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Infinium Arrays

Infinium HTS Assay Manual v1.2

Overview

The Infinium HTS Assay Manual workflow includes the following functionality.

Preconfigured Infinium HTS Assay Manual protocols.
Automatic placement of samples when necessary.
Automatic step transition when required.
Automatic calculation or display of reagents at every step in the protocol.

Protocol 1: Prep Sample (Infinium HTS Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Infinium Kit (Infinium HTS Assay Manual v1.2)

Master Step Name = Select Infinium Kit-Infinium HTS v1.2
Step Type = No Outputs

Automations

Set Infinium HTS Kit Name

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 'input.::Infinium Kit Name:: = step.::Infinium HTS Kits::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

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

Step 2: Quantify DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Quantify DNA-Infinium PicoGreen v1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1X TE
- Lambda DNA
- PicoGreen dsDNA quantification reagent

Automations

Calculate Stock Lambda DNA and PicoGreen Dilution

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.::Stock Lambda DNA for A1 (uL):: = (233.3 * 75) / step.::Stock Lambda DNA (ng/uL):: ; step.::1X TE for A1 (uL):: = 233.3 - step.::Stock Lambda DNA for A1 (uL):: ; if (step.::No. of QDNA Plates:: == 1) {step.::PicoGreen (uL):: = 115 ; step.::1X TE (mL):: = 23} ; if (step.::No. of QDNA Plates:: == 2) {step.::PicoGreen (uL):: = 215 ; step.::1X TE (mL):: = 43} ; if (step.::No. of QDNA Plates:: == 3) {step.::PicoGreen (uL):: =  315 ; step.::1X TE (mL):: = 63}' -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

Record Details

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

Step 3: Amplify DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Amplify DNA-Infinium HTS v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MA2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MSM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH

Automations

Validate MSA3 Plate Barcode and Set Sample Placement Information

Trigger Location = Placement
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 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA3:: ) ) {fail ( ::Invalid MSA3 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA3:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

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.::Infinium Kit Name:: = input.::Infinium Kit Name::' -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 = Same Shape
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 = Row
- Table Columns - Global Fields

Step 4: Incubate DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Incubate DNA-Infinium v1.2
Step Type = No Outputs

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)

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

Step 5: Fragment DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Fragment DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- FMS-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: Precipitate DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Precipitate DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- 100% 2-propanol
- PM1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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

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

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 7: Resuspend DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Resuspend DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: BeadChip Processing (Infinium HTS Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to HTS BeadChip (Infinium HTS Assay Manual v1.2)

Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- PB2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Generate Sample Placement for Infinium BeadChip

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/infinium/placementpatterns"

Validate BeadChip Barcode

Trigger Location = Placement
Trigger Style = Automatic upon exit

/usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

Copy Sample Information

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.::Infinium Kit Name:: = input.::Infinium Kit Name:: ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode:: ; output.::Sample_Plate:: = input.::Sample_Plate:: ; output.::Sample_Well:: = input.::Sample_Well:: ; output.::BeadChip Barcode:: = output.container.name ; output.::BeadChip Position:: = output.well' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 24x1 HTS BeadChip Multichannel
- 24x1 HTS BeadChip
- 24x1 HD BeadChip

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

Step 2: Wash BeadChip (Infinium HTS Assay Manual v1.2)

Master Step Name = Wash BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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

Step 3: Extend and Stain BeadChip (Infinium HTS Assay Manual v1.2)

Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- ATM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- EDTA
- EML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- SML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC3-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC4-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Set Array Instrument

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 -exp 'input.::Array Instrument:: = ::iScan::' -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}"

Routing Script - iScan

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 'Array Instrument' \
--FIELD_VALUE 'iScan' \
--WORKFLOW 'iScan v1.0' \
--STEP 'Image Infinium BeadChip (iScan v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

Queue/Ice Bucket

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

Record Details

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

Infinium HTS Assay Manual v1.2

Overview

The Infinium HTS Assay Manual workflow includes the following functionality.

Preconfigured Infinium HTS Assay Manual protocols.
Automatic placement of samples when necessary.
Automatic step transition when required.
Automatic calculation or display of reagents at every step in the protocol.

Protocol 1: Prep Sample (Infinium HTS Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Infinium Kit (Infinium HTS Assay Manual v1.2)

Master Step Name = Select Infinium Kit-Infinium HTS v1.2
Step Type = No Outputs

Automations

Set Infinium HTS Kit Name

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 'input.::Infinium Kit Name:: = step.::Infinium HTS Kits::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

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

Step 2: Quantify DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Quantify DNA-Infinium PicoGreen v1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1X TE
- Lambda DNA
- PicoGreen dsDNA quantification reagent

Automations

Calculate Stock Lambda DNA and PicoGreen Dilution

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.::Stock Lambda DNA for A1 (uL):: = (233.3 * 75) / step.::Stock Lambda DNA (ng/uL):: ; step.::1X TE for A1 (uL):: = 233.3 - step.::Stock Lambda DNA for A1 (uL):: ; if (step.::No. of QDNA Plates:: == 1) {step.::PicoGreen (uL):: = 115 ; step.::1X TE (mL):: = 23} ; if (step.::No. of QDNA Plates:: == 2) {step.::PicoGreen (uL):: = 215 ; step.::1X TE (mL):: = 43} ; if (step.::No. of QDNA Plates:: == 3) {step.::PicoGreen (uL):: =  315 ; step.::1X TE (mL):: = 63}' -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

Record Details

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

Step 3: Amplify DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Amplify DNA-Infinium HTS v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MA2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MSM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH

Automations

Validate MSA3 Plate Barcode and Set Sample Placement Information

Trigger Location = Placement
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 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA3:: ) ) {fail ( ::Invalid MSA3 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA3:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

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.::Infinium Kit Name:: = input.::Infinium Kit Name::' -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 = Same Shape
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 = Row
- Table Columns - Global Fields

Step 4: Incubate DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Incubate DNA-Infinium v1.2
Step Type = No Outputs

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)

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

Step 5: Fragment DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Fragment DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- FMS-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: Precipitate DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Precipitate DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- 100% 2-propanol
- PM1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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

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

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 7: Resuspend DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Resuspend DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: BeadChip Processing (Infinium HTS Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to HTS BeadChip (Infinium HTS Assay Manual v1.2)

Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- PB2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Generate Sample Placement for Infinium BeadChip

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/infinium/placementpatterns"

Validate BeadChip Barcode

Trigger Location = Placement
Trigger Style = Automatic upon exit

/usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

Copy Sample Information

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.::Infinium Kit Name:: = input.::Infinium Kit Name:: ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode:: ; output.::Sample_Plate:: = input.::Sample_Plate:: ; output.::Sample_Well:: = input.::Sample_Well:: ; output.::BeadChip Barcode:: = output.container.name ; output.::BeadChip Position:: = output.well' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 24x1 HTS BeadChip Multichannel
- 24x1 HTS BeadChip
- 24x1 HD BeadChip

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

Step 2: Wash BeadChip (Infinium HTS Assay Manual v1.2)

Master Step Name = Wash BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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

Step 3: Extend and Stain BeadChip (Infinium HTS Assay Manual v1.2)

Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- ATM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- EDTA
- EML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- SML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC3-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC4-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Set Array Instrument

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 -exp 'input.::Array Instrument:: = ::iScan::' -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}"

Routing Script - iScan

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 'Array Instrument' \
--FIELD_VALUE 'iScan' \
--WORKFLOW 'iScan v1.0' \
--STEP 'Image Infinium BeadChip (iScan v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

The workflow version and step version for the Array Instrument may vary depending on the version of the IPP.

Queue/Ice Bucket

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

Record Details

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

Infinium XT Assay Manual v1.2

Overview

The Infinium XT Assay Manual workflow includes the following functionality.

Preconfigured protocols to prepare 96 DNA samples for use with the 24x4 BeadChip.
Support for custom content for XT format.
Automated calculation of sample and buffer volumes.
Automatic placement of samples when necessary.
Automatic step transition when required.
Automatic calculation or display of reagents at every step in the protocol.

Protocol 1: Prep Sample (Infinium XT Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Amplify DNA (Infinium XT Assay Manual v1.2)

Master Step Name = Amplify DNA-Infinium XT v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MA2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH
- RAM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Validate MSA7 Plate Barcode and Set Sample Information

Trigger Location = Placement
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 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA7:: ) ) {fail ( ::Invalid MSA7 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA7:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Set Infinium XT Kit Name and 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 'output.::Infinium Kit Name:: = step.::Infinium XT Kits:: ; 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

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

Step 2: Incubate DNA (Infinium XT Assay Manual v1.2)

Master Step Name = Incubate DNA-Infinium v1.2
Step Type = No Outputs

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)

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

Step 3: Fragment DNA (Infinium XT Assay Manual v1.2)

Master Step Name = Fragment DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- FMS-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: Precipitate DNA (Infinium XT Assay Manual v1.2)

Master Step Name = Precipitate DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- 100% 2-propanol
- PM1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: Resuspend DNA (Infinium XT Assay Manual v1.2)

Master Step Name = Resuspend DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: BeadChip Processing (Infinium XT Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to XT BeadChip (Infinium XT Assay Manual v1.2)

Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- PB2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Generate Sample Placement for Infinium BeadChip

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/infinium/placementpatterns"

Validate BeadChip Barcode

Trigger Location = Placement
Trigger Style = Automatic upon exit

/usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

Copy Sample Information

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.::Infinium Kit Name:: = input.::Infinium Kit Name:: ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode:: ; output.::Sample_Plate:: = input.::Sample_Plate:: ; output.::Sample_Well:: = input.::Sample_Well:: ; output.::BeadChip Barcode:: = output.container.name ; output.::BeadChip Position:: = output.well' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 24x4 XT BeadChip

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

Step 2: Wash BeadChip (Infinium XT Assay Manual v1.2)

Master Step Name = Wash BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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

Step 3: Extend and Stain BeadChip (Infinium XT Assay Manual v1.2)

Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- 70% EtOH
- ATM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- EDTA
- EML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- SML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC3-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Set Array Instrument

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 -exp 'input.::Array Instrument:: = ::iScan::' -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}"

Routing Script - iScan

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 'Array Instrument' \
--FIELD_VALUE 'iScan' \
--WORKFLOW 'iScan v1.0' \
--STEP 'Image Infinium BeadChip (iScan v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

Queue/Ice Bucket

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

Record Details

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

Infinium LCG Assay Manual v1.2

Overview

The Infinium LCG Assay Manual workflow includes the following functionality.

Preconfigured protocols to prepare 96 DNA samples for use with 8x1 LCG BeadChip products.
Automated calculation of sample and buffer volumes.
Automatic placement of samples when necessary.
Automatic step transition when required.
Automatic calculation or display of reagents at every step in the protocol.

Protocol 1: Prep Sample (Infinium LCG Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Infinium Kit (Infinium LCG Assay Manual v1.2)

Master Step Name = Select Infinium Kit-Infinium LCG v1.2
Step Type = No Outputs

Automations

Set Infinium LCG Kit Name

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 'input.::Infinium Kit Name:: = step.::Infinium LCG Kits::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

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

Step 2: Quantify DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Quantify DNA-Infinium PicoGreen v1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1X TE
- Lambda DNA
- PicoGreen dsDNA quantification reagent

Automations

Calculate Stock Lambda DNA and PicoGreen Dilution

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.::Stock Lambda DNA for A1 (uL):: = (233.3 * 75) / step.::Stock Lambda DNA (ng/uL):: ; step.::1X TE for A1 (uL):: = 233.3 - step.::Stock Lambda DNA for A1 (uL):: ; if (step.::No. of QDNA Plates:: == 1) {step.::PicoGreen (uL):: = 115 ; step.::1X TE (mL):: = 23} ; if (step.::No. of QDNA Plates:: == 2) {step.::PicoGreen (uL):: = 215 ; step.::1X TE (mL):: = 43} ; if (step.::No. of QDNA Plates:: == 3) {step.::PicoGreen (uL):: =  315 ; step.::1X TE (mL):: = 63}' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Placement = Enabled

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

Record Details

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

Step 3: Amplify DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Amplify DNA-Infinium LCG v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MSM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH
- RPM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Validate MSA6 Plate Barcode and Set Sample Placement Information

Trigger Location = Placement
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 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA6:: ) ) {fail ( ::Invalid MSA6 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA6:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

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.::Infinium Kit Name:: = input.::Infinium Kit Name::' -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 = Same Shape
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 = Row
- Table Columns - Global Fields

Step 4: Incubate DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Incubate DNA-Infinium v1.2
Step Type = No Outputs

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)

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

Step 5: Fragment DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Fragment DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- FMS-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: Precipitate DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Precipitate DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- 100% 2-propanol
- PM1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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 7: Resuspend DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Resuspend DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: BeadChip Processing (Infinium LCG Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to LCG BeadChip (Infinium LCG Assay Manual v1.2)

Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- PB2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC4-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Generate Sample Placement for Infinium BeadChip

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/infinium/placementpatterns"

Validate BeadChip Barcode

Trigger Location = Placement
Trigger Style = Automatic upon exit

/usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

Copy Sample Information

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.::Infinium Kit Name:: = input.::Infinium Kit Name:: ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode:: ; output.::Sample_Plate:: = input.::Sample_Plate:: ; output.::Sample_Well:: = input.::Sample_Well:: ; output.::BeadChip Barcode:: = output.container.name ; output.::BeadChip Position:: = output.well' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 8x1 LCG BeadChip

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

Step 2: Wash BeadChip (Infinium LCG Assay Manual v1.2)

Master Step Name = Wash BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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

Step 3: Extend and Stain BeadChip (Infinium LCG Assay Manual v1.2)

Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- 70% EtOH
- ATM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- EML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- SML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC3-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC4-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Set Array Instrument

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 -exp 'input.::Array Instrument:: = ::iScan::' -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}"

Routing Script - iScan

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 'Array Instrument' \
--FIELD_VALUE 'iScan' \
--WORKFLOW 'iScan v1.0' \
--STEP 'Image Infinium BeadChip (iScan v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

Queue/Ice Bucket

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

Record Details

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

Infinium HD Methylation Assay Manual v1.2

Overview

The Infinium HD Methylation Assay Manual workflow includes the following functionality.

Preconfigured protocols to prepare 96 DNA samples for use with the 8x1 HD BeadChip products.
Automated calculation of sample and buffer volumes.
Automatic placement of samples when necessary.
Automatic step transition when required.
Automatic calculation or display of reagents at every step in the protocol.

Protocol 1: Prep Sample (Infinium HD Methylation Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Infinium Kit (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Select Infinium Kit-Infinium HD Methylation v1.2
Step Type = No Outputs

Automations

Set Infinium HD Methylation Kit Name

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 'input.::Infinium Kit Name:: = step.::Infinium HD Methylation Kits::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

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

Step 2: Quantify DNA (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Quantify DNA-Infinium PicoGreen v1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1X TE
- Lambda DNA
- PicoGreen dsDNA quantification reagent

Automations

Calculate Stock Lambda DNA and PicoGreen Dilution

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.::Stock Lambda DNA for A1 (uL):: = (233.3 * 75) / step.::Stock Lambda DNA (ng/uL):: ; step.::1X TE for A1 (uL):: = 233.3 - step.::Stock Lambda DNA for A1 (uL):: ; if (step.::No. of QDNA Plates:: == 1) {step.::PicoGreen (uL):: = 115 ; step.::1X TE (mL):: = 23} ; if (step.::No. of QDNA Plates:: == 2) {step.::PicoGreen (uL):: = 215 ; step.::1X TE (mL):: = 43} ; if (step.::No. of QDNA Plates:: == 3) {step.::PicoGreen (uL):: =  315 ; step.::1X TE (mL):: = 63}' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Placement = Enabled

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

Record Details

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

Step 3: Bisulfite Conversion (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Bisulfite Conversion-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- EZ DNA Methylation Kit
  - Supplier = Zymo Research
  - Website = https://www.zymoresearch.com/collections/ez-dna-methylation-kits

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)

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

Step 4: Create BCD Plate (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Create BCD Plate-Infinium v1.2
Step Type = Standard
Reagent Kits
- EZ DNA Methylation Kit
  - Supplier = Zymo Research
  - Website = https://www.zymoresearch.com/collections/ez-dna-methylation-kits

Automations

Set DNA Plate Barcode

Trigger Location = Placement
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 'output.::DNA Plate Barcode:: = input.container.name' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

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.::Infinium Kit Name:: = input.::Infinium Kit Name::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Record Details

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

Step 5: Amplify DNA (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Amplify DNA-Infinium HD Methylation v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MSM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH
- RPM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Validate MSA4 Plate Barcode and Set Sample Placement Information

Trigger Location = Placement
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 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA4:: ) ) {fail ( ::Invalid MSA4 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA4:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode::}' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

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.::Infinium Kit Name:: = input.::Infinium Kit Name::' -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 = Same Shape
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 = Row
- Table Columns - Global Fields

Step 6: Incubate DNA (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Incubate DNA-Infinium v1.2
Step Type = No Outputs

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)

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

Step 7: Fragment DNA (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Fragment DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- FMS-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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 8: Precipitate DNA (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Precipitate DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- 100% 2-propanol
- PM1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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 9: Resuspend DNA (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Resuspend DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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: BeadChip Processing (Infinium HD Methylation Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to HD BeadChip (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 70% EtOH
- PB2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC4-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Generate Sample Placement for Infinium BeadChip

Trigger Location = Placement
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/infinium/placementpatterns"

Validate BeadChip Barcode

Trigger Location = Placement
Trigger Style = Automatic upon exit

/usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

Copy Sample Information

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.::Infinium Kit Name:: = input.::Infinium Kit Name:: ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode:: ; output.::Sample_Plate:: = input.::Sample_Plate:: ; output.::Sample_Well:: = input.::Sample_Well:: ; output.::BeadChip Barcode:: = output.container.name ; output.::BeadChip Position:: = output.well' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 8x1 HD BeadChip

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

Step 2: Wash BeadChip (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Wash BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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)

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

Step 3: Extend and Stain BeadChip (Infinium HD Methylation Assay Manual v1.2)

Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
- ATM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- EDTA
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- STM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- TEM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC3-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC4-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Set Array Instrument

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 -exp 'input.::Array Instrument:: = ::iScan::' -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}"

Routing Script - iScan

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 'Array Instrument' \
--FIELD_VALUE 'iScan' \
--WORKFLOW 'iScan v1.0' \
--STEP 'Image Infinium BeadChip (iScan v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

Queue/Ice Bucket

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

Record Details

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