Library Preparation v1.1
Protocol 1: Library Prep (AmpliSeq for Illumina Custom DNA Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Dilute DNA (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina Custom DNA Panel)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"
Calculate Input Amount, Total Volume & Low TE - Custom DNA Panel
Trigger Location = Record Details
Trigger Style = Manual button
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.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL)::' \
-log {compoundOutputFileLuid0}"
Calc Input Amount, Total Volume & Low TE - Custom DNA - Final Conc.
Trigger Location = Not Used
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.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Final Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Desired Final Concentration (ng/uL):: = step.::Desired Final Concentration (ng/uL)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
Trigger Location = Not Used
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}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 2: Qubit (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Qubit (AmpliSeq for Illumina v1.1)
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Assign QC flags (Qubit QC)
Trigger Location = Record Details
Trigger Style = Manual button
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"
Set Next Step and Copy Concentration
Trigger Location = Record Details
Trigger Style = Automatic upon exit
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
QC Log File - Automatically attached
QC Result File - Automatically attached
Upload File - Manually uploaded
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina Custom DNA Panel)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"
Calc Input Amount, Total Volume & Low TE - Custom DNA - Final Conc.
Trigger Location = Record Details
Trigger Style = Manual button
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.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Final Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Desired Final Concentration (ng/uL):: = step.::Desired Final Concentration (ng/uL)::' \
-log {compoundOutputFileLuid0}"
Calculate Input Amount, Total Volume & Low TE - Custom DNA Panel
Trigger Location = Not Used
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.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
Trigger Location = Not Used
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}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 4: Amplify Targets - One Primer Pool (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Custom DNA Panel for Illumina
Catalog Number = 20020495
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool
Trigger Location = Record Details
Trigger Style = Manual button
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
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 Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Placement Pattern = Column
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 5: Amplify Targets - Two Primer Pools (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Custom DNA Panel for Illumina
Catalog Number = 20020495
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Record Details
Trigger Style = Manual button
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
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 Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Placement Pattern = Column
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 6: Amplify Targets - Three Primer Pool (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Custom DNA Panel for Illumina
Catalog Number = 20020495
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Record Details
Trigger Style = Manual button
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
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 Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 7: Amplify Targets - Four Primer Pool (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Custom DNA Panel for Illumina
Catalog Number = 20020495
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Record Details
Trigger Style = Manual button
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
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 Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Not Used
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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Placement Pattern = Column
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 8: Partially Digested Amplicons (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina v1.1)
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
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}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 9: Ligate Indexes (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Ligate Indexes (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
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}"
Route AmpliSeq Samples - Custom DNA Panel
Trigger Style = Automatic upon exit
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - Immune Repertoire Panel
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - BRCA
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina BRCA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina BRCA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - Childhood Cancer Panel
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - CHP v2
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - CP
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - Focus Panel
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - Immune Response Panel
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples - Myeloid Panel
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Route AmpliSeq Samples -Transcriptome Human GEx Panel
Trigger Location = Not Used
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 {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Add Labels
Label Groups
AmpliSeq CD Indexes Set A for Illumina
AmpliSeq CD Indexes Set B for Illumina
AmpliSeq CD Indexes Set C for Illumina
AmpliSeq CD Indexes Set D for Illumina
AmpliSeq UD Indexes for Illumina (24 Indexes)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
