Illumina DNA PCR-Free Library Prep Manual v1.1

Overview

The Illumina DNA PCR-Free Library Prep Manual workflow includes the following functionality.

Preset Illumina DNA PCR-Free Library Prep Manual protocols that support the preparation of up to 96 dual-indexed paired-end single-stranded libraries from DNA using the Illumina DNA PCR-Free Library Prep workflow.
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: Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Sort Sample (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
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 - DNA PCR-Free Lib Prep

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::gDNA:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::gDNA:: && input.::Protocol Type:: == ::Hybex::) {nextStep = ::Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Whole Blood:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Whole Blood Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Dried Blood Spot:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Dried Blood Spot Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Saliva:: && input.::Protocol Type::  == ::Thermal Cycler::) {nextStep = ::Saliva Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::}' \
-log {compoundOutputFileLuid0}"

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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 = Column
- Table Columns - Global Fields

Step 2: Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

The version of Qubit - Hybex master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type for DNA PCR-Free Lib Prep

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.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-log {compoundOutputFileLuid0}"

Assign QC flags

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"

Set Next Step-REMOVE and Copy Concentration & Sample Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ; input.::Sample Type:: = output.::Sample Type::' -log {compoundOutputFileLuid0}"

Routing - gDNA Hybex

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 'Sample Type' \
--FIELD_VALUE 'gDNA' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Queue/Ice Bucket

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

Record Details

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

Step 3: Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

The version of Qubit - Thermal Cycler master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type for DNA PCR-Free Lib Prep

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.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-log {compoundOutputFileLuid0}"

Assign QC flags

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"

Set Next Step-REMOVE, Set Prep Input Type, Copy Concentration & Sample Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::REMOVE:: ; \
if (output.::Concentration:: >= 25 && output.::Concentration:: <= 99) {output.::Prep Input Type:: = ::Low::} ; \
if (output.::Concentration:: >= 100 && output.::Concentration:: <= 2000) {output.::Prep Input Type:: = ::Standard::} ; \
input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ; input.::Sample Type:: = output.::Sample Type::' -log {compoundOutputFileLuid0}"

Routing - gDNA Thermal Cycler

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 Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Queue/Ice Bucket

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

Record Details

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

Step 4: Whole Blood Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Whole Blood Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina Lysis Reagent Kit
  - Supplier = Illumina
  - Catalog Number = 20042221
  - Website = www.illumina.com

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

Automations

Calculate Whole Blood Lysis Master Mix & Copy Sample Type

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::MLB (uL):: = step.::Total Samples:: * 30 *1.1 ; \
step.:: PK1 (uL):: = step.::Total Samples:: * 2 * 1.1 ; \
step.:: Nuclease-free water (uL):: = step.::Total Samples:: * 248 * 1.1 ; \
output.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep::' \
-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 - Whole Blood Lysis

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 'Sample Type' \
--FIELD_VALUE 'Whole Blood' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Placement = Enabled

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

Record Details

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

Step 5: Dried Blood Spot Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Dried Blood Spot Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina Lysis Reagent Kit
  - Supplier = Illumina
  - Catalog Number = 20042221
  - Website = www.illumina.com

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

Automations

Calculate Dried Blood Lysis 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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::10x Lysis Buffer (uL):: = step.::Total Samples:: * 30 *1.1 ; \
step.:: PK1 (uL):: = step.::Total Samples:: * 2 * 1.1 ; \
step.:: Nuclease-free water (uL):: = step.::Total Samples:: * 268 * 1.1 ; \
output.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep::' \
-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 - Dried Blood Spot Lysis

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 'Sample Type' \
--FIELD_VALUE 'Dried Blood Spot' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Placement = Enabled

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

Record Details

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

Step 6: Saliva Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Saliva Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina Lysis Reagent Kit
  - Supplier = Illumina
  - Catalog Number = 20042221
  - Website = www.illumina.com

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

Automations

Copy Sample Type for DNA PCR-Free Lib Prep

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.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-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 - Saliva Lysis

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 'Sample Type' \
--FIELD_VALUE 'Saliva' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Placement = Enabled

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

Record Details

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

Protocol 2: Library Prep - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Tagment Genomic DNA (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

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

Automations

Copy Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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

Calculate DNA Volume & Copy Desired DNA Input

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'output.::DNA (uL):: = (step.::Desired DNA Input (ng):: / output.::Concentration::) ; \
output.::RSB (uL):: = (25 - output.::DNA (uL)::) ; \
output.::Desired DNA Input (ng):: = step.::Desired DNA Input (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 = Column
Sample Table (Column Headers)

Placement = Enabled

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

Record Details

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

Step 2: Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = No Outputs
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

The version of Post Tagmentation Cleanup master step name may be different depending on the version of IPP installed.

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}"

Copy Desired DNA Input

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 {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

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

Step 3: Ligate Indexes (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Ligate Indexes (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}-{AppliedReagentLabels}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

The version of Ligate Indexes master step name may be different depending on the version of IPP installed.

Automations

Calculate Dilution for HP3 & Copy Desired DNA Input

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.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng):: ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::HP3 (uL):: = step.::Total Samples:: * 6 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 54' \
-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 = Column
- Placement Pattern = Column
Destination Containers
- 96 well plate

Add Labels

Label Groups
- 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 = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 4: Clean Up Libraries (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Clean Up Libraries (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

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

Automations

Copy Desired DNA Input

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.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"

Set Next Step-Remove & Prep Input Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::REMOVE:: ; \
output.::Prep Input Type:: = ::Standard::' -log {compoundOutputFileLuid0}"

Routing - Quantify & Pool 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 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

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

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Record Details

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

Protocol 3: Library Prep - Thermal Cycler Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Tagment Genomic DNA - Standard Input v1.0.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

The version of Tagment Genomic DNA - Standard Input master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type & Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
 -t false \
-h false \
-exp 'output.::Sample Type:: = input.::Sample Type:: ; \
if (output.::Sample Type:: == ::gDNA::) {output.::Concentration:: = input.::Concentration::} else {output.::Concentration:: = 0} ; \
if (output.::Sample Type:: == ::gDNA::) {output.::Conc. Units:: = input.::Conc. Units::} else {output.::Conc. Units:: = ::NA::}' \
-log {compoundOutputFileLuid0}"

Calculate Dilution & BLT-PF Volumes and Copy Desired DNA Input

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 false \
-h false \
-exp 'output.::Desired DNA Input (ng):: = step.::Desired DNA Input (ng):: ; \
if (output.::Sample Type:: == ::gDNA::) {output.::DNA (uL):: = output.::Desired DNA Input (ng):: / output.::Concentration::} ; \
if (output.::Sample Type:: == ::Whole Blood::) {output.::DNA (uL):: = 30} ; \
if (output.::Sample Type:: == ::Dried Blood Spot::) {output.::DNA (uL):: = 30} ; \
if (output.::Sample Type:: == ::Saliva::) {output.::DNA (uL):: = 30} ; \
if (output.::Sample Type:: == ::gDNA::) {output.::RSB (uL):: = 25 - output.::DNA (uL)::} ; \
if (output.::Sample Type:: == ::Whole Blood::) {output.::RSB (uL):: = 0} ; \
if (output.::Sample Type:: == ::Dried Blood Spot::) {output.::RSB (uL):: = 0} ; \
if (output.::Sample Type:: == ::Saliva::) {output.::RSB (uL):: = 0} ; \
if (output.::Sample Type:: == ::gDNA::) {output.::BLT-PF (uL):: = 15} ; \
if (output.::Sample Type:: == ::Whole Blood::) {output.::BLT-PF (uL):: = 10} ; \
if (output.::Sample Type:: == ::Dried Blood Spot::) {output.::BLT-PF (uL):: = 10} ; \
if (output.::Sample Type:: == ::Saliva::) {output.::BLT-PF (uL):: = 10}' \
-log {compoundOutputFileLuid0}"

Set Next Step-Post TAG

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.::Sample Type:: == ::Whole Blood::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type:: == ::Dried Blood Spot::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type:: == ::Saliva::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type:: == ::gDNA::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::}' \
-log {compoundOutputFileLuid0}"

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

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Placement = Enabled

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

Record Details

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

Step 2: Tagment Genomic DNA - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Tagment Genomic DNA - Low Input v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

Automations

Calculate Tag Master Mix and Copy Concentration & Sample Type

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
output.::Sample Type:: = input.::Sample Type:: ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::BLT-PF (uL):: = step.::Total Samples:: * 11 ; \
step.::TB1 (uL):: = step.::Total Samples:: * 11' \
-log {compoundOutputFileLuid0}"

Calculate Dilution and Copy Desired DNA Input

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 false \
-h false \
-exp 'output.::Desired DNA Input (ng):: = step.::Desired DNA Input (ng):: ; \
output.::DNA (uL):: = output.::Desired DNA Input (ng):: / output.::Concentration:: ; \
output.::RSB (uL):: = 30 - output.::DNA (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 = Column
Sample Table (Column Headers)

Placement = Enabled

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

Record Details

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

Step 3: Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Post Tagmentation Cleanup v1.0.1
Step Type = No Outputs
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

The version of Post Tagmentation Cleanup master step name may be different depending on the version of IPP installed.

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}"

Copy Desired DNA Input & Sample Type

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 {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Sample Type:: = input.::Sample Type:: ; \
output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

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

Step 4: Ligate Indexes - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Ligate Indexes - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}-{AppliedReagentLabels}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

The version of Ligate Indexes - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual) master step name may be different depending on the version of IPP installed.

Automations

Calculate Dilution for HP3 & Copy Desired DNA Input

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.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng):: ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::HP3 (uL):: = step.::Total Samples:: * 6 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 54' \
-log {compoundOutputFileLuid0}"

Set Next Step - Clean Up Libraries

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 (output.::Desired DNA Input (ng):: >= 100) {nextStep = ::Clean Up Libraries - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (output.::Desired DNA Input (ng):: <= 99) {nextStep = ::Clean Up Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::}' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Add Labels

Label Groups
- 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 = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 5: Clean Up Libraries - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Clean Up Libraries - Thermal Cycler v1.0.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

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

Automations

Copy Desired DNA Input

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.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"

Set Next Step-Remove & Prep Input Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::REMOVE:: ; \
if (output.::Desired DNA Input (ng):: >= 300) {output.::Prep Input Type:: = ::Standard::} else {output.::Prep Input Type:: = ::Low::}' \
-log {compoundOutputFileLuid0}"

Routing - Quantify & Pool 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 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Record Details

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

Step 6: Clean Up Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Clean Up Libraries - Thermal Cycler v1.0.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

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

Automations

Copy Desired DNA Input

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.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"

Set Next Step-Remove & Prep Input Type

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::REMOVE:: ; \
if (output.::Desired DNA Input (ng):: >= 300) {output.::Prep Input Type:: = ::Standard::} else {output.::Prep Input Type:: = ::Low::}' \
-log {compoundOutputFileLuid0}"

Routing - Quantify & Pool 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 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Record Details

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

Protocol 4: Quantify and Pool Libraries - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Pool Samples (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Reagent Kits
- Illumina DNA PCR-Free Library Prep
  - Supplier = Illumina
  - Catalog Number = 24 - 20041794; 96 - 20041795
  - Website = www.illumina.com

The version of Pool Samples (Illumina DNA PCR-Free Library Prep Manual) master step name may be different depending on the version of IPP installed.

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 = Column
Sample Table (Column Headers)

Pooling

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

Record Details

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

Step 2: Qubit (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Qubit (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

The version of Qubit (Illumina DNA PCR-Free Library Prep Manual) master step name may be different depending on the version of IPP installed.

Automations

Assign QC flags

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"

Set Next Step-Remove and Copy Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
- QC Log File - Automatically attached
- QC Result File - Automatically attached
- Upload File - Manually uploaded
Sample Table
- 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

Protocol 5: Quantify and Pool Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = KAPA Sample Prep - Illumina/Universal v1.0.1
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 0.05% Tween® 20
- 10 mM Tris-HCl, pH 8.0 – 8.5 (25°C)
Control Types
- KAPA DNA Standard 1
  - Supplier = Roche
  - Catalog Number = KK4828-07960166001
  - Website = www.roche.com
  - Conc. = 20 pM
  - Control Use
    Single step only = No
- KAPA DNA Standard 2
  - Supplier = Roche
  - Catalog Number = KK4828-07960166001
  - Website = www.roche.com
  - Conc. = 2 pM
  - Control Use
    Single step only = No
- KAPA DNA Standard 3
  - Supplier = Roche
  - Catalog Number = KK4828-07960166001
  - Website = www.roche.com
  - Conc. = 0.2 pM
  - Control Use
    Single step only = No
- KAPA DNA Standard 4
  - Supplier = Roche
  - Catalog Number = KK4828-07960166001
  - Website = www.roche.com
  - Conc. = 0.02 pM
  - Control Use
    Single step only = No
- KAPA DNA Standard 5
  - Supplier = Roche
  - Catalog Number = KK4828-07960166001
  - Website = www.roche.com
  - Conc. = 0.002 pM
  - Control Use
    Single step only = No
- KAPA DNA Standard 6
  - Supplier = Roche
  - Catalog Number = KK4828-07960166001
  - Website = www.roche.com
  - Conc. = 0.0002
  - Control Use
    Single step only = No
- KAPA Library Quantification Dilution Control
  - Supplier = Roche
  - Catalog Number = KK4906
  - Website = www.roche.com
  - Conc. = 200 pM
  - Control Use
    Single step only = No
- KAPA NTC
  - Control Use
    Single step only = No

The version of KAPA Sample Prep - Illumina/Universal master step name may be different depending on the version of IPP installed.

Automations

Copy Desired DNA Input for KAPA

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 'if (output.name.contains(::KAPA DNA Standard 1::)) {output.::Desired DNA Input (ng):: = 0.005952} ; \
if (output.name.contains(::KAPA DNA Standard 2::)) {output.::Desired DNA Input (ng):: = 0.000595}  ; \
if (output.name.contains(::KAPA DNA Standard 3::)) {output.::Desired DNA Input (ng):: = 0.00006}  ; \
if (output.name.contains(::KAPA DNA Standard 4::)) {output.::Desired DNA Input (ng):: = 0.000006}  ; \
if (output.name.contains(::KAPA DNA Standard 5::)) {output.::Desired DNA Input (ng):: = 0.0000006}  ; \
if (output.name.contains(::KAPA DNA Standard 6::)) {output.::Desired DNA Input (ng):: = 0.00000006}  ; \
if (output.name.contains(::KAPA Library Quantification Dilution Control::)) {output.::Desired DNA Input (ng):: = 0.059524} ; \
if (output.name.contains(::KAPA NTC::)) {output.::Desired DNA Input (ng):: = 0} ; \
if (!output.name.contains(::KAPA::)) {output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::}' \
-log {compoundOutputFileLuid0}"

Calculate Expected Concentration & Dilution Factor

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'output.::Expected Concentration (pM):: = output.::Desired DNA Input (ng):: * 3.36 * 1000 ; \
if (output.::Expected Concentration (pM):: >= 84000 && output.::Expected Concentration (pM):: <= 188000) {output.::Dilution Factor:: = 10000} ; \
if (output.::Expected Concentration (pM):: >= 189000 && output.::Expected Concentration (pM):: <= 333000) {output.::Dilution Factor:: = 20000} ; \
if (output.::Expected Concentration (pM):: <= 83000) {output.::Dilution Factor:: = 0}' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'if (output.::Expected Concentration (pM):: > 333000) {fail(::Expected Concentration is too high, please edit Dilution Factor and recalculate::)}' \
-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 = Column
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 = Column
- Table Columns - Global Fields

Step 2: KAPA qPCR Prep & Analysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = KAPA qPCR Prep & Analysis - Illumina/Universal v1.0
Step Type = Standard QC
Measurement Generation = Variable
Naming Convention = {InputItemName}
Reagent Kits
- KAPA qPCR library quantification kit - Illumina/Universal
  - Supplier = Roche
  - Catalog Number = 07960166001
  - Website = www.roche.com

Automations

Assign QC flags

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"

Calculate Average Cq

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:computeReplicateAverage \
 -src 'Cq' \
 -dest 'Average Cq' \
 -log {compoundOutputFileLuid0}"

Calculate qPCR Master Mix & Sample Volume

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; \
if (step.::Reaction Volume (uL):: == 20) {step.::KAPA SYBR FAST qPCR Master Mix + Primer Premix (uL):: = step.::Total Samples:: * 12} else {step.::KAPA SYBR FAST qPCR Master Mix + Primer Premix (uL):: = step.::Total Samples:: * 6} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::Yes::) {step.::ROX (uL):: = step.::Total Samples:: * 0.4} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::No::) {step.::ROX (uL):: = 0} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::Yes::) {step.::ROX (uL):: = step.::Total Samples:: * 0.2} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::No::) {step.::ROX (uL):: = 0} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::Yes::) {step.::PCR-grade water (uL):: = step.::Total Samples:: * 3.6} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::No::) {step.::PCR-grade water (uL):: = step.::Total Samples:: * 4} ; \
if (step.::Reaction Volume (uL):: == 10) {step.::PCR-grade water (uL):: = 0} ; \
if (step.::Reaction Volume (uL):: == 20) {output.::qPCR master mix (uL):: = 16} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::Yes::) {output.::qPCR master mix (uL):: = 6.2} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::No::) {output.::qPCR master mix (uL):: = 6} ; \
output.::Sample (uL):: = 4' \
-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 = Column
Sample Table (Column Headers)

Placement = Enabled

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

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
- QC Log File - Automatically attached
- QC Result File - Automatically attached
- Upload File - Manually uploaded
Sample Table
- 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

Step 3: KAPA Library Quantification (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = KAPA Library Quantification - Illumina/Universal v1.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Calculate Library Length Ratio & Copy Dilution Factor and Average Cq

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.::Library Length Ratio:: = 452 / step.::Library Length (bp):: ; \
output.::Average Cq:: = input.::Average Cq:: ; \
output.::Dilution Factor:: = input.::Dilution Factor::' \
-log {compoundOutputFileLuid0}"

Assign QC flags

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"

Calculate Concentration

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.::Diluted Avg. Conc. (pM)::  = 10 ** ((output.::Average Cq:: - step.::Standard Curve Y-Intercept::) / step.::Standard Curve Slope::) ; \
if (output.::Dilution Factor::.toFloat() >= 1) {output.::Concentration (pM):: = output.::Diluted Avg. Conc. (pM):: * step.::Library Length Ratio:: * output.::Dilution Factor::.toFloat()} else {output.::Concentration (pM):: = output.::Diluted Avg. Conc. (pM):: * step.::Library Length Ratio::} ; \
output.::Concentration (nM):: = 0.001 * output.::Concentration (pM)::' \
-log {compoundOutputFileLuid0}"

Set Next Step-KAPA Lib Quant

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.name.contains(::KAPA::)) {nextStep = ::REMOVE::} else {nextStep = ::ADVANCE::} ; \
input.::Concentration (nM):: = output.::Concentration (nM)::' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

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 {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 = Column
Sample Table (Column Headers)

Record Details

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

Step 4: Dilute Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Dilute Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Resuspension Buffer (RSB)

Automations

Copy Concentration (nM)

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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

Calculate Dilution Volumess

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 false \
-h false \
-exp 'output.::Sample (uL):: = (step.::Final Concentration (nM):: * step.::Final Volume (uL)::) / output.::Concentration (nM):: ; \
output.::RSB (uL):: = step.::Final Volume (uL):: - output.::Sample (uL):: ; \
output.::Final Concentration (nM):: = step.::Final Concentration (nM)::' \
-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 = Column
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 = Column
- Table Columns - Global Fields

Step 5: Pool Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Pool Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}

Automations

Copy Final Concentration (nM)

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration (nM):: = input.::Final Concentration (nM)::' \
-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 = Column
Sample Table (Column Headers)

Pooling

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

Record Details

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