Illumina DNA Prep with Enrichment (S) Tagmentation v1.2

Protocol 1: Prep Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = No Outputs

Automations

Sort & Set Next Step
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (input.::NFE Sample Type:: == ::Blood:: ) {nextStep=::Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \
if (input.::NFE Sample Type:: == ::Saliva:: ) {nextStep=::Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \
if (input.::NFE Sample Type:: == ::gDNA:: ) {nextStep=::Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \
if (input.::NFE Sample Type:: == ::FFPE DNA::) {nextStep=::Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: }' \
-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 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

      NFE Sample Type

      Text Dropdown

      Required Field

      Presets

      • Blood

      • Saliva

      • gDNA

      • FFPE DNA

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 2: Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Agencourt AMPure XP beads, 5 ml

    • Flex Lysis Reagent Kit

Automations

Calculate Total Samples & Master Mix
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
step.::BLB (uL):: = step.::Total Samples:: * 1.1 * 7 ; \
step.::PK1 (uL):: = step.::Total Samples:: * 1.1 * 2 ; \
step.::Water (uL):: = step.::Total Samples:: * 1.1 * 31' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
Route NFE - Blood
  • Trigger Location = Step

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'NFE Sample Type' \
--FIELD_VALUE 'Blood' \
--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.2' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    BLB (uL)

    Numeric

    Decimal Places Displayed = 2

    PK1 (uL)

    Numeric

    Decimal Places Displayed = 2

    Thermal Cycler Program

    Text

    Default = BLP

    Total Samples

    Numeric

    Default = 0

    Water (uL)

    Numeric

    Decimal Places Displayed = 2

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 3: Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Agencourt AMPure XP, 5 ml

      • Supplier = Beckman Coulter

      • Catalog Number = A63880

Automations

Copy NFE Sample Type and Set UDFs
  • 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.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
output.::Sample Volume (uL):: = 30 ; \
output.::80% EtOH (uL):: = 150 ; \
output.::Water for Resuspension (uL):: = 30' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::REMOVE::' -log {compoundOutputFileLuid0}"
Route NFE - Saliva
  • 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 'NFE Sample Type' \
--FIELD_VALUE 'Saliva' \
--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.2' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

  • 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

      80% EtOH (uL)

      Numeric

      Derived Sample

      NFE Sample Type

      Text Dropdown

      Required Field

      Presets

      • Blood

      • Saliva

      • gDNA

      • FFPE DNA

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Water for Resuspension (uL)

      Numeric

      Default = 30

      Project

      Project Name

      Built-in

Step 4: Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Assign QC flags
  • Trigger Location = Record Details

  • Trigger Style = Manual button

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

      • File Attachment Method = Manual

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      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 5: Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Copy Concentration
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

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

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'if (!output.hasValue(::Conc. Units::) || output.::Conc. Units:: != ::ng/uL::) { fail(::This automation expects Conc. Units to be ng/uL.::) ; };\
output.::Sample Volume (uL):: = (step.::Desired gDNA Concentration (ng/uL):: * step.::Total Volume (uL)::) / output.::Concentration::;\
output.::Dilution Volume (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::;\
output.::Final Concentration:: = step.::Desired gDNA Concentration (ng/uL)::;' \
-log {compoundOutputFileLuid0}"
Set Next Step - Remove & Copy NFE Sample Type
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::REMOVE:: ; \
output.::NFE Sample Type:: = input.::NFE Sample Type:: ;' \
-log {compoundOutputFileLuid0}"
Route NFE - gDNA
  • 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 'NFE Sample Type' \
--FIELD_VALUE 'gDNA' \
--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.2' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = 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 gDNA Concentration (ng/uL)

    Numeric

    Decimal Places Displayed = 2

    Dilution Buffer

    Text Dropdown

    Custom Entries

    Presets

    • RSB

    • 10 mM Tris-HCI, pH 7.5–8.5

    Total Volume (uL)

    Numeric

    Decimal Places Displayed = 2

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • File Column Options

      • File Column Display = Show

      • File Attachment Method = Manual

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      Required Field

      Derived Sample

      Dilution Volume (uL)

      Numeric

      Derived Sample

      Final Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (uL)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 6: Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Assign QC flags
  • Trigger Location = Record Details

  • Trigger Style = Manual button

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

      • File Attachment Method = Manual

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      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 7: Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Copy Concentration
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

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

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'if (!output.hasValue(::Conc. Units::) || output.::Conc. Units:: != ::ng/uL::) { fail(::This automation expects Conc. Units to be ng/uL.::) ; };\
output.::Sample Volume (uL):: = (step.::Desired gDNA Concentration (ng/uL):: * step.::Total Volume (uL)::) / output.::Concentration::;\
output.::Dilution Volume (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::;\
output.::Final Concentration:: = step.::Desired gDNA Concentration (ng/uL)::;' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance & Copy NFE Sample Type
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE:: ; \
output.::NFE Sample Type:: = input.::NFE Sample Type:: ;' \
-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 gDNA Concentration (ng/uL)

    Numeric

    Decimal Places Displayed = 2

    Dilution Buffer

    Text Dropdown

    Custom Entries

    Presets

    • RSB

    • 10 mM Tris-HCI, pH 7.5–8.5

    Total Volume (uL)

    Numeric

    Decimal Places Displayed = 2

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • File Column Options

      • File Column Display = Show

      • File Attachment Method = Manual

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      Required Field

      Derived Sample

      Dilution Volume (uL)

      Numeric

      Derived Sample

      Final Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (uL)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Protocol 2: Library Prep (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA Prep -Tagmentation (S) Beads

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

    • Illumina DNA/RNA Prep - Tagmentation PCR Reagents

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

Automations

Calculate Total Samples and Master Mix & Copy Conc. & NFE Sample Type
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
step.::eBLT (uL):: = step.::Total Samples:: * 1.1 * 11.5 ; \
step.::TB1 (uL):: = step.::Total Samples:: * 1.1 * 11.5 ; \
if (output.::NFE Sample Type::.contains(::Saliva::) || output.::NFE Sample Type::.contains(::Blood::)) {output.::Concentration:: = 100 ; output.::Conc. Units:: = ::ng/uL::} ; \
if (input.hasValue(::Final Concentration::)) {output.::Concentration:: = input.::Final Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::}' \
-log {compoundOutputFileLuid0}"
Calculate Sample Volume & Water
  • 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.::Sample Volume (uL):: = step.::Desired Input Amount (ng):: / output.::Concentration:: ; \
output.::Nuclease-free water (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Desired Input Amount (ng):: = step.::Desired Input Amount (ng):: ; ' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Desired Input Amount (ng)

    Numeric

    Range = 50 To 1000

    eBLT (uL)

    Numeric

    Notes

    Multiline Text

    Default = Desired Input Amount should be between 50-1000 ng.

    TB1 (uL)

    Numeric

    Thermal Cycler Instructions

    Multiline Text

    Default = Choose the preheat lid option and set to 100C Set the reaction volume to 50 uL 55C for 5 minutes Hold at 10C

    Thermal Cycler Program

    Text

    Default = TAG

    Total Samples

    Numeric

    Default = 0

    Total Volume (uL)

    Numeric

    Default = 30

  • 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

      Text

      Required Field

      Derived Sample

      Desired Input Amount (ng)

      Numeric

      Derived Sample

      NFE Sample Type

      Text Dropdown

      Required Field

      Presets

      • Blood

      • Saliva

      • gDNA

      • FFPE DNA

      Derived Sample

      Nuclease-free water (uL)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (uL)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 2: Post Tagmentation Cleanup (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Post Tagmentation Cleanup (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = No Outputs

  • Reagent Kits

    • Illumina DNA/RNA Prep - Tagmentation Buffers

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

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 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

      NFE Sample Type

      Text Dropdown

      Required Field

      Presets

      • Blood

      • Saliva

      • gDNA

      • FFPE DNA

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 3: Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Add Labels

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA Fast Hyb - Enrichment PCR + Buffers

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

Automations

Calculate Total Samples, Master Mix, Copy NFE Sample Type and Set PCR Cycles
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \
step.::EPM (uL):: = step.::Total Samples:: * 1.1 * 23 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 1.1 * 23 ; \
if (output.::NFE Sample Type:: == ::Saliva::) {output.::PCR Cycles:: = 9} ; \
if (output.::NFE Sample Type:: == ::Blood::) {output.::PCR Cycles:: = 9} ; \
if (output.::NFE Sample Type:: == ::gDNA::) {if (input.::Desired Input Amount (ng):: >= 10 && input.::Desired Input Amount (ng):: <= 49) {output.::PCR Cycles:: = 12}} ; \
if (output.::NFE Sample Type:: == ::gDNA::) {if (input.::Desired Input Amount (ng):: >= 50 && input.::Desired Input Amount (ng):: <= 1000) {output.::PCR Cycles:: = 9}} ; \
if (output.::NFE Sample Type:: == ::FFPE DNA::) {if (input.::Desired Input Amount (ng):: >= 50 && input.::Desired Input Amount (ng):: <= 1000) {output.::PCR Cycles:: = 12}}' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Placement = Enabled

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

    • Placement Pattern = Row

  • Destination Containers

    • 96 well plate

Add Labels

  • Label Groups

    • IDT for Illumina DNA-RNA UD Indexes Set A Tagmentation

    • IDT for Illumina DNA-RNA UD Indexes Set A-D Tagmentation

    • IDT for Illumina DNA-RNA UD Indexes Set B Tagmentation

    • IDT for Illumina DNA-RNA UD Indexes Set C Tagmentation

    • IDT for Illumina DNA-RNA UD Indexes Set D Tagmentation

    • Illumina DNA-RNA UD Indexes Set A B C D Tagmentation

    • Illumina DNA-RNA UD Indexes Set A Tagmentation

    • Illumina DNA-RNA UD Indexes Set B Tagmentation

    • Illumina DNA-RNA UD Indexes Set C Tagmentation

    • Illumina DNA-RNA UD Indexes Set D Tagmentation

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    EPM (uL)

    Numeric

    Nuclease-free water (uL)

    Numeric

    Thermal Cycler Program

    Text

    Default = eBLT PCR

    Thermal Cycler Program Instructions

    Multiline Text

    Default = Choose the preheat lid option and set to 100°C Set the reaction volume to 50 uL 72C for 3 minutes 98C for 3 minutes X cycles of: X = 98C for 20 seconds X = 0C for 30 seconds X = 72C for 1 minute 72C for 3 minutes Hold at 10C

    Total Samples

    Numeric

    Default = 0

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      NFE Sample Type

      Text Dropdown

      Required Field

      Presets

      • Blood

      • Saliva

      • gDNA

      • FFPE DNA

      Derived Sample

      PCR Cycles

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 4: Clean Up Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Clean Up Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Agencourt AMPure XP Beads

      • Supplier = Thermo

      • Catalog Number = NC9959336; NC9933872

    • Illumina DNA Prep -Tagmentation (S) Beads

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

      • Website = 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

    80% EtOH Prep Date

    Date

  • 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 5: Bioanalyzer QC Qualify Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Bioanalyzer QC Qualify Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Generate Bioanalyzer driver file
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \
      script:driver_file_generator \
        -i {processURI:v2} \
        -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv \
        -o {compoundOutputFileLuid0}.csv \
        -l {compoundOutputFileLuid1}  \
      && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:addBlankLines \
        -i {stepURI:v2} \
        -f {compoundOutputFileLuid0}.csv \
        -l {compoundOutputFileLuid1} \
        -sep COMMA \
        -b ',False,' \
        -h 1 \
        -c LIMSID \
        -pre 'Sample '"
Parse Bioanalyzer XML and assign QC flags
  • Trigger Location = Record Details

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Placement = Enabled

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

    • Placement Pattern = Row

  • Destination Containers

    • BioAnalyzer DNA High Sensitivity Chip

    • BioAnalyzer DNA 1000 Chip

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 = Peak 2 Size - bp

    Criteria 1 - Threshold Value

    Numeric

    Default = 300

    Criteria 2 - Operator

    Text

    Default = <=

    Criteria 2 - Source Data Field

    Text

    Default = Peak 2 Size - bp

    Criteria 1 - Threshold Value

    Numeric

    Default = 400

    Use strict matching for Bioanalyzer results

    Toggle Switch

    Default = None Set

  • Step File Placeholders

    • Bioanalyzer Input File - Automatically attached

    • Bioanalyzer Input File Generation Log File - Automatically attached

    • Bioanalyzer XML Result File (required) - Manually uploaded

    • Result File (optional) - Manually uploaded

    • PDF Summary File (optional) - Manually uploaded

    • Bioanalyzer XML Parsing Log File - Automatically attached

    • QC Assignment Log File - Automatically attached

    • QC Assignment Report - Automatically attached

  • Sample Table

    • Enable QC Flags = Yes

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • File Column Options

      • File Column Display = Show

      • File Attachment Method = Manual

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Measurement

      A260/280 ratio

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Number of Peaks found

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Number of Regions found

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 1 % Integrated Area

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 1 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 1 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 1 MW

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 1 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 2 % Integrated Area

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 2 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 2 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 2 MW

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 2 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 3 % Integrated Area

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 3 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 3 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 3 MW

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 3 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 4 % Integrated Area

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 4 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 4 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 4 MW

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 4 Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 5 % Integrated Area

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 5 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 5 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Peak 5 MW

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Peak 5 Size - bp

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 1 % of Total

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 1 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 1 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 1 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 2 % of Total

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 2 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 2 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 2 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 3 % of Total

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 3 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 3 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 3 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 4 % of Total

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 4 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 4 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 4 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 5 % of Total

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 5 Average Size - bp

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Region 5 Conc.

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Region 5 Molarity

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Sample Comment

      Text

      Project

      Project Name

      Built-in

Step 6: Pool Pre-Enriched Libraries - Volume (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Pool Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Pooling

  • Aliquot Generation = Fixed, 1

  • Naming Convention = {PoolName}

  • Reagent Kits

    • Agencourt AMPure XP Beads

      • Supplier = Thermo

      • Catalog Number = NC9959336; NC9933872

    • Illumina DNA Prep -Tagmentation (S) Beads

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

      • Website = illumina.com

Automations

Calculate Pre-Enriched Library Volume & RSB Volume
  • Trigger Location = Record Details

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (step.::Library Pool Plexity:: == ::1-plex::) {output.::Pre-Enriched Library Volume (uL):: = 14} ; \
if (step.::Library Pool Plexity:: == ::12-plex::) {output.::Pre-Enriched Library Volume (uL):: = 2.5} ; \
output.::RSB Volume (uL):: = step.::Total Pooled Volume (uL):: - output.::Pre-Enriched Library Volume (uL)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Hybridize Probes
  • 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 = ::Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)::' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Pooling

  • Label Uniqueness = On

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

Placement = Enabled

  • Defaults

    • Well Sort Order = Row

    • Placement Pattern = Row

  • Destination Containers

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Library Pool Plexity

    Text Dropdown

    • Required Field

    • Custom Entries

    Presets

    • 1-plex

    • 12-plex

    Total Pooled Volume (uL)

    Numeric

    • Read Only

    Default = 30

  • 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

      Pre-Enriched Library Volume (uL)

      Numeric

      Derived Sample

      RSB Volume (uL)

      Numeric

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 7: Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Assign QC flags
  • Trigger Location = Record Details

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"
Set Next Step 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 1 - 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

      Sample Name

      Built-in

      Measurement

      Concentration

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Conc. Units

      Text

      Project

      Project Name

      Built-in

Step 8: Pool Pre-Enriched Libraries - Mass (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Pool Pre-Enriched Libraries - Mass (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Pooling

  • Aliquot Generation = Fixed, 1

  • Naming Convention = {PoolName}

Automations

Copy Concentration
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
 -t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-log {compoundOutputFileLuid0}"
Calculate Pre-Enriched Library Volume & RSB Volume
  • Trigger Location = Record Details

  • Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (step.::Library Pool Plexity:: == ::1-plex::) {output.::Pre-Enriched Library Volume (uL):: = 14} ; \
if (step.::Library Pool Plexity:: == ::12-plex::) {output.::Pre-Enriched Library Volume (uL):: = 2.5} ; \
output.::RSB Volume (uL):: = step.::Total Pooled Volume (uL):: - output.::Pre-Enriched Library Volume (uL)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Pooling

  • Label Uniqueness = On

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

Placement = Enabled

  • Defaults

    • Well Sort Order = Row

    • Placement Pattern = Row

  • Destination Containers

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Library Pool Plexity

    Text Dropdown

    Required Field

    Presets

    • 1-plex

    • 12-plex

    Pre-Enriched Library Sample (ng)

    Numeric

    Read Only

    Default = 500

    Total Pooled Volume (uL)

    Numeric

    Read Only

    Default = 30

  • 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

      Text

      Required Field

      Derived Sample

      Pre-Enriched Library Volume (uL)

      Numeric

      Derived Sample

      RSB Volume (uL)

      Numeric

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 9: Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA Fast Hyb - Enrichment Beads + Buffers

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

    • Illumina DNA Fast Hyb - Enrichment PCR + Buffers

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

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

    PCR Cycles

    Numeric

    Thermal Cycler Program

    Text

    Default = NF-HYB program

  • 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 10: Capture Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Capture Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA Fast Hyb - Enrichment Beads + Buffers

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

    • Illumina DNA Fast Hyb - Enrichment PCR + Buffers

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

Automations

Calculate Total Samples and Calculate Master Mix
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::EE1 (uL):: = step.::Total Samples:: * 1.1 * 28.5 ; \
step.::HP3 (uL):: = step.::Total Samples:: * 1.1 * 1.5 ;' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    EE1 (uL)

    Numeric

    Decimal Places Displayed = 2

    HP3 (uL)

    Numeric

    Decimal Places Displayed = 2

    Total Samples

    Numeric

    Default = 0

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 11: Amplify Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Amplify Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA Fast Hyb - Enrichment PCR + Buffers

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

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

    PCR Cycles

    Numeric

    Thermal Cycler Program

    Text

    Default = AMP

  • 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 12: Clean Up Amplified Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Master Step Name = Clean Up Amplified Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Agencourt AMPure XP Beads

      • Supplier = Thermo

      • Catalog Number = NC9959336; NC9933872

    • Illumina DNA Prep -Tagmentation (S) Beads

      • Supplier = Illumina

      • Catalog Number = 20025519; 20025520

      • Website = 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 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

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