Illumina DNA Prep (M) Tagmentation v1.0

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

The version of Sort Sample master step name may be different depending on the version of IPP installed.

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}"

ℹ The version of the nextStep step names may be different depending on the version of IPP installed.

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' "

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

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}

The version of DNA Quantification master step name may be different depending on the version of IPP installed.

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' "

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
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
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Measurement
  Concentration (ng/ul)
  Numeric
  Decimal Places Displayed = 2
  Measurement
  DNA Amount (ng)
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Prep Sample Type - Tagmentation
  Text
  Read Only
  Measurement
  Sample Volume (ul)
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Project
  Project Name
  Built-in

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

The version of Blood Lysis master step name may be different depending on the version of IPP installed.

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' "

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
80% Ethanol Prep Date
Date
BLB (uL)
Numeric
Decimal Places Displayed = 2
Comment
Multiline Text
Nuclease-free water (uL)
Numeric
Decimal Places Displayed = 2
PK1 (uL)
Numeric
Decimal Places Displayed = 2
Thermal Cycler Program
Text
Default = BLP
Total Samples
Numeric
Default = 0
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

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

The version of Saliva Lysis master step name may be different depending on the version of IPP installed.

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)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
80% Ethanol Prep Date
Date
Comment
Multiline Text
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

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)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Desired DNA Amount (ng)
Numeric
Decimal Places Displayed = 1
Directions
Multiline Text
Default = If Sample Type is Small Genome, please enter a Desired DNA Amount (ng) at the top of the screen & press blue button. If Sample Type is Large Complex Genome please enter Sample Volume (ul).
Thermal Cycler Program
Text
Default = TAG
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Nuclease-free water (ul)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Project
  Project Name
  Built-in

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)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Thermal Cycler Program
Text
Default = PTC
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

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)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

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)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Thermal Cycler Program
Text
Default = BLT PCR
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  PCR Cycles
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

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

The version of Clean Up Libraries master step name may be different depending on the version of IPP installed.

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)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
80% EtOH Prep Date
Date
Comment
Multiline Text
Nuclease-free water (ul)
Numeric
Decimal Places Displayed = 2
SPB (ul)
Numeric
Decimal Places Displayed = 2
Total Samples
Numeric
Default = 0
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Pool Samples?
  Text Dropdown
  Required Field
  Presets
  YES
  NO
  Derived Sample
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

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)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

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
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

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}"

Set Next Step - Output PASS/FAIL

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 -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {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} && /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.::Concentration:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}"

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {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}"

Parse Bioanalyzer XML, Calculate nM and assign QC flags

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {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 'output.::Concentration:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -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}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- BioAnalyzer DNA High Sensitivity Chip
- BioAnalyzer DNA 1000 Chip

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,500.00

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 350.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 500.00

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 200.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Targeted RNA Expression Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 700.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

Step Data
- Group of Defaults = Nextera DNA Flex Library Validation
- Master Step Fields
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Criteria 1 - Operator
  Text Dropdown
  Custom Entries
  Presets
  >=
  <=
  =
  !=
  Criteria 1 - Source Data Field
  Text Dropdown
  Presets
  Concentration
  Conc. Units
  Number of Peaks found
  Peak 1 Size - bp
  Peak 1 Conc.
  Peak 1 Molarity
  Peak 2 Size - bp
  Peak 2 Conc.
  Peak 2 Molarity
  Peak 3 Size - bp
  Peak 3 Conc.
  Peak 3 Molarity
  Peak 4 Size - bp
  Peak 4 Conc.
  Peak 4 Molarity
  Peak 5 Size - bp
  Peak 5 Conc.
  Peak 5 Molarity
  Number of Regions found
  Region 1 Average Size - bp
  Region 1 Conc.
  Region 1 Molarity
  Region 2 Average Size - bp
  Region 2 Conc.
  Region 2 Molarity
  Region 3 Average Size - bp
  Region 3 Conc.
  Region 3 Molarity
  Region 4 Average Size - bp
  Region 4 Conc.
  Region 4 Molarity
  Region 5 Average Size - bp
  Region 5 Conc.
  Region 5 Molarity
  Criteria 1 - Threshold Value
  Numeric
  Decimal Places Displayed = 2
  Criteria 2 - Operator
  Text Dropdown
  Custom Entries
  Presets
  >=
  <=
  =
  !=
  Criteria 2 - Source Data Field
  Text Dropdown
  Presets
  Concentration
  Conc. Units
  Number of Peaks found
  Peak 1 Size - bp
  Peak 1 Conc.
  Peak 1 Molarity
  Peak 2 Size - bp
  Peak 2 Conc.
  Peak 2 Molarity
  Peak 3 Size - bp
  Peak 3 Conc.
  Peak 3 Molarity
  Peak 4 Size - bp
  Peak 4 Conc.
  Peak 4 Molarity
  Peak 5 Size - bp
  Peak 5 Conc.
  Peak 5 Molarity
  Number of Regions found
  Region 1 Average Size - bp
  Region 1 Conc.
  Region 1 Molarity
  Region 2 Average Size - bp
  Region 2 Conc.
  Region 2 Molarity
  Region 3 Average Size - bp
  Region 3 Conc.
  Region 3 Molarity
  Region 4 Average Size - bp
  Region 4 Conc.
  Region 4 Molarity
  Region 5 Average Size - bp
  Region 5 Conc.
  Region 5 Molarity
  Criteria 2 - Threshold Value
  Numeric
  Decimal Places Displayed = 2
  Use strict matching for Bioanalyzer results
  Toggle Switch
  Default = None Set
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
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Derived Sample
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Measurement
  BA Sample Name
  Text
  Measurement
  Concentration
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Conc. Units
  Text
  Measurement
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Number of Peaks found
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Number of Regions found
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 1 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 1 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 1 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 2 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 2 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 2 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 3 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 3 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 3 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 4 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 4 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 4 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 5 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 5 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 5 Size - bp
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 1 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 1 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 1 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 2 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 2 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 2 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 3 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 3 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 3 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 4 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 4 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 4 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 5 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 5 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 5 Molarity
  Numeric
  Decimal Places Displayed = 2

Step 7: Normalize Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Normalize Libraries 1 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

The version of Normalize Libraries 1 master step name may be different depending on the version of IPP installed.

Automations

Normalization Calculations - Option 1

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.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Final Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = (step.::Target Normalization (nM):: * step.::Final Volume (ul):: ) / input.::Molarity (nM):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -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}"

Routing script - Normalize Libraries

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -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 'Sequencing Instrument' \
--FIELD_VALUE 'MiSeq' \
--WORKFLOW 'MiSeq Sequencing v3.2' \
--STEP 'Library Pooling (MiSeq v3.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq' \
--WORKFLOW 'NextSeq 500/550 Sequencing v1.2' \
--STEP 'Library Pooling (NextSeq 500/550 v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 2.0' \
--WORKFLOW 'NovaSeq 6000 v2.3' \
--STEP 'Define Run Format (NovaSeq 6000 v2.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 3.0' \
--WORKFLOW 'NovaSeq 6000 v3.8' \
--STEP 'Define Run Format (NovaSeq 6000 v3.8)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeqDx' \
--WORKFLOW 'NovaSeqDx v1.2' \
--STEP 'Define Run Format (NovaSeqDx v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000' \
--WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series' \
--WORKFLOW 'NovaSeq X Series v1.1' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \
--WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Final Volume (ul)
Numeric
Required Field
Decimal Places Displayed = 2
Target Normalization (nM)
Numeric
Required Field
Default = 2
Decimal Places Displayed = 2
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Buffer Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Normalized Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sequencing Instrument
  Text Dropdown
  Required Field
  Presets
  MiSeq
  NextSeq
  NextSeq 1000/2000
  NextSeq 1000/2000 On-Prem
  NovaSeq 2.0
  NovaSeq 3.0
  NovaSeq X Series
  NovaSeqDx
  Project
  Project Name
  Built-in

PreviousIllumina DNA PCR-Free Library Prep Manual v1.1 NextOther RNA Protocols

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hashtagOverview

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

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPlacement = Enabled

hashtagAdd Labels

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPooling

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPlacement = Enabled

hashtagRecord Details

hashtagStep 7: Normalize Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

Overview

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

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Placement = Enabled

Add Labels

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Pooling

Record Details

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

Automations

Queue/Ice Bucket

Placement = Enabled

Record Details

Step 7: Normalize Libraries (Illumina DNA Prep (M) Tagmentation v1.0.9)

Automations

Queue/Ice Bucket

Record Details