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
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Input Amount, Total Volume & Low TE - Custom DNA Panel
Trigger Location = Record Details
Trigger Style = Manual button
Calc Input Amount, Total Volume & Low TE - Custom DNA - Final Conc.
Trigger Location = Not Used
Set Next Step - Advance
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step 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
Assign QC flags (Qubit QC)
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step and Copy Concentration
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: 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
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calc Input Amount, Total Volume & Low TE - Custom DNA - Final Conc.
Trigger Location = Record Details
Trigger Style = Manual button
Calculate Input Amount, Total Volume & Low TE - Custom DNA Panel
Trigger Location = Not Used
Set Next Step - Advance
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step 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
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
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 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
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 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
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step 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
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool
Trigger Location = Not Used
Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 8: Partially Digested Amplicons (AmpliSeq for Illumina Custom DNA Panel v1.1)
Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina v1.1)
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 9: 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
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Route AmpliSeq Samples - Custom DNA Panel
Trigger Style = Automatic upon exit
Route AmpliSeq Samples - Immune Repertoire Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - BRCA
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Childhood Cancer Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - CHP v2
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - CP
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Focus Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Immune Response Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Myeloid Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples -Transcriptome Human GEx Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Label Groups
AmpliSeq CD Indexes Set A for Illumina
AmpliSeq CD Indexes Set B for Illumina
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = If enough DNA is available, dilute to intermediate concentration of ~20-50 ng/uL.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Criteria 1 - Threshold Value
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
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
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
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
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Column
Decimal Places Displayed = 1
Recommended Prep Input (ng)
Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
Decimal Places Displayed = 0
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
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
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Column
Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
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
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
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
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Column
Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Sample Table (Column Headers)
Additional Options and Dropdown Items
AmpliSeq CD Indexes Set C for Illumina
AmpliSeq CD Indexes Set D for Illumina
AmpliSeq UD Indexes for Illumina (24 Indexes)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Desired Concentration (ng/uL)
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Desired Final Concentration (ng/uL)
Additional Options and Dropdown Items
2X AmpliSeq Custom DNA Panel
Decimal Places Displayed = 1
5X AmpliSeq HiFi Mix (uL)
Additional Options and Dropdown Items
Recommended Prep Input (ng)
Additional Options and Dropdown Items
Recommended Prep Input (ng)
Additional Options and Dropdown Items
Recommended Prep Input (ng)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp '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}"
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}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"
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}"
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}"
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}"
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}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::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}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::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}"
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}"
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}"
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}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::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}"
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}"
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}"
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}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::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}"
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}"
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}"
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}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::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}"
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}"
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}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -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'"
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'"
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'"
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'"
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'"
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'"
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'"
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'"
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'"
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'"
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Desired Final Concentration (ng/uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Diluted DNA Conc. (ng/uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 0
5X AmpliSeq HiFi Mix (uL)
Decimal Places Displayed = 1
Diluted DNA Conc. (ng/uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 0
5X AmpliSeq HiFi Mix (uL)
Decimal Places Displayed = 1
Diluted DNA Conc. (ng/uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 0
5X AmpliSeq HiFi Mix (uL)
Decimal Places Displayed = 1
Diluted DNA Conc. (ng/uL)
Decimal Places Displayed = 2
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
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
