TruSight Tumor 170 v2.0 TruSight Tumor 170 v2.0 includes the following functionality:
Preconfigured TruSight Tumor 170 v2.0 protocol that supports the preparation of samples for the detection of gene variants across 170 gene targets in nucleic acids extracted from FFPE cancer tissue samples.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples (when necessary).
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
Routing script that allows sequencing of libraries using any Illumina sequencing instrument.
Protocol 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0)
Master Step Name = DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0.10)
Derived Sample Generation = Fixed, 2
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
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)
Protocol 2: RNA QC and cDNA Synthesis (TruSight Tumor 170 v2.0)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Qubit RNA QC (TruSight Tumor 170 v2.0)
Master Step Name = Qubit RNA QC (TruSight Tumor 170 v2.0.10)
Measurement 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: Denature and Anneal RNA (TruSight Tumor 170 v2.0)
Master Step Name = Denature and Anneal RNA (TruSight Tumor 170 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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: First Strand cDNA Synthesis (TruSight Tumor 170 v2.0)
Master Step Name = First Strand cDNA Synthesis 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: Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0)
Master Step Name = Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0.10)
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 5: cDNA Clean Up (TruSight Tumor 170 v2.0)
Master Step Name = cDNA Clean Up (TruSight Tumor 170 v2.0.10)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
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)
Protocol 3: DNA QC and Fragmentation (TruSight Tumor 170 v2.0)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Qubit DNA QC (TruSight Tumor 170 v2.0)
Master Step Name = Qubit DNA QC (TruSight Tumor 170 v2.0.10)
Measurement 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: Fragment DNA (TruSight Tumor 170 v2.0)
Master Step Name = Fragment DNA (TruSight Tumor 170 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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Protocol 4: Library Prep (TruSight Tumor 170 v2.0)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: End Repair and A-Tailing (TruSight Tumor 170 v2.0)
Master Step Name = End Repair and A-Tailing (TruSight Tumor 170 v2.0.10)
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: Ligate Adapters (TruSight Tumor 170 v2.0)
Master Step Name = Ligate Adapters (TruSight Tumor 170 v2.0.10)
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 3: Clean Up Ligation (TruSight Tumor 170 v2.0)
Master Step Name = Clean Up v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
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: Index PCR (TruSight Tumor 170 v2.0)
Master Step Name = Index PCR (TruSight Tumor 170 v2.0.10)
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
Label Groups
TruSight Tumor 170 Index List
Step Data (Master Step Fields)
Protocol 5: Hybridization (TruSight Tumor 170 v2.0)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Perform First Hybridization (TruSight Tumor 170 v2.0)
Master Step Name = Hybridize v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
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 2: Perform First Capture (TruSight Tumor 170 v2.0)
Master Step Name = Perform First Capture (TruSight Tumor 170 v2.0.10)
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 3: Perform Second Hybridization (TruSight Tumor 170 v2.0)
Master Step Name = Perform Second Hybridization (TruSight Tumor 170 v2.0.10)
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 4: Perform Second Capture (TruSight Tumor 170 v2.0)
Master Step Name = Perform Second Capture (TruSight Tumor 170 v2.0.10)
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 5: Amplify Enriched Library (TruSight Tumor 170 v2.0)
Master Step Name = Amplify Enriched Library 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 6: Clean Up Amplified Enriched Library (TruSight Tumor 170 v2.0)
Master Step Name = Clean Up v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
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)
Protocol 6: Library QC and Normalization (TruSight Tumor 170 v2.0)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Quantify Libraries (TruSight Tumor 170 v2.0)
Master Step Name = Quantify Libraries (TruSight Tumor 170 v2.0.10)
Derived Sample Generation = Fixed, 3
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Normalize Libraries (TruSight Tumor 170 v2.0)
Master Step Name = Normalize Libraries (TruSight Tumor 170 v2.0.10)
Derived Sample Generation = Fixed, 1
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 = {LIST:{SubmittedSampleName}_DNA,{SubmittedSampleName}_RNA}
Reagent Kits
QIAGEN AllPrep DNA/RNA FFPE Kit
ℹ 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
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Sample Table
Column Headers
Additional Options and Dropdown Items
Default = Concentration (ng/ul)
Criteria 1 - Threshold Value
Decimal Places Displayed = 2
Criteria 2 - Source Data Field
Default = Concentration (ng/ul)
Criteria 2 - Threshold Value
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Qubit Result File - Manually uploaded
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
TruSight Tumor 170, Box 1
Catalog Number = OP-101-1004
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 1
Step File Placeholders
Calculation Log File - Automatically attached
NextStep Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
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
TruSight Tumor 170, Box 1
Catalog Number = OP-101-1004
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}_cDNA
Reagent Kits
TruSight Tumor 170, Box 3
Catalog Number = OP-101-1004
ℹ 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
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Sample Table
Column Headers
Additional Options and Dropdown Items
Default = Concentration (ng/ul)
Criteria 1 - Threshold Value
Decimal Places Displayed = 2
Criteria 2 - Source Data Field
Default = Concentration (ng/ul)
Criteria 2 - Threshold Value
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Qubit Result File - 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}_DNA
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Column
Decimal Places Displayed = 0
Minimum Final Volume (uL)
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSight Tumor 170, Box 2
Catalog Number = OP-101-1004
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
TruSight Tumor 170, Box 2
Catalog Number = OP-101-1004
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
Reagent Kits
TruSight Tumor 170, Box 3
Catalog Number = OP-101-1004
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
TruSight Tumor 170, Box 2
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 4
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 5
Catalog Number = OP-101-1004
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
Reagent Kits
TruSight Tumor 170, Box 6
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 7
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 8
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 9
Catalog Number = OP-101-1004
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
TruSight Tumor 170, Box 6
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 7
Catalog Number = OP-101-1004
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
TruSight Tumor 170, Box 6
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 7
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 8
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 9
Catalog Number = OP-101-1004
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
TruSight Tumor 170, Box 6
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 7
Catalog Number = OP-101-1004
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
TruSight Tumor 170, Box 7
Catalog Number = OP-101-1004
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
Reagent Kits
TruSight Tumor 170, Box 3
Catalog Number = OP-101-1004
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}
Control Types
Blank Solution (TruSight Tumor 170 v2.0.10)
DNA Standard (TruSight Tumor 170 v2.0.10)
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Column
Step File Placeholders
Log File - Manually uploaded
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSight Tumor 170, Box 6
Catalog Number = OP-101-1004
TruSight Tumor 170, Box 7
Catalog Number = OP-101-1004
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
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Dilution Concentration (ng/ul)
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
Dilution Concentration (ng/ul)
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
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 'if (output.name.endsWith(::_RNA::)) {output.::Sample Type:: = ::RNA::}; if (output.name.endsWith(::_DNA::)) {output.::Sample Type:: = ::DNA::}' -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 -l -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 {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'Qubit RNA QC (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'Qubit DNA QC (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid2} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 true -h false -exp 'output.::Sample Volume (ul):: = (step.::Dilution Concentration (ng/ul):: * 17) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 17 - 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 '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.::Sample Type:: = ::cDNA::' -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 -l -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 {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'End Repair and A-Tailing (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
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:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid1} && /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.::Concentration (ng/ul):: = output.::Concentration (ng/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 true -h false -exp 'output.::Sample Volume (ul):: = (step.::Dilution Concentration (ng/ul):: * step.::Minimum Final Volume (uL)::) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = step.::Minimum 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 '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 '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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Library Volume (ul):: = 200 / input.::Concentration (ng/ul):: ; output.::RSB Volume (ul):: = 10 - output.::Library 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 '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 '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:computeReplicateAverage -src 'Concentration (ng/ul)' -dest 'Concentration (ng/ul)' -exclude 'Exclude' -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 'if(input.::Concentration (ng/ul):: >= 3) { output.QC = true } else { output.QC = false } ; input.QC = output.QC' -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 true -h false -excludeControls true -exp 'if (input.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 {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 = 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
=
144
16
=
54
Decimal Places Displayed = 0
138
Decimal Places Displayed = 0
456
Decimal Places Displayed = 0
24
Decimal Places Displayed = 0
456
Decimal Places Displayed = 0
24
Decimal Places Displayed = 0
32
Decimal Places Displayed = 0
704
Decimal Places Displayed = 0
128
Decimal Places Displayed = 0
608
Decimal Places Displayed = 0
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
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
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
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
