TruSeq DNA PCR-Free v2.0

Protocol 1: TruSeq DNA PCR-Free v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Fragment DNA (TruSeq DNA PCR-Free v2.0)

• Master Step Name = Fragment DNA v1.0

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box

    • Supplier = Illumina

    • Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

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 ( step.::Target Insert Size (bp):: == 350 ) { output.::Sample Volume (ul):: = 1000 / output.::Concentration:: } ; if ( step.::Target Insert Size (bp):: == 550 ) { output.::Sample Volume (ul):: = 2000 / output.::Concentration:: } ; output.::RSB Volume (ul):: = 55 - output.::Sample Volume (ul):: ; output.::Target Insert Size (bp):: = step.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

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

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if ( step.::Target Insert Size (bp):: == 350 ) { output.::Sample Volume (ul):: = 100 / output.::Concentration:: } ; if ( step.::Target Insert Size (bp):: == 550 ) { output.::Sample Volume (ul):: = 200 / output.::Concentration:: } ; output.::RSB Volume (ul):: = 52.5 - output.::Sample Volume (ul):: ; output.::Target Insert Size (bp):: = step.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table

  • Column Headers

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Cycles/Burst	Numeric Dropdown	Custom Entries	Presets 200
  Duration (seconds)	Numeric Dropdown	Custom Entries	Presets 65 50 45 25 Decimal Places Displayed = 0
  Duty Factor (%)	Numeric Dropdown	Custom Entries	Presets 20 5 10 Decimal Places Displayed = 0
  Intensity	Numeric Dropdown	Custom Entries	Presets 5 2 Decimal Places Displayed = 1
  Mode	Text Dropdown	Custom Entries	Presets Frequency sweeping -
  Peak/Displayed Power (W)	Numeric Dropdown	Custom Entries	Presets 50 175 23 14 9 7 Decimal Places Displayed = 0
  Target Insert Size (bp)	Numeric Dropdown	Required Field Custom Entries	Presets 350 550 Decimal Places Displayed = 0
  Temperature (oC)	Numeric Dropdown	Custom Entries	Presets 20 6
  80% EtOH Prep Date	Date

• Step File Placeholders

  • Log file - 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	Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Conc. Units	Text	Required Field
    Derived Sample	RSB Volume (ul)	Numeric	Read Only	Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Project	Project Name	Built-in

Step 2: Repair Ends and Select Library Size (TruSeq DNA PCR-Free v2.0)

• Master Step Name = Repair Ends v1.0

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box

    • Supplier = Illumina

    • Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

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 Number of Samples:: = step.::Total Number of 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 'if(input.::Target Insert Size (bp):: == 350) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 109.25) / 1000} ; if(input.::Target Insert Size (bp):: == 350) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 74.75) / 1000 } ; if(input.::Target Insert Size (bp):: == 550) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 92) / 1000} ; if(input.::Target Insert Size (bp):: == 550) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 92) / 1000 } ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

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

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table

  • Column Headers

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  SPB (ml)	Numeric		Decimal Places Displayed = 2
  PCR Grade Water (ml)	Numeric		Decimal Places Displayed = 2
  Thermal Cycler Program	Text		Default = ERP

• Step File Placeholders

  • Next Step 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	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Project	Project Name	Built-in

Step 3: Adenylate 3' Ends (TruSeq DNA PCR-Free v2.0)

• Master Step Name = Adenylate 3' Ends v2.0

• Step Type = No Outputs

• Reagent Kits

  • TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box

    • Supplier = Illumina

    • Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

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	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Thermal Cycler Program	Text		Default = ATAIL70

• Step File Placeholders

  • Log File - 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	Sample Name	Built-in
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Project	Project Name	Built-in

Step 4: Ligate Adapters (TruSeq DNA PCR-Free v2.0)

• Master Step Name = Ligate Adapters v2.0

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box

    • Supplier = Illumina

    • Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

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.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

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

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

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table

  • Column Headers

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

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

Add Labels

• Label Groups

  • TruSeq DNA HT

  • TruSeq DNA LT

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Thermal Cycler Program	Text		Default = LIG
  80% EtOH Prep Date	Date

• Step File Placeholders

  • Log File - 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	Reagent Name	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Project	Project Name	Built-in

Step 5: Clean Up Ligated Fragments (TruSeq DNA PCR-Free v2.0)

• Master Step Name = Clean Up Ligated Fragments (TruSeq DNA PCR-Free v2.0.10)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

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

Automations

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.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp '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
  Comment	Multiline Text
  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 6: Validate Libraries (TruSeq DNA PCR-Free v2.0)

• Master Step Name = Validate Libraries (TruSeq DNA PCR-Free v2.0.10)

• Step Type = Standard QC

• Measurement Generation = Fixed, 4

• Naming Convention = {SubmittedSampleName}_{OutputItemSubsetNumber} of {OutputItemSubsetTotal}

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

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (output.name.contains(::_1 of 4::)) {output.::Dilution Factor:: = ::1:10000::} ; if (output.name.contains(::_2 of 4::)) {output.::Dilution Factor:: = ::1:10000::} ; if (output.name.contains(::_3 of 4::)) {output.::Dilution Factor:: = ::1:20000::} ; if (output.name.contains(::_4 of 4::)) {output.::Dilution Factor:: = ::1:20000::}' -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp ' if (output.::Dilution Factor:: == ::1:10000:: && input.::Target Insert Size (bp):: == 350) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 10000) * (452 / 470)) / 1000} ; if (output.::Dilution Factor:: == ::1:20000:: && input.::Target Insert Size (bp):: == 350) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 20000) * (452 / 470)) / 1000} ; if (output.::Dilution Factor:: == ::1:10000:: && input.::Target Insert Size (bp):: == 550) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 10000) * (452 / 670)) / 1000} ; if (output.::Dilution Factor:: == ::1:20000:: && input.::Target Insert Size (bp):: == 550) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 10000) * (452 / 670)) / 1000}' -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:computeReplicateAverage -src 'Molarity (nM)' -dest 'Molarity (nM)' -exclude 'Exclude' -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 true -h false -exp 'if (output.::Molarity (nM):: >= 2 && output.::Molarity (nM):: <= 75) { output.QC = true } else { output.QC = false } ; if (input.::Molarity (nM):: >= 2 && input.::Molarity (nM):: <= 75) { input.QC = true } else { input.QC = false }' -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -excludeControls true -exp 'if (input.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -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 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
    Derived Sample	Concentration (pM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Dilution Factor	Text Dropdown	Required Field Custom Entries	Presets 1:10000 1:20000
    Derived Sample	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Target Insert Size (bp)	Numeric Dropdown	Custom Entries	Presets 350 550 Decimal Places Displayed = 0
    Measurement	Concentration (pM)	Numeric		Decimal Places Displayed = 2
    Measurement	Dilution Factor	Text	Read Only
    Measurement	Exclude	Toggle Switch		Default = None Set
    Measurement	Molarity (nM)	Numeric		Decimal Places Displayed = 2

Step 7: Normalize Libraries (TruSeq DNA PCR-Free v2.0)

• Master Step Name = Normalize Libraries 2 v2.0.10

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

ℹ️ The version of Normalized Libraries 2 master step name may be different depending on the version of IPP installed.

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = step.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = ((output.::Molarity (nM):: * step.::Sample Volume (ul)::) / step.::Target Normalization (nM)::) - step.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -log {compoundOutputFileLuid0}"

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

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'MiSeq' \
--WORKFLOW 'MiSeq Sequencing v3.2' \
--STEP 'Library Pooling (MiSeq v3.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq' \
--WORKFLOW 'NextSeq 500/550 Sequencing v1.2' \
--STEP 'Library Pooling (NextSeq 500/550 v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 2.0' \
--WORKFLOW 'NovaSeq 6000 v2.3' \
--STEP 'Define Run Format (NovaSeq 6000 v2.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 3.0' \
--WORKFLOW 'NovaSeq 6000 v3.8' \
--STEP 'Define Run Format (NovaSeq 6000 v3.8)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeqDx' \
--WORKFLOW 'NovaSeqDx v1.2' \
--STEP 'Define Run Format (NovaSeqDx v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000' \
--WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series' \
--WORKFLOW 'NovaSeq X Series v1.1' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \
--WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

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
  Comment	Multiline Text
  Sample Volume (ul)	Numeric	Required Field	Default = 10 Decimal Places Displayed = 0
  Target Normalization (nM)	Numeric	Required Field	Default = 10 Decimal Places Displayed = 0

• Step File Placeholders

  • Log File - 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	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Buffer Volume (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sequencing Instrument	Text Dropdown	Required Field	Presets MiSeq NextSeq NextSeq 1000/2000 NextSeq 1000/2000 On-Prem NovaSeq 2.0 NovaSeq 3.0 NovaSeq X Series NovaSeqDx
    Project	Project Name	Built-in

    ℹ️ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.