Library Preparation v1.1

Protocol 1: Library Prep (AmpliSeq for Illumina Custom DNA Panel v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Dilute DNA (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Dilute DNA (AmpliSeq for Illumina Custom DNA Panel)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • Website = www.illumina.com

Automations

Copy Concentration and Set Sample Volume

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"

Calculate Input Amount, Total Volume & Low TE - Custom DNA Panel

• 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.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL)::' \
        -log {compoundOutputFileLuid0}"

Calc Input Amount, Total Volume & Low TE - Custom DNA - Final Conc.

• 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 true \
        -h false \
        -exp 'output.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Final Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Desired Final Concentration (ng/uL):: = step.::Desired Final Concentration (ng/uL)::' \
        -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 = Row

• Sample Table (Column Headers)

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Desired Concentration (ng/uL)	Numeric		Range = 20 To 50
  Directions	Multiline Text	Read Only	Default = If enough DNA is available, dilute to intermediate concentration of ~20-50 ng/uL.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Conc. Units	Numeric	Required Field
    Derived Sample	Input Amount (ng)	Numeric		Decimal Places Displayed = 0
    Derived Sample	Low TE (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Total Volume (uL)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

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

• Master Step Name = Qubit (AmpliSeq for Illumina v1.1)

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName}

Automations

Assign QC flags (Qubit QC)

• Trigger Location = Record Details

• Trigger Style = Manual button

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

Set Next Step 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 = ::ADVANCE:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Criteria 1 - Operator	Text		Default = >=
  Criteria 1 - Source Data Field	Text		Default = Concentration
  Criteria 1 - Threshold Value	Numeric
  Criteria 2 - Operator	Text		Default = <=
  Criteria 2 - Source Data Field	Text		Default = Concentration
  Criteria 2 - Threshold Value	Numeric

• 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 = Row

  • File Column Options

    • File Column Display = Hide

    • File Attachment Method = Auto

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Conc. Units	Text	Required Field
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Project	Project Name	Built-in

Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Dilute DNA (AmpliSeq for Illumina Custom DNA Panel)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • Website = www.illumina.com

Automations

Copy Concentration and Set Sample Volume

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"

Calc Input Amount, Total Volume & Low TE - Custom DNA - Final Conc.

• 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.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Final Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Desired Final Concentration (ng/uL):: = step.::Desired Final Concentration (ng/uL)::' \
        -log {compoundOutputFileLuid0}"

Calculate Input Amount, Total Volume & Low TE - Custom DNA Panel

• 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 true \
        -h false \
        -exp 'output.::Input Amount (ng):: = output.::Concentration:: * output.::Sample Volume (uL):: ; \
output.::Total Volume (uL):: = output.::Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL)::' \
        -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 = Row

• Sample Table (Column Headers)

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Desired Final Concentration (ng/uL)	Numeric		Range = 2 To 8

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Conc. Units	Numeric	Required Field
    Derived Sample	Desired Final Concentration (ng/uL)	Numeric
    Derived Sample	Low TE (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Total Volume (uL)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 4: Amplify Targets - One Primer Pool (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Custom DNA Panel for Illumina

    • Supplier = Illumina

    • Catalog Number = 20020495

    • Website = www.illumina.com

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • Website = www.illumina.com

Automations

Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

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

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  2X AmpliSeq Custom DNA Panel	Numeric		Decimal Places Displayed = 1
  5X AmpliSeq HiFi Mix (uL)	Numeric		Decimal Places Displayed = 1
  PCR Cycles	Numeric
  Recommended Prep Input (ng)	Multiline Text	Read Only	Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
  Thermal Cycler Program	Text		Default = AMP_DNA
  Total Samples	Numeric		Default = 0 Decimal Places Displayed = 0

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Diluted DNA Conc. (ng/uL)	Numeric
    Derived Sample	DNA Volume (uL)	Numeric
    Derived Sample	Master Mix (uL)	Numeric
    Derived Sample	Nuclease-free water (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Prep Input Amount (ng)	Numeric	Required Field	Range = 2 To 200 Decimal Places Displayed = 0
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 5: Amplify Targets - Two Primer Pools (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Custom DNA Panel for Illumina

    • Supplier = Illumina

    • Catalog Number = 20020495

    • Website = www.illumina.com

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • Website = www.illumina.com

Automations

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

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

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  PCR Cycles	Numeric
  Recommended Prep Input (ng)	Multiline Text	Read Only	Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
  Thermal Cycler Program	Text		Default = AMP_DNA

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	5X AmpliSeq HiFi Mix (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Diluted DNA Conc. (ng/uL)	Numeric
    Derived Sample	DNA Volume (uL)	Numeric
    Derived Sample	Nuclease-free water (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Prep Input Amount (ng)	Numeric	Required Field	Range = 2 To 200 Decimal Places Displayed = 0
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 6: Amplify Targets - Three Primer Pool (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Custom DNA Panel for Illumina

    • Supplier = Illumina

    • Catalog Number = 20020495

    • Website = www.illumina.com

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • Website = www.illumina.com

Automations

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  PCR Cycles	Numeric
  Recommended Prep Input (ng)	Multiline Text	Read Only	Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
  Thermal Cycler Program	Text		Default = AMP_DNA

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	5X AmpliSeq HiFi Mix (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Diluted DNA Conc. (ng/uL)	Numeric
    Derived Sample	DNA Volume (uL)	Numeric
    Derived Sample	Nuclease-free water (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Prep Input Amount (ng)	Numeric	Required Field	Range = 2 To 200 Decimal Places Displayed = 0
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 7: Amplify Targets - Four Primer Pool (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Amplify Targets (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Custom DNA Panel for Illumina

    • Supplier = Illumina

    • Catalog Number = 20020495

    • Website = www.illumina.com

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • Website = www.illumina.com

Automations

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 4 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 9 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 22.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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

Copy Desired Final Conc. & Calculate Master Mix, Total Sample, DNA Volume, Water - Custom DNA 1 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::Master Mix (uL):: = 14 ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::5X AmpliSeq HiFi Mix (uL):: = step.::Total Samples:: *1.1* 4 ; \
step.::2X AmpliSeq Custom DNA Panel:: = step.::Total Samples:: * 1.1 * 10 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 6) {output.::Nuclease-free water (uL):: = 20 -(output.::Master Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 2 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 7.5) {output.::Nuclease-free water (uL):: = 12.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Copy Desired DNA Conc. and Calc DNA Vol & Water - Custom DNA 3 Primer Pool

• 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.::Diluted DNA Conc. (ng/uL):: = input.::Desired Final Concentration (ng/uL):: ; \
output.::5X AmpliSeq HiFi Mix (uL):: = 5 ; \
output.::DNA Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Diluted DNA Conc. (ng/uL):: ; \
if (output.::DNA Volume (uL):: < 10.5) {output.::Nuclease-free water (uL):: = 17.5 - (output.::5X AmpliSeq HiFi Mix (uL):: + output.::DNA Volume (uL)::)}' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

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

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  PCR Cycles	Numeric
  Recommended Prep Input (ng)	Multiline Text	Read Only	Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
  Thermal Cycler Program	Text		Default = AMP_DNA

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	5X AmpliSeq HiFi Mix (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Diluted DNA Conc. (ng/uL)	Numeric
    Derived Sample	DNA Volume (uL)	Numeric
    Derived Sample	Nuclease-free water (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Prep Input Amount (ng)	Numeric	Required Field	Range = 2 To 200 Decimal Places Displayed = 0
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 8: Partially Digested Amplicons (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina v1.1)

• Step Type = No Outputs

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • 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)

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Thermal Cycler Program	Text		Default = FUPA

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

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

Step 9: Ligate Indexes (AmpliSeq for Illumina Custom DNA Panel v1.1)

• Master Step Name = Ligate Indexes (AmpliSeq for Illumina v1.1)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

    • 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}"

Route AmpliSeq Samples - Custom DNA Panel

• 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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - Immune Repertoire Panel

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - BRCA

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina BRCA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina BRCA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - Childhood Cancer Panel

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - CHP v2

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - CP

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - Focus Panel

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - Immune Response Panel

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples - Myeloid Panel

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Route AmpliSeq Samples -Transcriptome Human GEx Panel

• Trigger Location = Not Used

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 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ️ The workflow version and step version for the routing script 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)

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

Add Labels

• Label Groups

  • AmpliSeq CD Indexes Set A for Illumina

  • AmpliSeq CD Indexes Set B for Illumina

  • AmpliSeq CD Indexes Set C for Illumina

  • AmpliSeq CD Indexes Set D for Illumina

  • AmpliSeq UD Indexes for Illumina (24 Indexes)

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Thermal Cycler Program	Text		Default = LIGATE

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	AmpliSeq Workflow	Text Dropdown	Required Field	Preset Standard Workflow Equalizer Workflow
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in