaluateDynamicExpression -t false -h false -exp '(step.::A-Tailing Mix Volume (ul):: = step.::Total samples:: * 12.5) ; (step.::Water Volume (ul):: = step.::Total samples:: * 17.5)' -log {compoundOutputFileLuid1}"
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.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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 '(step.::Total samples:: = step.::Total samples:: + 1)' -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 true -h false -exp '(step.::Enhanced PCR Mix Volume (ul):: = step.::Total samples:: * 20 * 1.1) ; (step.::PCR Primer Cocktail Volume (ul):: = step.::Total samples:: * 5 * 1.1) ; (step.::Water Volume (ul):: = step.::Total samples:: * 25 * 1.1)' -log {compoundOutputFileLuid1}"
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/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 true -h false -exp 'output.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Final Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = (step.::Target Normalization (nM):: * step.::Final Volume (ul):: ) / input.::Molarity (nM):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -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 = ::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'"
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Decimal Places Displayed = 2
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NextSeq 1000/2000 On-Prem
