Protocol 1: Prep Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Automations
Sort & Set Next Step
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 'if (input.::NFE Sample Type:: == ::Blood:: ) {nextStep=::Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \
if (input.::NFE Sample Type:: == ::Saliva:: ) {nextStep=::Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \
if (input.::NFE Sample Type:: == ::gDNA:: ) {nextStep=::Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \
if (input.::NFE Sample Type:: == ::FFPE DNA::) {nextStep=::Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: }' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 2: Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
Agencourt AMPure XP beads, 5 ml
Supplier = Beckman Coulter
Flex Lysis Reagent Kit
Catalog Number = 20015884
Automations
Calculate Total Samples & Master Mix
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 '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.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
step.::BLB (uL):: = step.::Total Samples:: * 1.1 * 7 ; \
step.::PK1 (uL):: = step.::Total Samples:: * 1.1 * 2 ; \
step.::Water (uL):: = step.::Total Samples:: * 1.1 * 31' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove
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 = ::REMOVE::' -log {compoundOutputFileLuid0}"
Route NFE - Blood
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 'NFE Sample Type' \
--FIELD_VALUE 'Blood' \
--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.2' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "
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 = Collapse
Table Columns - Global Fields
Step 3: Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
Agencourt AMPure XP, 5 ml
Supplier = Beckman Coulter
Automations
Copy NFE Sample Type and Set UDFs
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.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
output.::Sample Volume (uL):: = 30 ; \
output.::80% EtOH (uL):: = 150 ; \
output.::Water for Resuspension (uL):: = 30' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove
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 = ::REMOVE::' -log {compoundOutputFileLuid0}"
Route NFE - Saliva
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 'NFE Sample Type' \
--FIELD_VALUE 'Saliva' \
--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.2' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "
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: Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Assign QC flags
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 -u {username} -p {password} \
script:assignQC \
-i {processURI:v2} \
-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 = Show
File Attachment Method = Manual
Table Columns - Global Fields
Step 5: Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Copy Concentration
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::' \
-log {compoundOutputFileLuid0}"
Calculate Dilution Volume & Sample Volume
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 'if (!output.hasValue(::Conc. Units::) || output.::Conc. Units:: != ::ng/uL::) { fail(::This automation expects Conc. Units to be ng/uL.::) ; };\
output.::Sample Volume (uL):: = (step.::Desired gDNA Concentration (ng/uL):: * step.::Total Volume (uL)::) / output.::Concentration::;\
output.::Dilution Volume (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::;\
output.::Final Concentration:: = step.::Desired gDNA Concentration (ng/uL)::;' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove & Copy NFE Sample Type
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 = ::REMOVE:: ; \
output.::NFE Sample Type:: = input.::NFE Sample Type:: ;' \
-log {compoundOutputFileLuid0}"
Route NFE - gDNA
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 'NFE Sample Type' \
--FIELD_VALUE 'gDNA' \
--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.2' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "
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
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Step 6: Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Assign QC flags
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 -u {username} -p {password} \
script:assignQC \
-i {processURI:v2} \
-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 = Show
File Attachment Method = Manual
Table Columns - Global Fields
Step 7: Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Copy Concentration
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::' \
-log {compoundOutputFileLuid0}"
Calculate Dilution Volume & Sample Volume
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 'if (!output.hasValue(::Conc. Units::) || output.::Conc. Units:: != ::ng/uL::) { fail(::This automation expects Conc. Units to be ng/uL.::) ; };\
output.::Sample Volume (uL):: = (step.::Desired gDNA Concentration (ng/uL):: * step.::Total Volume (uL)::) / output.::Concentration::;\
output.::Dilution Volume (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::;\
output.::Final Concentration:: = step.::Desired gDNA Concentration (ng/uL)::;' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance & Copy NFE Sample Type
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:: ; \
output.::NFE Sample Type:: = input.::NFE Sample Type:: ;' \
-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
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Protocol 2: Library Prep (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
Illumina DNA Prep -Tagmentation (S) Beads
Catalog Number = 20025519; 20025520
Illumina DNA/RNA Prep - Tagmentation PCR Reagents
Catalog Number = 20025519; 20025520
Automations
Calculate Total Samples and Master Mix & Copy Conc. & NFE Sample Type
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 '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.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
step.::eBLT (uL):: = step.::Total Samples:: * 1.1 * 11.5 ; \
step.::TB1 (uL):: = step.::Total Samples:: * 1.1 * 11.5 ; \
if (output.::NFE Sample Type::.contains(::Saliva::) || output.::NFE Sample Type::.contains(::Blood::)) {output.::Concentration:: = 100 ; output.::Conc. Units:: = ::ng/uL::} ; \
if (input.hasValue(::Final Concentration::)) {output.::Concentration:: = input.::Final Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::}' \
-log {compoundOutputFileLuid0}"
Calculate Sample Volume & Water
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.::Sample Volume (uL):: = step.::Desired Input Amount (ng):: / output.::Concentration:: ; \
output.::Nuclease-free water (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Desired Input Amount (ng):: = step.::Desired Input Amount (ng):: ; ' \
