MiSeq i100 Series Sequencing v2.0

Protocol 1: MiSeq i100 Series Sequencing v2.0

Protocol Type = Sequencing

Next Steps Configuration

• Step(s):

  • 1: Assign Analysis Configuration Template (MiSeq i100 Series Sequencing v2.0)

    • Start Next Step = Manual

    • Assign Next Step = Automatic

  • 2: Make Bulk Pool (MiSeq i100 Series Sequencing v2.0)

    • Start Next Step = Manual

    • Assign Next Step = Automatic

  • 3: Load to Dry Cartridge (MiSeq i100 Series Sequencing v2.0)

    • Start Next Step = Manual

    • Assign Next Step = Automatic

  • 4: AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing v2.0)

    • Start Next Step = Manual

    • Assign Next Step = Automatic

  • 5: AUTOMATED - Analysis Run (MiSeq i100 Series Sequencing v2.0)

    • Assign Next Step = Manual

Step	To Step 1	To Step 2	To Step 3	To Step 4	To Step 5
1		✓	✓	❌	❌
2			✓	❌	❌
3				✓	❌
4					✓
5

Step 1: Assign Analysis Configuration Template (MiSeq i100 Series Sequencing v2.0)

• Master Step Name = Assign Analysis Configuration Template (MiSeq i100 Series Sequencing v2.0)

• Step Type = No Outputs

• Instrument Types

  • MiSeq i100 Series

    • Vendor = Illumina

The Instrument Types is only applicable to the on-premise integration.

The version of Assign Analysis Configuration Template (MiSeq i100 Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Validate Sample Names and Register Step Started

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'submittedSamples.each { sample -> if ( !sample.name.matches( ::[A-Za-z0-9_-]+:: ) ) { fail ( ::Submitted sample :: + sample.name + :: should only have alphanumeric, dash, and underscore characters. Please rename and try again.:: ) } }' -log {compoundOutputFileLuid1} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

1. Retrieve ACT List

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/miseqi100series/automation/miseqi100series-automation.jar script:retrieve_act_list -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -n 'INSTRUMENT_USED' -t true"

2. Retrieve ACT Information

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/miseqi100series/automation/miseqi100series-automation.jar script:retrieve_act_info -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -a '{udf:Analysis Configuration Template}' -n 'INSTRUMENT_USED'"

Validate Reagent Labels and Apply Selected ACT to Samples and 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.hasValue(::Molarity (nM)::)) { fail(::The Molarity cannot be empty.::) ; } else if (input.::Molarity (nM):: <= 0) { fail(::The Molarity cannot be negative or zero.::) ;  }' -log {compoundOutputFileLuid1} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/miseqi100series/automation/miseqi100series-automation.jar -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -a '{udf:Analysis Configuration Template}' -n 'INSTRUMENT_USED' --derivedSampleInstrumentIdUdf 'Instrument ID' script:validate_indexes script:assign_act && /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.::Skip Pooling:: == true) { nextStep = ::Load to Dry Cartridge (MiSeq i100 Series Sequencing v2.0):: } else { nextStep = ::Make Bulk Pool (MiSeq i100 Series Sequencing v2.0):: }' -log {compoundOutputFileLuid1}"

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Register Step Completed

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

• 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

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
  Analysis Configuration Template	Text		Default = No Analysis
  Application	Text	Read Only
  Application Version	Text	Read Only
  Index Adapter Kit	Text	Read Only
  Library Prep Kit	Text	Read Only
  Reference Genome	Text	Read Only
  Secondary Analysis Mode	Text	Read Only
  Skip Pooling	Toggle Switch	Required Field	Default = False

• 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	Well	Built-in
    Derived Sample	ACT Name	Text	Read Only
    Derived Sample	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in

Step 2: Make Bulk Pool (MiSeq i100 Series Sequencing v2.0)

• Master Step Name = Make Bulk Pool (MiSeq i100 Series Sequencing v2.0)

• Step Type = Pooling

• Aliquot Generation = Fixed, 1

• Naming Convention = {PoolName}

• Reagent Kits

  • MiSeq i100 Series Library Denature (KLD)

  • Resuspension Buffer (RSB)

The version of Make Bulk Pool (MiSeq i100 Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Validate Analysis Configurations

• Trigger Location = Pooling

• 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.hasValue(::Instrument ID::)) {output.::Instrument ID:: = input.::Instrument ID::}' -log {compoundOutputFileLuid1} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/miseqi100series/automation/miseqi100series-automation.jar -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -m PerPool -n 'INPUT.Instrument ID' script:validate_analysis_config script:validate_physical_logical_configurations"

Calculate Volumes

• 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} -log {compoundOutputFileLuid1} \
      script:evaluateDynamicExpression \
      -exp 'if (!input.hasValue(::Molarity (nM)::)) { return; }; if (output.hasValue(::Number of Samples in Pool::)) { output.::Number of Samples in Pool:: = output.::Number of Samples in Pool:: + 1; } else { output.::Number of Samples in Pool:: = 1; };' -t true \
      script:evaluateDynamicExpression \
      -exp 'output.::MiSeq i100 Series Flowcell Type:: = step.::Flowcell Type::; \
      input.::Per Sample Volume (ul):: = 0.01 * step.::Final Loading Concentration (pM):: * step.::Bulk Pool Volume (ul):: / input.::Molarity (nM):: / output.::Number of Samples in Pool::; \
      output.::Bulk Pool Volume (ul):: = step.::Bulk Pool Volume (ul)::; \
      if (step.::% PhiX Spike In:: == 0) { step.::RSB Volume for PhiX Stock (ul):: = 0; output.::Diluted PhiX Volume (ul):: = 0; }; \
      else if (step.::% PhiX Spike In:: < 10) { step.::RSB Volume for PhiX Stock (ul):: = (10 / step.::Final Loading Concentration (pM):: * 1000 / 6) - 1; output.::Diluted PhiX Volume (ul):: = 30 * step.::% PhiX Spike In:: / (60 + 0.4 * step.::% PhiX Spike In::) }; \
      else { step.::RSB Volume for PhiX Stock (ul):: = (20 / step.::Final Loading Concentration (pM):: * 1000 / 10) - 2; output.::Diluted PhiX Volume (ul):: = 3 * step.::% PhiX Spike In:: / 10 };' -t true \
      script:calculate_multipool_adjusted_per_sample_volume -t \
      script:evaluateDynamicExpression \
      -exp 'if (output.hasValue(::Total Sample Volume (ul)::)) { output.::Total Sample Volume (ul):: = output.::Total Sample Volume (ul):: + input.::Adjusted Per Sample Volume (ul)::; } else { output.::Total Sample Volume (ul):: = input.::Adjusted Per Sample Volume (ul)::; };' -t true \
      script:evaluateDynamicExpression \
      -exp 'if (output.::Bulk Pool Volume (ul):: > output.::Total Sample Volume (ul)::) { output.::RSB Volume (ul):: = output.::Bulk Pool Volume (ul):: - output.::Total Sample Volume (ul):: } else { output.::RSB Volume (ul):: = 0 }; \
      output.::Diluted Bulk Pool Volume (ul):: = 30 - output.::Diluted PhiX Volume (ul):: ; \
      output.::KLD Volume (ul):: = 270; \
      output.::Final Loading Concentration (pM):: = step.::Final Loading Concentration (pM)::;
      output.::Final Loading Volume (ul):: = step.::Final Loading Volume (ul)::; ' -t true \
      && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} script:driver_file_generator \
      -t /opt/gls/clarity/extensions/conf/driverfiletemplates/MiSeqi100Series_Bulk_Pool1.csv -o 1.csv \
      script:driver_file_generator \
      -t /opt/gls/clarity/extensions/conf/driverfiletemplates/MiSeqi100Series_Bulk_Pool2.csv -o 2.csv \
      script:driver_file_generator \
      -t /opt/gls/clarity/extensions/conf/driverfiletemplates/MiSeqi100Series_Bulk_Pool3.csv -o 3.csv \
      script:driver_file_generator \
      -t /opt/gls/clarity/extensions/conf/driverfiletemplates/MiSeqi100Series_Bulk_Pool4.csv -o 4.csv \
      && if [ {udf:% PhiX Spike In} != '0' ]; then \
      cat 1.csv 2.csv 3.csv 4.csv > {compoundOutputFileLuid0}.csv; \
      else \
      cat 1.csv 2.csv 4.csv > {compoundOutputFileLuid0}.csv; \
      fi \
      && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} -log {compoundOutputFileLuid1} \
      script:evaluateDynamicExpression \
      -exp 'output.::Number of Samples in Pool:: = ::::; output.::Total Sample Volume (ul):: = ::::;' -t true \
      && echo 'Calculate Volume calculated successfully.'"

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} -log {compoundOutputFileLuid1} \
      script:evaluateDynamicExpression -exp 'if (!input.hasValue(::Molarity (nM)::)){ return; }; nextStep = ::ADVANCE::;'"

Register Pools and Register Step Completed

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar -i {stepURI:v2} -u {username} -p {password} script:executeUPAAutomationScript -s 'com/illumina/upa/scripts/common/pooling.groovy' script:executeUPAAutomationScript -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

• 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

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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  % PhiX Spike In	Numeric	Required Field	Default = 0 Decimal Places Displayed = 1
  Bulk Pool Volume (ul)	Numeric	Required Field	Default = 30 Decimal Places Displayed = 1
  Final Loading Concentration (pM)	Numeric	Required Field	Decimal Places Displayed = 0
  Final Loading Volume (ul)	Numeric	Required Field Read Only	Default = 250 Decimal Places Displayed = 2
  Flowcell Type	Text Dropdown	Required Field	Presets 5M 25M 50M 100M
  Minimum Per Sample Volume (ul)	Numeric	Required Field	Default = 2 Decimal Places Displayed = 2

• 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
    Derived Sample	Diluted Bulk Pool Volume (ul)	Numeric	Read Only	Decimal Places Displayed = 1
    Derived Sample	Diluted PhiX Volume (ul)	Numeric	Read Only	Decimal Places Displayed = 1
    Derived Sample	Final Loading Concentration (pM)	Numeric	Required Field	Presets 225 400 Decimal Places Displayed = 0
    Derived Sample	Final Loading Volume (ul)	Numeric	Read Only	Decimal Places Displayed = 2
    Derived Sample	KLD Volume (ul)	Numeric	Read Only	Decimal Places Displayed = 1
    Derived Sample	MiSeq i100 Series Flowcell Type	Text Dropdown	Required Field Read Only	Presets 5M 25M 50M 100M
    Derived Sample	RSB Volume (ul)	Numeric	Read Only	Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 3: Load to Dry Cartridge (MiSeq i100 Series Sequencing v2.0)

• Master Step Name = Load to Dry Cartridge (MiSeq i100 Series Sequencing v2.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

The version of Load to Dry Cartridge (MiSeq i100 Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Validate Single Pool and Register Step Started

• Trigger Location = Step

• 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:validateSampleCount -min 1 -max 1 && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_started.groovy'"

Validate Dry Cartridge Barcode

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:validate_output_containers -l {compoundOutputFileLuid1} -r 'MiSeq i100 Series Dry Cartridge:SC[0-9]{7}-SC3' -min 1 -max 1"

Validate Run Setup and Create Sample Sheet

• 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 \
          -exp 'if (!step.::Run Name::.matches(::[a-zA-Z0-9-_]+[a-zA-Z0-9-_. ]*::)) { fail(::Run Name contains prohibited characters. Please check to make sure Run Name only contains alphanumeric characters, spaces, dashes and underscores. Run Name must start with alphanumeric, a dash or an underscore::); }; if (step.::Run Name::.length() > 255) { fail(::Run Name shall not exceed 255 characters.::); };  if (step.::Index 2 Cycles:: > 0 && step.::Index 1 Cycles:: == 0) { fail(::Index 1 Cycles cannot be zero if Index 2 Cycles is non-zero::); };' \
          -log {compoundOutputFileLuid1} \
          -t true \
          && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/miseqi100series/automation/miseqi100series-automation.jar  script:generate_sample_sheet -i {stepURI:v2} -u {username} -p {password} -c {compoundOutputFileLuid0} -l {compoundOutputFileLuid1} -n 'INPUT.Instrument ID' --instrumentType '{udf:Instrument Type}' --verifyIndexLength"

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 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid1}"

Register Step Completed

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

• 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	Instrument ID ℹ Only applicable for on-premise integration	Text	Read Only
  Derived Sample	MiSeq i100 Series Flowcell Type	Text Dropdown	Required Field Read Only	Presets 5M 25M 50M 100M
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

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	MiSeq i100 Series Flowcell Type	Text Dropdown	Required Field Read Only	Presets 5M 25M 50M 100M
  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

  • MiSeq i100 Series Dry Cartridge

    • Rows

      • Number: 1

      • Naming: Alphabetic

    • Columns

      • Number: 1

      • Naming: Numeric

      • Start at: 1

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Create Planned Run	Toggle Switch	Required Field	Default = True
  Index 1 Cycles	Numeric	Required Field	Presets 0 6 8
  Index 2 Cycles	Numeric	Required Field	Presets 0 6 8
  Instrument ℹ Only applicable for on-premise integration.	Text	Read Only
  Read 1 Cycles	Numeric	Required Field	Presets 51 151 301 501
  Read 2 Cycles	Numeric	Required Field	Presets 51 151 301 501
  Run Name	Text	Required Field

• 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
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 4: AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing v2.0)

• Master Step Name = AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing v2.0)

• Step Type = Analysis

• Measurement Generation = Variable

• Naming Convention = Lane {OutputItemNumber}

• Reagent Kits

  • MiSeq i100 Series Dry Cartridge

    • Supplier = Illumina

  • MiSeq i100 Series Wet Cartridge

    • Supplier = Illumina

The version of AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started and Register MiSeq i100 Series Run and Register MiSeq i100 Series Run Association and Register MiSeq i100 Series RunStarted

• Trigger Location = Step

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_started.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/miseqi100series/register_miseqi100series_run.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/miseqi100series/miseqi100series_associate_seqrun.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/miseqi100series/miseqi100series_seqrun_started.groovy'"

Register MiSeq i100 Series RunCompleted and Register Step Completed

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/miseqi100series/miseqi100series_seqrun_completed.groovy' && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_completed.groovy'"

Queue

• 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
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

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
  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
  Current Cycle	Text	Read Only
  Current Read	Text	Read Only
  Dry Cartridge Barcode Serial Number	Text	Read Only
  Dry Cartridge Expiration Date	Text	Read Only
  Flow Cell ID	Text	Read Only
  Flow Cell Type	Text	Read Only
  Instrument Control Software Version	Text	Read Only
  Instrument ID	Text	Read Only
  Instrument Type	Text	Read Only
  Output Folder	Text	Read Only
  Run Name	Text	Read Only
  Run Status	Text	Read Only
  Sequencing Log	Multiline Text	Read Only
  Wet Cartridge Expiration Date	Text	Read Only
  Wet Cartridge Serial Number	Text	Read Only

• 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	% Aligned R1	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% Aligned R2	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% Bases >=Q30 R1	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% Bases >=Q30 R2	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% Error Rate R1	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% Error Rate R2	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% Occupied	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% PF	Numeric	Read Only	Decimal Places Displayed = 2
    Container	% Phasing R1	Numeric	Read Only	Decimal Places Displayed = 3
    Container	% Phasing R2	Numeric	Read Only	Decimal Places Displayed = 3
    Container	% Prephasing R1	Numeric	Read Only	Decimal Places Displayed = 3
    Container	% Prephasing R2	Numeric	Read Only	Decimal Places Displayed = 3
    Container	Container Name	Built-in
    Container	Intensity Cycle 1 R1	Numeric	Read Only
    Container	Intensity Cycle 1 R2	Numeric	Read Only
    Container	LIMS ID (Container)	Built-in
    Container	Reads PF	Numeric	Read Only	Decimal Places Displayed = 2
    Container	Yield (Gb) R1	Numeric	Read Only	Decimal Places Displayed = 2
    Container	Yield (Gb) R2	Numeric	Read Only	Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	% Aligned R1	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	% Aligned R2	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	% Bases >=Q30 R1	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	% Bases >=Q30 R2	Numeric	Read Only
    Measurement	% Error Rate R1	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	% Error Rate R2	Numeric	Read Only
    Measurement	% Occupied	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	% PF	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	% Phasing R1	Numeric	Read Only	Decimal Places Displayed = 3
    Measurement	% Phasing R2	Numeric	Read Only	Decimal Places Displayed = 3
    Measurement	% Prephasing R1	Numeric	Read Only	Decimal Places Displayed = 3
    Measurement	% Prephasing R2	Numeric	Read Only	Decimal Places Displayed = 3
    Measurement	Intensity Cycle 1 R1	Numeric	Read Only
    Measurement	Intensity Cycle 1 R2	Numeric	Read Only
    Measurement	Reads PF	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	Yield (Gb) R1	Numeric	Read Only	Decimal Places Displayed = 2
    Measurement	Yield (Gb) R2	Numeric	Read Only	Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 5: AUTOMATED - Analysis Run (MiSeq i100 Series Sequencing v2.0)

• Master Step Name = AUTOMATED - Analysis Run (MiSeq i100 Series Sequencing v2.0)

• Step Type = Demultiplexing

• Measurement Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName} {AppliedReagentLabels}

The version of AUTOMATED - Analysis Run (MiSeq i100 Series Sequencing) master step name may be different depending on the version of IPP installed.

Queue

• 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
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

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
  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
  Analysis Result Location	Text	Read Only
  Analysis Status	Text	Read Only
  Log	Multiline Text	Read Only

• 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
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in