Illumina DNA Prep (M) Tagmentation v1.0

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Overview

The Illumina DNA Prep (M) Tagmentation workflow includes the following functionality.

Preset Illumina DNA Prep (M) Tagmentation protocols that support the generation of enriched libraries for dual-indexed, paired-end sequencing.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.

Protocol 1: Prep Sample (Illumina DNA Prep (M) Tagmentation v1.0.9)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample Type (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Sort Sample v2.0.8
Step Type = No Outputs

Automations

Set Next Step - Tagmentation

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 true -h false -exp 'if (input.::Prep Sample Type - Tagmentation:: == ::Large Complex Genomes::) {nextStep = ::REMOVE::} ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Small Genomes::) {nextStep = ::DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Saliva::) {nextStep = ::Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Blood::) {nextStep = ::Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ' -log {compoundOutputFileLuid0}"

Route Samples - Large Complex Genome

Trigger Location = Step
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 'Prep Sample Type - Tagmentation' \
--FIELD_VALUE 'Large Complex Genomes' \
--WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \
--INPUTS_OR_OUTPUTS 'INPUTS' "

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 2: DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Calculate DNA Amount & Assign QC

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::DNA Amount (ng):: = output.::Concentration (ng/ul):: * output.::Sample Volume (ul)::' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (output.::DNA Amount (ng):: >= 0.33 && output.::DNA Amount (ng):: <= 100) { output.QC = true } else { output.QC = false } ; input.::DNA Amount (ng):: = output.::DNA Amount (ng):: ; input.::Concentration (ng/ul):: = output.::Concentration (ng/ul):: ; output.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation::' -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 Samples - Small Genomes

Trigger Location = Step
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 'Prep Sample Type - Tagmentation' \
--FIELD_VALUE 'Small Genomes' \
--WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \
--INPUTS_OR_OUTPUTS 'INPUTS' "

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Row
- File Column Options
  - File Column Display = Show
  - File Attachment Method = Manual
- Table Columns - Global Fields

Step 3: Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1
  - Supplier = Illumina
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Flex Lysis Reagent Kit
  - Supplier = Illumina

Automations

Count Samples and Calculate 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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \
step.::BLB (uL):: = step.::Total Samples:: * 7 ; \
step.::PK1 (uL):: = step.::Total Samples:: * 2 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 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 Samples - Blood

Trigger Location = Step
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 'Prep Sample Type - Tagmentation' \
--FIELD_VALUE 'Blood' \
--WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 4: Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1
  - Supplier = Illumina

Automations

Copy Prep Sample Type - Tagmentation

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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Protocol 2: Library Prep (Illumina DNA Prep (M) Tagmentation v1.0.9)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Tagment Genomic DNA v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 2
  - Supplier = Illumina
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 3
  - Supplier = Illumina

Automations

Copy Prep Sample Type - Tagmentation, DNA Amount & Set Blood and Saliva Sample Volume

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Blood:: || input.::Prep Sample Type - Tagmentation:: == ::Saliva::) {output.::Sample Volume (ul):: = 30} ; \
if (input.hasValue(::DNA Amount (ng)::)) {output.::DNA Amount (ng):: = input.::DNA Amount (ng)::}' -log {compoundOutputFileLuid0}"

Calculate DNA Amount for SMALL GENOMES

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.::Prep Sample Type - Tagmentation:: == ::Small Genomes:: && !step.hasValue(::Desired DNA Amount (ng)::)) {fail(::Please enter Desired DNA Amount (ng)::)} else {if (output.::Prep Sample Type - Tagmentation:: == ::Small Genomes:: && step.hasValue(::Desired DNA Amount (ng)::)) {output.::Sample Volume (ul):: = step.::Desired DNA Amount (ng):: / input.::Concentration (ng/ul):: ; output.::Nuclease-free water (ul):: = 30 - output.::Sample Volume (ul)::}}' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 2: Post Tagmentation Clean Up (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Post Tagmentation Clean Up v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1
  - Supplier = Illumina

Automations

Copy Prep Sample Type - Tagmentation & DNA Amount

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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \
if (input.hasValue(::DNA Amount (ng)::)) {output.::DNA Amount (ng):: = input.::DNA Amount (ng)::}' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 3: Amplify Tagmented DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Amplify Tagmented DNA v3.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 2
  - Supplier = Illumina

Automations

Set Prep Sample Type - Tagmentation & Set PCR Cycles

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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Small Genomes::) {if (input.::DNA Amount (ng):: >= 1 && input.::DNA Amount (ng):: <= 9) {output.::PCR Cycles:: = 12} ; \
if (input.::DNA Amount (ng):: >=10 && input.::DNA Amount (ng):: <= 24) {output.::PCR Cycles:: = 8} ; \
if (input.::DNA Amount (ng):: >=25 && input.::DNA Amount (ng):: <= 49) {output.::PCR Cycles:: = 6} ; \
if (input.::DNA Amount (ng):: >=50 && input.::DNA Amount (ng):: <= 100) {output.::PCR Cycles:: = 5}} else {output.::PCR Cycles:: = 5}' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 96 well plate

Add Labels

Label Groups
- IDT for Illumina DNA-RNA UD Indexes Set A Tagmentation
- IDT for Illumina DNA-RNA UD Indexes Set A-D Tagmentation
- 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
- IDT for Illumina Nextera DNA UD Indexes Set A for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set A-D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set B for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set C for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 4: Clean Up Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Clean Up Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1
  - Supplier = Illumina

Automations

Set Prep Sample Type - Tagmentation, Count Samples & Calculate 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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \
step.::SPB (ul):: = step.::Total Samples:: * 45 ; \
step.::Nuclease-free water (ul):: = step.::Total Samples:: * 40' -log {compoundOutputFileLuid0}"

Set Next Step - Optional Pooling

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 (output.::Pool Samples?:: == ::YES::) {nextStep = ::Optional Pool Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \
if (output.::Pool Samples?:: == ::NO::) {nextStep = ::Bioanalyzer Library QC (Illumina DNA Prep (M) Tagmentation v1.0.9)::}' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 5: Optional Pool Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Pool Libraries v2.0
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Pooling

Label Uniqueness = On
Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 6: Bioanalyzer Library QC (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

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/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -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 script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -f {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} -sep COMMA -b ',False,' -h 1 -c LIMSID -pre 'Sample '"

Parse Bioanalyzer XML, Copy nM and 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 -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /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 {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"