Illumina DNA Prep with Enrichment (S) Tagmentation v1.2 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)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log - Automatically attached
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
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 version of the workflow and step for the routing 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)
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
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 version of the workflow and step for the routing 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)
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
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 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
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
chevron-right hashtag Trigger Style = Automatic upon exit
ℹ The version of the workflow and step for the routing 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)
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
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 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
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)
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
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 2: Post Tagmentation Cleanup (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Post Tagmentation Cleanup (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log - Automatically attached
Step 3: Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Label Groups
IDT for Illumina DNA-RNA UD Indexes Set A Tagmentation
IDT for Illumina DNA-RNA UD Indexes Set A-D Tagmentation
Step Data (Master Step Fields)
Step 4: Clean Up Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Clean Up Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
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: Bioanalyzer QC Qualify Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Bioanalyzer QC Qualify Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Measurement 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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 6: Pool Pre-Enriched Libraries - Volume (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Pool Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Aliquot 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
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Step Data (Master Step Fields)
Step 7: Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
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 8: Pool Pre-Enriched Libraries - Mass (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Pool Pre-Enriched Libraries - Mass (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Aliquot 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
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Step Data (Master Step Fields)
Step 9: Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
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 10: Capture Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Capture Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
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 11: Amplify Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Amplify Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
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 12: Clean Up Amplified Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
Master Step Name = Clean Up Amplified Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
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 File Placeholders
Log - Automatically attached
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
Agencourt AMPure XP beads, 5 ml
Supplier = Beckman Coulter
Flex Lysis Reagent Kit
Catalog Number = 20015884
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Agencourt AMPure XP, 5 ml
Supplier = Beckman Coulter
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}
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 = Show
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Presets
10 mM Tris-HCI, pH 7.5–8.5
Decimal Places Displayed = 2
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
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 = Show
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Presets
10 mM Tris-HCI, pH 7.5–8.5
Decimal Places Displayed = 2
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
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
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = Desired Input Amount should be between 50-1000 ng.
Thermal Cycler Instructions
Default =
Choose the preheat lid option and set to 100C
Set the reaction volume to 50 uL
55C for 5 minutes
Hold at 10C
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Illumina DNA/RNA Prep - Tagmentation Buffers
Catalog Number = 20025519; 20025520
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
Illumina DNA Fast Hyb - Enrichment PCR + Buffers
Catalog Number = 20025519; 20025520
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
IDT for Illumina DNA-RNA UD Indexes Set B Tagmentation
IDT for Illumina DNA-RNA UD Indexes Set C Tagmentation
IDT for Illumina DNA-RNA UD Indexes Set D Tagmentation
Illumina DNA-RNA UD Indexes Set A B C D Tagmentation
Illumina DNA-RNA UD Indexes Set A Tagmentation
Illumina DNA-RNA UD Indexes Set B Tagmentation
Illumina DNA-RNA UD Indexes Set C Tagmentation
Illumina DNA-RNA UD Indexes Set D Tagmentation
Thermal Cycler Program Instructions
Default =
Choose the preheat lid option and set to 100°C Set the reaction volume to 50 uL
72C for 3 minutes
98C for 3 minutes
X cycles of:
X = 98C for 20 seconds
X = 0C for 30 seconds
X = 72C for 1 minute
72C for 3 minutes Hold at 10C
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Agencourt AMPure XP Beads
Catalog Number = NC9959336; NC9933872
Illumina DNA Prep -Tagmentation (S) Beads
Catalog Number = 20025519; 20025520
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}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Destination Containers
BioAnalyzer DNA High Sensitivity Chip
BioAnalyzer DNA 1000 Chip
Default = Peak 2 Size - bp
Criteria 1 - Threshold Value
Criteria 2 - Source Data Field
Default = Peak 2 Size - bp
Criteria 1 - Threshold Value
Use strict matching for Bioanalyzer results
Step File Placeholders
Bioanalyzer Input File - Automatically attached
Bioanalyzer Input File Generation Log File - Automatically attached
Bioanalyzer XML Result File (required) - Manually uploaded
Result File (optional) - Manually uploaded
PDF Summary File (optional) - Manually uploaded
Bioanalyzer XML Parsing Log File - Automatically attached
QC Assignment Log File - Automatically attached
QC Assignment Report - Automatically attached
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {PoolName}
Reagent Kits
Agencourt AMPure XP Beads
Catalog Number = NC9959336; NC9933872
Illumina DNA Prep -Tagmentation (S) Beads
Catalog Number = 20025519; 20025520
Sample Table (Column Headers)
Additional Options and Dropdown Items
Well Sort Order = Row
Destination Containers
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 1 - 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 = {PoolName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Well Sort Order = Row
Destination Containers
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina DNA Fast Hyb - Enrichment Beads + Buffers
Catalog Number = 20025519; 20025520
Illumina DNA Fast Hyb - Enrichment PCR + Buffers
Catalog Number = 20025519; 20025520
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
Illumina DNA Fast Hyb - Enrichment Beads + Buffers
Catalog Number = 20025519; 20025520
Illumina DNA Fast Hyb - Enrichment PCR + Buffers
Catalog Number = 20025519; 20025520
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Illumina DNA Fast Hyb - Enrichment PCR + Buffers
Catalog Number = 20025519; 20025520
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
Agencourt AMPure XP Beads
Catalog Number = NC9959336; NC9933872
Illumina DNA Prep -Tagmentation (S) Beads
Catalog Number = 20025519; 20025520
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
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
Desired gDNA Concentration (ng/uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Desired gDNA Concentration (ng/uL)
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Desired Input Amount (ng)
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
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Pre-Enriched Library Sample (ng)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 2
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 (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}"
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.::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}"
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 {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' "
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.::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}"
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 {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' "
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} \
script:assignQC \
-i {processURI:v2} \
-log {compoundOutputFileLuid1} \
-qcResult {compoundOutputFileLuid2}"
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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-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 '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}"
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:: ; \
output.::NFE Sample Type:: = input.::NFE Sample Type:: ;' \
-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 {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' "
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} \
script:assignQC \
-i {processURI:v2} \
-log {compoundOutputFileLuid1} \
-qcResult {compoundOutputFileLuid2}"
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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-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 '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}"
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:: ; \
output.::NFE Sample Type:: = input.::NFE Sample Type:: ;' \
-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 '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}"
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 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):: ; ' \
-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 'output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
step.::EPM (uL):: = step.::Total Samples:: * 1.1 * 23 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 1.1 * 23 ; \
if (output.::NFE Sample Type:: == ::Saliva::) {output.::PCR Cycles:: = 9} ; \
if (output.::NFE Sample Type:: == ::Blood::) {output.::PCR Cycles:: = 9} ; \
if (output.::NFE Sample Type:: == ::gDNA::) {if (input.::Desired Input Amount (ng):: >= 10 && input.::Desired Input Amount (ng):: <= 49) {output.::PCR Cycles:: = 12}} ; \
if (output.::NFE Sample Type:: == ::gDNA::) {if (input.::Desired Input Amount (ng):: >= 50 && input.::Desired Input Amount (ng):: <= 1000) {output.::PCR Cycles:: = 9}} ; \
if (output.::NFE Sample Type:: == ::FFPE DNA::) {if (input.::Desired Input Amount (ng):: >= 50 && input.::Desired Input Amount (ng):: <= 1000) {output.::PCR Cycles:: = 12}}' \
-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/DriverFileGenerator.jar -u {username} -p {password} \
script:driver_file_generator \
-i {processURI:v2} \
-t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv \
-o {compoundOutputFileLuid0}.csv \
-l {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
script:addBlankLines \
-i {stepURI:v2} \
-f {compoundOutputFileLuid0}.csv \
-l {compoundOutputFileLuid1} \
-sep COMMA \
-b ',False,' \
-h 1 \
-c LIMSID \
-pre 'Sample '"
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:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"
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 (step.::Library Pool Plexity:: == ::1-plex::) {output.::Pre-Enriched Library Volume (uL):: = 14} ; \
if (step.::Library Pool Plexity:: == ::12-plex::) {output.::Pre-Enriched Library Volume (uL):: = 2.5} ; \
output.::RSB Volume (uL):: = step.::Total Pooled Volume (uL):: - output.::Pre-Enriched 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 = ::Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)::' \
-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} \
script:assignQC \
-i {processURI:v2} \
-log {compoundOutputFileLuid1} \
-qcResult {compoundOutputFileLuid2}"
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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-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 (step.::Library Pool Plexity:: == ::1-plex::) {output.::Pre-Enriched Library Volume (uL):: = 14} ; \
if (step.::Library Pool Plexity:: == ::12-plex::) {output.::Pre-Enriched Library Volume (uL):: = 2.5} ; \
output.::RSB Volume (uL):: = step.::Total Pooled Volume (uL):: - output.::Pre-Enriched 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 '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.::EE1 (uL):: = step.::Total Samples:: * 1.1 * 28.5 ; \
step.::HP3 (uL):: = step.::Total Samples:: * 1.1 * 1.5 ;' \
-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}" Website =
Decimal Places Displayed = 2
Water for Resuspension (uL)
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
Desired Input Amount (ng)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 1 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 2 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 3 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 4 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Region 5 Average Size - bp
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Pre-Enriched Library Volume (uL)
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Pre-Enriched Library Volume (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
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
