TruSeq ChIP-Seq v1.0 Protocol 1: TruSeq ChIP-Seq v1.0
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Normalize DNA (TruSeq ChIP-Seq v1.0)
Master Step Name = Normalize DNA (TruSeq ChIP-Seq v1.0)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: End Repair (TruSeq ChIP-Seq v1.0)
Master Step Name = Repair Ends v1.0
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Adenylate 3' Ends (TruSeq ChIP-Seq v1.0)
Master Step Name = Adenylate 3' Ends v2.0
chevron-right hashtag 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: Ligate Indexed Paired-End Adapters (TruSeq ChIP-Seq v1.0)
Master Step Name = Ligate Adapters v2.0
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 5: Purify Ligation Products (TruSeq ChIP-Seq v1.0)
Master Step Name = Purify Ligation Products (TruSeq ChIP-Seq v1.0)
Derived Sample Generation = Fixed, 1
chevron-right hashtag 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: Enrich DNA Fragments (TruSeq ChIP-Seq v1.0)
Master Step Name = Enrich DNA Fragments (TruSeq ChIP-Seq v1.0)
Derived Sample Generation = Fixed, 1
chevron-right hashtag 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 (Library Validation) (TruSeq ChIP-Seq v1.0)
Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Measurement Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Group of Defaults
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
chevron-right hashtag Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Step Data
Group of Defaults = TruSeq ChIP-Seq Library Validation
Step 8: Normalize Libraries (TruSeq ChIP-Seq v1.0)
Master Step Name = Normalize Libraries 2 v2.0.10
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Naming Convention = {SubmittedSampleName}
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Reagent Kits
AMPure XP Beads
Supplier = Beckman Coulter Genomics
TruSeq ChIP Sample Prep Kit, Box A or B
Catalog Number = 15034288; 15034289
Sample Table
Column Headers
Additional Options and Dropdown Items
Step File Placeholders
Next Step Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSeq ChIP Sample Prep Kit, Box A or B
Catalog Number = 15034288; 15034289
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
AMPure XP Beads
Supplier = Beckman Coulter Genomics
TruSeq ChIP Sample Prep Kit, Box A or B
Catalog Number = 15034288; 15034289
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
50X TAE buffer
Catalog Number = 161-0743
Certified low-range ultra agarose
Catalog Number = 161-3107
MinElute Gel Extraction Kit
Supplier = QIAGEN, part # 28604
SYBR Gold Nucleic acid gel stain
TruSeq ChIP Sample Prep Kit, Box A or B
Catalog Number = 15034288; 15034289
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 = {SubmittedSampleName}
Reagent Kits
AMPure XP Beads
Supplier = Beckman Coulter Genomics
TruSeq ChIP Sample Prep Kit, Box A or B
Catalog Number = 15034288; 15034289
TruSeq ChIP Sample Prep Kit, PCR Box
Catalog Number = 15027084
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
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 value and the actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Target Normalization (nM)
Decimal Places Displayed = 0
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
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
Copy 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.::Input Amount (pg/ul):: / 1000) * step.::Final Volume (ul)::) / input.::Concentration::) ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul)::' -log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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}"
Copy 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 Number of Samples:: = step.::Total Number of 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 'if(input.::Target Insert Size (bp):: == 350) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 109.25) / 1000} ; if(input.::Target Insert Size (bp):: == 350) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 74.75) / 1000 } ; if(input.::Target Insert Size (bp):: == 550) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 92) / 1000} ; if(input.::Target Insert Size (bp):: == 550) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 92) / 1000 } ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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 '"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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}"
Copy 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 true -h false -exp 'output.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = step.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = ((output.::Molarity (nM):: * step.::Sample Volume (ul)::) / step.::Target Normalization (nM)::) - step.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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 = 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 = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
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
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
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
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Additional Options and Dropdown Items
NextSeq 1000/2000 On-Prem
