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Standard v1.1

Protocol 1: Standard Workflow (AmpliSeq for Illumina Custom DNA Panel v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)

Step 2: Amplify Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs

Automations

Count Samples and Calculate Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Calculate Total Samples and Calculate Master Mix

Trigger Location = Not Used

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)

Step 3: Perform Second Clean Up (AmpliSeq for Illumina Custom DNA Panel v1.1)

Master Step Name = Perform Second Clean Up (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)

Standard v1.1

Protocol 1: Standard Workflow (AmpliSeq for Illumina Custom DNA Panel v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)

Step 2: Amplify Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs

Automations

Count Samples and Calculate Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Calculate Total Samples and Calculate Master Mix

Trigger Location = Not Used

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)

Step 3: Perform Second Clean Up (AmpliSeq for Illumina Custom DNA Panel v1.1)

Master Step Name = Perform Second Clean Up (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)

Category

Field Name

Field Type

Options

Additional Options and Dropdown Items

Container

Container Name

Built-in

Container

LIMS ID (Container)

Built-in

Category

Field Name

Field Type

Options

Additional Options and Dropdown Items

Container

Container Name

Built-in

Container

LIMS ID (Container)

Built-in

Category

Field Name

Field Type

Options

Additional Options and Dropdown Items

Container

Container Name

Built-in

Container

LIMS ID (Container)

Built-in

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
      -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'step.::1X Lib AMP Mix (uL):: = step.::Total Samples:: * 1.1 * 45 ; \
step.::10X Library Amp Primers (uL):: = step.::Total Samples:: * 1.1 * 5' \
      -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \ -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \ step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \ -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
      -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'step.::1X Lib AMP Mix (uL):: = step.::Total Samples:: * 1.1 * 45 ; \
step.::10X Library Amp Primers (uL):: = step.::Total Samples:: * 1.1 * 5' \
      -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \ -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \ step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \ -log {compoundOutputFileLuid0}"

Standard v1.1

hashtagProtocol 1: Standard Workflow (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagStep 1: Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 2: Amplify Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 3: Perform Second Clean Up (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

Standard v1.1

hashtagProtocol 1: Standard Workflow (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagStep 1: Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 2: Amplify Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 3: Perform Second Clean Up (AmpliSeq for Illumina Custom DNA Panel v1.1)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

Protocol 1: Standard Workflow (AmpliSeq for Illumina Custom DNA Panel v1.1)

Step 1: Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Automations

Queue/Ice Bucket

Record Details

Step 2: Amplify Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Automations

Queue/Ice Bucket

Record Details

Step 3: Perform Second Clean Up (AmpliSeq for Illumina Custom DNA Panel v1.1)

Automations

Queue/Ice Bucket

Record Details

Protocol 1: Standard Workflow (AmpliSeq for Illumina Custom DNA Panel v1.1)

Step 1: Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Automations

Queue/Ice Bucket

Record Details

Step 2: Amplify Library (AmpliSeq for Illumina Custom DNA Panel v1.1)

Automations

Queue/Ice Bucket

Record Details

Step 3: Perform Second Clean Up (AmpliSeq for Illumina Custom DNA Panel v1.1)

Automations

Queue/Ice Bucket

Record Details