TruSight Oncology 500 ctDNA v1.1 TruSight Oncology 500 ctDNA v1.1 includes the following functionality:
Preconfigured TruSight Oncology 500 ctDNA v1.1 protocol that supports the preparation of 48 libraries from cfDNA.
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. A routing script that allows sequencing of libraries using any Illumina sequencing instrument.
Protocol 1: TruSight Oncology 500 ctDNA v1.1
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)
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 = 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: Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)
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: Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)
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: Index PCR (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Index PCR (TruSight Oncology 500 ctDNA v1.1)
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 Oncology 500 ctDNA NovaSeq
Step Data (Master Step Fields)
Step 5: Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)
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: Capture Target One (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)
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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 7: Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)
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 8: Capture Target Two (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)
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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 9: Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
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 10: Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
Master Step Name = Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
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)
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 ctDNA, Box 2
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 3
Catalog Number = 20039252; 20039253; 20039254
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Column
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSight Oncology 500 ctDNA, Box 1
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 2
Catalog Number = 20039252; 20039253; 20039254
Sample Table (Column Headers)
Additional Options and Dropdown Items
Add UMI1 (uL) to each well
Default = Immediately after ligation: add 5ul STL
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 ctDNA, Box 3
Catalog Number = 20039252; 20039253; 20039254
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}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 ctDNA, Box 5
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 6
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 7
Catalog Number = 20039252; 20039253; 20039254
Sample Table (Column Headers)
Additional Options and Dropdown Items
Add TCB1 (uL) to each well
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 ctDNA, Box 5
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 6
Catalog Number = 20039252; 20039253; 20039254
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
TruSight Oncology 500 ctDNA, Box 5
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 6
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 7
Catalog Number = 20039252; 20039253; 20039254
Sample Table (Column Headers)
Additional Options and Dropdown Items
Add TCB1 (uL) to each well
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 ctDNA, Box 3
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 5
Catalog Number = 20039252; 20039253; 20039254
TruSight Oncology 500 ctDNA, Box 6
Catalog Number = 20039252; 20039253; 20039254
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSight Oncology 500 ctDNA, Box 6
Catalog Number = 20039252; 20039253; 20039254
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}
Reagent Kits
TruSight Oncology 500 ctDNA, Box 3
Catalog Number = 20039252; 20039253; 20039254
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
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Add ALB1 (uL) to each well
Add LIG3 (uL) to each well
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Add EPM (uL) to each well
Add UPxx (uL) to each well
Additional Options and Dropdown Items
Add OPD2 (uL) to each well
Add TCA1 (uL) to each well
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Additional Options and Dropdown Items
Add OPD2 (uL) to each well
Add TCA1 (uL) to each well
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Add EPM (uL) to each well
Add PPC3 (uL) to each well
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 '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 'output.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
step.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-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.::Desired Input (ng):: / output.::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 '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 '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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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 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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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}" Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
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
TruSight Oncology 500 v1.1 Protocol 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)
Master Step Name = DNA/RNA FFPE Extraction (TSO 500 HT v1.1)
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
chevron-right hashtag Trigger Location = Not Used
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Protocol 2: RNA QC and cDNA Synthesis (TruSight Oncology 500 v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Qubit RNA QC (TruSight Oncology 500 v1.1)
Master Step Name = Qubit RNA QC (TSO 500 v1.1)
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: Denature and Anneal RNA (TruSight Oncology 500 v1.1)
Master Step Name = Denature and Anneal RNA (TSO 500 v1.1)
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 = 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 Oncology 500 v1.1)
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 Oncology 500 v1.1)
Master Step Name = Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
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: cDNA Clean Up (TruSight Oncology 500 v1.1)
Master Step Name = cDNA Clean Up (TSO 500 v1.1)
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
chevron-right hashtag Trigger Location = Not Used
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Protocol 3: DNA QC and Fragmentation (TruSight Oncology 500 v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Qubit DNA QC (TruSight Oncology 500 v1.1)
Master Step Name = Qubit DNA QC (TruSight Oncology 500 HT v1.1)
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 Oncology 500 v1.1)
Master Step Name = Fragment DNA (TruSight Oncology 500 HT v1.1)
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 Oncology 500 v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: End Repair and A-Tailing (TruSight Oncology 500 v1.1)
Master Step Name = End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Ligate Adapters (TruSight Oncology 500 v1.1)
Master Step Name = Ligate Adapters (TruSight Oncology 500 HT v1.1)
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: Clean Up Ligation (TruSight Oncology 500 v1.1)
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 Oncology 500 v1.1)
Master Step Name = Index PCR (TruSight Oncology 500 HT v1.1)
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 Oncology 500 NextSeq
Step Data (Master Step Fields)
Protocol 5: Hybridization (TruSight Oncology 500 v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Set Up First Hybridization (TruSight Oncology 500 v1.1)
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: Capture Targets One (TruSight Oncology 500 v1.1)
Master Step Name = Capture Targets One (TSO 500 v1.1)
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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Set Up Second Hybridization (TruSight Oncology 500 v1.1)
Master Step Name = Set Up Second Hybridization (TSO 500 v1.1)
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: Capture Targets Two (TruSight Oncology 500 v1.1)
Master Step Name = Capture Targets Two (TSO 500 v1.1)
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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 5: Amplify Enriched Library (TruSight Oncology 500 v1.1)
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 Oncology 500 v1.1)
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)
TruSight Oncology 500 HT v1.1 Protocol 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 HT v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
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}
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 Oncology 500, Box 1
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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 Oncology 500, Box 4
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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
Reagent Kits
TruSight Oncology 500, Box 4
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
Sample Table
Column Headers
Additional Options and Dropdown Items
Placement Pattern = Column
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
TruSight Oncology 500, Box 3
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
TruSight Oncology 500, Box 2
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 3
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 Oncology 500, Box 4
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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 Oncology 500, Box 5
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 4
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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 Oncology 500, Box 6
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 7
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 8
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 9
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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 Oncology 500, Box 6
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 7
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSight Oncology 500, Box 6
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 7
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 8
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 9
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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 Oncology 500, Box 6
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
TruSight Oncology 500, Box 7
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
Sample Table
Column Headers
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
TruSight Oncology 500, Box 7
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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 Oncology 500, Box 6
Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
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
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
Step 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 HT v1.1)
Master Step Name = DNA/RNA FFPE Extraction (TSO 500 HT v1.1)
Derived Sample Generation = Fixed, 2
Naming Convention = {LIST:{SubmittedSampleName}_DNA,{SubmittedSampleName}_RNA}
Reagent Kits
QIAGEN AllPrep DNA/RNA FFPE Kit
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
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
chevron-right hashtag Trigger Location = Not Used
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Protocol 2: RNA QC and cDNA Synthesis (TruSight Oncology 500 HT v1.1)
Protocol Type = Library Prep
Step 1: Qubit RNA QC (TruSight Oncology 500 HT v1.1)
Master Step Name = Qubit RNA QC (TSO 500 v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Step File Placeholders
Log File - Automatically attached
Qubit Result File - Manually uploaded
Sample Table
Sample Display Default = Expand
Step 2: Denature and Anneal RNA (TruSight Oncology 500 HT v1.1)
Master Step Name = Denature and Anneal RNA (TSO 500 v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 HT, Box 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
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Dilution Concentration (ng/ul)
Step File Placeholders
Calculation Log File - Automatically attached
NextStep Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Step 3: First Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
Master Step Name = First Strand cDNA Synthesis v2.0
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 4: Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
Master Step Name = Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
Reagent Kits
TruSight Oncology 500 HT, Box 1
Catalog Number = 20007000
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 5: cDNA Clean Up (TruSight Oncology 500 HT v1.1)
Master Step Name = cDNA Clean Up (TSO 500 v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_cDNA
Reagent Kits
TruSight Oncology 500 HT, Box 4
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
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
chevron-right hashtag Trigger Location = Not Used
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Protocol 3: DNA QC and Fragmentation (TruSight Oncology 500 HT v1.1)
Protocol Type = Library Prep
Step 1: Qubit DNA QC (TruSight Oncology 500 HT v1.1)
Master Step Name = Qubit DNA QC (TruSight Oncology 500 HT v1.1)
Measurement Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Step File Placeholders
Log File - Automatically attached
Qubit Result File - Automatically attached
Sample Table
Sample Display Default = Expand
Step 2: Fragment DNA (TruSight Oncology 500 HT v1.1)
Master Step Name = Fragment DNA (TruSight Oncology 500 HT v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}_DNA
Reagent Kits
TruSight Oncology 500 HT, Box 4
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Defaults
Sample Grouping = Group by Containers
Placement Pattern = Column
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Dilution Concentration (ng/ul)
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Protocol 4: Library Prep (TruSight Oncology 500 HT v1.1)
Protocol Type = Library Prep
Step 1: End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)
Master Step Name = End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)
Reagent Kits
TruSight Oncology 500 HT, Box 3
Catalog Number = 20007002
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 2: Ligate Adapters (TruSight Oncology 500 HT v1.1)
Master Step Name = Ligate Adapters (TruSight Oncology 500 HT v1.1)
Reagent Kits
TruSight Oncology 500 HT, Box 2
TruSight Oncology 500 HT, Box 3
Catalog Number = 20007002
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 3: Clean Up Ligation (TruSight Oncology 500 HT v1.1)
Master Step Name = Clean Up v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 HT, Box 4
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 4: Index PCR (TruSight Oncology 500 HT v1.1)
Master Step Name = Index PCR (TruSight Oncology 500 HT v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSight Oncology 500 HT, Box 3
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Label Groups
TruSight Oncology 500 HT NovaSeq
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Protocol 5: Hybridization (TruSight Oncology 500 HT v1.1)
Protocol Type = Library Prep
Step 1: Set Up First Hybridization (TruSight Oncology 500 HT v1.1)
Master Step Name = Hybridize v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 HT, Box 7
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 2: Capture Targets One (TruSight Oncology 500 HT v1.1)
Master Step Name = Capture Targets One (TSO 500 v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSight Oncology 500 HT, Box 6
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 3: Set Up Second Hybridization (TruSight Oncology 500 HT v1.1)
Master Step Name = Set Up Second Hybridization (TSO 500 v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSight Oncology 500 HT, Box 7
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 4: Capture Targets Two (TruSight Oncology 500 HT v1.1)
Master Step Name = Capture Targets Two (TSO 500 v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
TruSight Oncology 500 HT, Box 6
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 5: Amplify Enriched Library (TruSight Oncology 500 HT v1.1)
Master Step Name = Amplify Enriched Library v2.0
Reagent Kits
TruSight Oncology 500 HT, Box 7
Catalog Number = 20026144
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
Step 6: Clean Up Amplified Enriched Library (TruSight Oncology 500 HT v1.1)
Master Step Name = Clean Up v2.0
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
TruSight Oncology 500 HT, Box 6
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Additional Options and Dropdown Items
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Collapse
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 Oncology 500 v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 v1.1)' \
--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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 HT v1.1)' \
--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 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.::FSM (uL):: = step.::Total Samples:: * (27/3) ; \
step.::RVT (uL):: = step.::Total Samples:: * (3/3) ' \
-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):: * 8.5) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 8.5 - 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 Oncology 500 v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 v1.1)' \
--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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)' \
--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):: * 12) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 12 - 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 '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.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-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 '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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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 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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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 '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 Oncology 500 HT v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 HT v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 HT v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 HT v1.1)' \
--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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit RNA QC (TruSight Oncology 500 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'Qubit DNA QC (TruSight Oncology 500 v1.1)' \
--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 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.::FSM (uL):: = step.::Total Samples:: * (27/3) ; \
step.::RVT (uL):: = step.::Total Samples:: * (3/3) ' \
-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):: * 8.5) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 8.5 - 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 Oncology 500 HT v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 HT v1.1)' \
--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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'TruSight Oncology 500 v1.1' \
--STEP 'End Repair and A-Tailing (TruSight Oncology 500 v1.1)' \
--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):: * 12) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (uL):: = 12 - 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 '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.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-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 '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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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 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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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}" 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
=
=
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
Catalog Number = 80234
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Expanded View Fields
Additional Options and Dropdown Items
Well Sort Order = Column
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20007000
Decimal Places Displayed = 2
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20007003
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Expanded View Fields
Additional Options and Dropdown Items
Well Sort Order = Column
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20007003
Decimal Places Displayed = 2
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Website =
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20007003
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20007002
TruSight Oncology 500 HT, Box 5
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20026144
TruSight Oncology 500 HT, Box 8
Catalog Number = 20026138
TruSight Oncology 500 HT, Box 9
Catalog Number = 20007012
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20026143
TruSight Oncology 500 HT, Box 7
Catalog Number = 20026144
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20026144
TruSight Oncology 500 HT, Box 8
Catalog Number = 20026138
TruSight Oncology 500 HT, Box 9
Catalog Number = 20007012
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20026143
TruSight Oncology 500 HT, Box 7
Catalog Number = 20026144
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
Catalog Number = 20026143
Expanded View Fields
Additional Options and Dropdown Items
Table Columns - Global Fields
Additional Options and Dropdown Items
=
=
Additional Options and Dropdown Items
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
Additional Options and Dropdown Items
Decimal Places Displayed = 1
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
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
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Decimal Places Displayed = 0
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 = 0
Decimal Places Displayed = 0
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Additional Options and Dropdown Items
Additional Options and Dropdown Items
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
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
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Decimal Places Displayed = 2
Additional Options and Dropdown Items
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Additional Options and Dropdown Items
Additional Options and Dropdown Items
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Decimal Places Displayed = 2
Additional Options and Dropdown Items
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Additional Options and Dropdown Items
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Additional Options and Dropdown Items
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Additional Options and Dropdown Items
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Decimal Places Displayed = 2
Additional Options and Dropdown Items
Additional Options and Dropdown Items
NextSeq 1000/2000 On-Prem
