LogoLogo
Illumina KnowledgeIllumina SupportSign In
Clarity LIMS Software
  • Home
Clarity LIMS Software
  • Announcements
  • Clarity LIMS
    • Clarity & LabLink
  • API and Database
    • API Portal
      • REST
        • REST General Concepts
        • REST Web Services
        • HTTP Response Codes and Errors
        • XML UTF-8 Character Encoding
        • Requesting API Version Information
        • Viewing Paginated List Resources
        • Filtering List Resources
        • Working with User-Defined Fields (UDF) and Types (UDT)
        • Traversing a Genealogy
        • Working with Batch Resources
      • Getting Started with API
        • Understanding API Terminology (LIMS v5 and later)
        • API-Based URIs (LIMS v4 and later)
        • Development Prerequisites
        • Structure of REST Resources
        • The Life Cycle of a Sample: Stages Versus Steps
        • Integrating Scripts
      • Automation
        • Automation Triggers and Command Line Calls
        • Automation Execution Environment
        • Supported Command Line Interpreters
        • Automation Channels
        • Error Handling
        • Automation Tokens
          • Derived Sample Automation Tokens
          • Step Automation Tokens
          • Project Automation Tokens
        • Automation Testing
        • Troubleshooting Automation
      • Tips and Tricks
        • Accessing Step UDFs from a different Step
        • Obfuscating Sensitive Data in Scripts
        • Integrating Clarity LIMS with Upstream Sample Accessioning Systems
        • Creating Samples and Projects via the API
        • Displaying Files From an Earlier Step
        • Transitioning Output Artifacts into the Next Step
        • Determining the Workflow(s) to Which a Sample is Assigned
        • Standardizing Sample Naming via the API
        • Copying UDF Values from Source to Destination
        • Updating Preset Value of a Step UDF through API
        • Automating BCL Conversion
        • Finding QC Flags in Aggregate QC (Library Validation) via REST API
        • Setting the Value of a QC Flag on an Artifact
        • Creating Notifications When Files are Added via LabLink
        • Remote HTTP Filestore Setup
      • Cookbook
        • Get Started with the Cookbook
          • Tips and Troubleshooting
          • Obtain and Use the REST API Utility Classes
        • Work with EPP/Automation and Files
          • Automation Trigger Configuration
          • Process Execution with EPP/Automation Support
        • Work with Submitted Samples
          • Adding Samples to the System
          • Renaming Samples
          • Assigning Samples to Workflows
          • Updating Sample Information
          • Show the Relationship Between Samples and Analyte Artifacts (Derived Samples)
        • Work with Containers
          • Add an Empty Container to the System
          • Find the Contents of a Well Location in a Container
          • Filter Containers by Name
        • Work with Derived Sample Automations
          • Remove Samples from Workflows
          • Requeue Samples
          • Rearray Samples
        • Work with Process/Step Outputs
          • Update UDF/Custom Field Values for a Derived Sample Output
          • Rename Derived Samples Using the API
          • Find the Container Location of a Derived Sample
          • Traverse a Pooled and Demultiplexed Sample History/Genealogy
          • View the Inputs and Outputs of a Process/Step
        • Work with Projects and Accounts
          • Remove Information from a Project
          • Add a New Project to the System with UDF/Custom Field Value
          • Get a Project Name
          • Find an Account Registered in the System
          • Update Contact (User and Client) Information
        • Work with Multiplexing
          • Find the Index Sequence for a Reagent Label
          • Demultiplexing
          • Pool Samples with Reagent Labels
          • Apply Reagent Labels with REST
          • Apply Reagent Labels When Samples are Imported
          • Apply Reagent Labels by Adding Reagents to Samples
        • Working with User Defined Fields/Custom Fields
          • About UDFs/Custom Fields and UDTs
          • Performing Post-Step Calculations with Custom Fields/UDFs
        • Work with Processes/Steps
          • Filter Processes by Date and Type
          • Find Terminal Processes/Steps
          • Run a Process/Step
          • Update UDF/Custom Field Information for a Process/Step
          • Work with the Steps Pooling Endpoint
        • Work with Batch Resources
          • Introduction to Batch Resources
          • Update UDF/Custom Field Information with Batch Operations
          • Retrieve Multiple Entities with a Single API Interaction
          • Select the Optimal Batch Size
        • Work with Files
          • Attach a File with REST and Python
          • Attach Files Located Outside the Default File Storage Repository
          • Attach a File to a File Placeholder with REST
        • Work with Controls
          • Automated Removal of Controls from a Workflow
      • Application Examples
        • Python API Library (glsapiutil.py) Location
        • Scripts That Help Automate Steps
          • Route Artifacts Based Off a Template File
          • Invoking bcl2fastq from BCL Conversion and Demultiplexing Step
          • Email Notifications
          • Finishing the Current Step and Starting the Next
          • Adding Downstream Samples to Additional Workflows
          • Advancing/Completing a Protocol Step via the API
          • Setting a Default Next Action
          • Automatic Placement of Samples Based on Input Plate Map (Multiple Plates)
          • Automatic Placement of Samples Based on Input Plate Map
          • Publishing Files to LabLink
          • Automatic Pooling Based on a Sample UDF/Custom Field
          • Completing a Step Programmatically
          • Automatic Sample Placement into Existing Containers
          • Routing Output Artifacts to Specific Workflows/Stages
          • Creating Multiple Containers / Types for Placement
          • Starting a Protocol Step via the API
          • Setting Quality Control Flags
          • Applying Indexing Patterns to Containers Automatically
          • Assignment of Sample Next Steps Based On a UDF
          • Parsing Metadata into UDFs (BCL Conversion and Demultiplexing)
        • Scripts That Validate Step Contents
          • Validating Process/Step Level UDFs
          • Checking That Containers Are Named Appropriately
          • Checking for Index Clashes Based on Index Sequence
          • Validating Illumina TruSeq Index Adapter Combinations
        • Scripts Triggered Outside of Workflows/Steps
          • Repurposing a Process to Upload Indexes
          • Adding Users in Bulk
          • Moving Reagent Kits & Lots to New Clarity LIMS Server
          • Programatically Importing the Sample Submission Excel File
          • Generating an MS Excel Sample Submission Spreadsheet
          • Assigning Samples to New Workflows
        • Miscellaneous Scripts
          • Illumina LIMS Integration
          • Generating a Hierarchical Sample History
          • Protocol-based Permissions
          • Self-Incremental Counters
          • Generic CSV Parser Template (Python)
          • Renaming Samples to Add an Internal ID
          • Creating Custom Sample Sheets
          • Copying Output UDFs to Submitted Samples
          • Parsing Sequencing Meta-Data into Clarity LIMS
          • Submit to a Compute Cluster via PBS
          • Downloading a File and PDF Image Extraction
        • Resources and References
          • Understanding LIMS ID Prefixes
          • Container States
          • Useful Tools
          • Unsupported Artifact Types
          • Unsupported Process Types
          • Suggested Reading
          • API Training Videos
  • Illumina Preset Protocols
    • IPP v2.10
      • Release Notes
      • Installation and User Configuration
      • Manual Upgrade
    • IPP v2.9
      • Release Notes
      • Installation and User Configuration
    • IPP v2.8
      • Release Notes
      • Installation and User Configuration
      • Manual Upgrade
    • IPP v2.7
      • Release Notes
      • Installation and User Configuration
    • IPP v2.6
      • Release Notes
      • Installation and User Configuration
      • Manual Upgrade
  • Sample Prep
    • QC and Sample Prep
      • DNA Initial QC 5.1.2
      • RNA Initial QC 5.1.2
      • Library Validation QC 5.1.2
  • Library Prep
    • AmpliSeq for Illumina
      • BRCA Panel
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Cancer HotSpot Panel v2
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Childhood Cancer Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Comprehensive Cancer Panel
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Comprehensive Panel v3
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Custom DNA Panel
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Focus Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Immune Repertoire Panel
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Immune Response Panel
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Myeloid Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • TCR beta-SR Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
      • Transcriptome Human Gene Expression Panel
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
    • Library Prep Validation
    • Nextera
      • Nextera Mate Pair v1.0
      • Nextera Rapid Capture Custom Enrichment v2.0
      • Nextera XT v2.0
    • Targeted Enrichment
      • Illumina DNA Prep with Enrichment (S) Tagmentation v1.2
      • Illumina RNA Prep with Enrichment (L) Tagmentation v1.1
    • TruSeq
      • TruSeq ChIP-Seq v1.0
      • TruSeq Custom Amplicon v1.0
      • TruSeq DNA Exome v2.0
      • TruSeq DNA PCR-Free v2.0
      • TruSeq Methyl Capture EPIC v2.0
      • TruSeq Nano DNA v1.0
      • TruSeq RNA Access v2.0
      • TruSeq RNA Exome v1.0
      • TruSeq Small RNA v1.0
      • TruSeq Stranded mRNA v2.0
    • TruSight
      • TruSight Oncology 500 ctDNA v1.1
      • TruSight Oncology 500 HT v1.1
      • TruSight Oncology 500 v1.1
      • TruSight Tumor 170 v2.0
    • Other DNA Protocols
      • Illumina DNA PCR-Free Library Prep Manual v1.1
      • Illumina DNA Prep (M) Tagmentation v1.0
    • Other RNA Protocols
      • Illumina Stranded mRNA Prep Ligation 1.1
      • Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1
  • iLASS & Infinium Arrays
    • iLASS
      • iLASS Infinium Genotyping v1.1
        • iLASS Infinium Batch DNA v1.1
        • iLASS Infinium Genotyping Assay v1.1
        • iLASS Infinium Genotyping with PGx Assay v1.1
      • iLASS Infinium Genotyping v1.0
        • iLASS Infinium Genotyping Assay v1.0
        • iLASS Infinium Genotyping with PGx Assay v1.0
    • Infinium Arrays
      • Infinium HD Methylation Assay Manual v1.2
      • Infinium HTS Assay Manual v1.2
      • Infinium LCG Assay Manual v1.2
      • Infinium XT Assay Manual v1.2
      • GenomeStudio v1.0
  • Applications
    • IGA
      • IGA v2.1
        • IGA Library Prep Automated v2.1
        • IGA NovaSeq Sequencing v2.1
    • Viral Pathogen Protocols
      • CDC COVID-19 RT-PCR
        • Sort Specimens to Extraction v1.1
        • Qiagen QIAamp DSP Viral RNA Mini Kit v1.1
        • Qiagen EZ1 Advanced XL v1.1
        • Roche MagNA Pure LC v1.1
        • Roche MagNA Pure Compact v1.1
        • Roche MagNA Pure 96 v1.1
        • bioMerieux NucliSENS easyMAG Instrument v1.1
        • bioMerieux EMAG Instrument v1.1
        • Real-Time RT-PCR Prep v1.1
      • Illumina COVIDSeq v1.6
      • Respiratory Virus Panel v1.0
  • Instruments & Integrations
    • Compatibility
    • Integration Properties
      • Integration Properties Details
    • Clarity LIMS Product Analytics
      • Supported Workflows
      • Workflow Customization
      • Clarity LIMS Product Analytics v1.4.0
        • Configuration
      • Clarity LIMS Product Analytics v1.3.1
        • Configuration
      • Clarity LIMS Product Analytics v1.3.0
        • Configuration
      • Clarity LIMS Product Analytics v1.2.0
        • Configuration
    • Illumina Run Manager
      • Illumina Run Manager v1.0.0
        • Installation and User Interaction
    • iScan
      • iScan System
      • iScan v1.2.0
        • Release Notes
        • BeadChip Accessioning, Imaging, and Analysis
      • iScan v1.1.0
        • Release Notes
        • BeadChip Accessioning, Imaging, and Analysis
      • iScan System v1.0
    • iSeq 100 Run Setup v1.0
    • MiniSeq v1.0
    • MiSeq
      • MiSeq v8.3.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • MiSeq v8.2.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
    • MiSeq i100 (On-Prem)
      • MiSeq i100 On-Prem v1.0.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • MiSeq i100 (Hosted)
      • MiSeq i100 v1.0.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • MiSeqDx
      • MiSeqDx Sample Sheet Generation (v1.11.0 and later)
      • MiSeqDx v1.11.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • MiSeqDx v1.10.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Sample Sheet Generation
        • Manual Upgrade
    • Next Generation Sequencing Package
      • Release Notes
        • NGS Extensions v5.25.0
        • NGS Extensions v5.24.0
        • NGS Extensions v5.23.0
      • Accession Kit Lots
      • Auto-Placement of Reagent Indexes
      • Compute Replicate Average
      • Copy UDFs
      • Initialize Artifact UDFs
      • Label Non-Labeled Outputs
      • Linear Regression Calculation
      • Normalization Buffer Volumes
      • Process Summary Report
      • Routing Script
      • Set UDF
      • Validate Complete Plate
      • Validate Sample Count
      • Validate Unique Indexes
    • NextSeq 500/550
      • NextSeq 500/550 v2.5.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
      • NextSeq 500/550 v2.4.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NextSeq 500/550 v2.3.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NextSeq 1000/2000 (Hosted)
      • NextSeq 1000/2000 v2.5.1
        • Release Notes
      • NextSeq 1000/2000 v2.5.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
      • NextSeq 1000/2000 v2.4.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NextSeq 1000/2000 (On-Prem)
      • NextSeq 1000/2000 On-Prem v1.0.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq 6000 (API-based)
      • NovaSeq 6000 API-based v3.7.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NovaSeq 6000 API-based v3.6.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
    • NovaSeq 6000 (File-based)
      • NovaSeq 6000 File-based v2.6.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NovaSeq 6000 File-based v2.5.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq 6000Dx (API-based)
      • NovaSeq 6000Dx API-based v1.3.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NovaSeq 6000Dx API-based v1.2.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq X Series (Hosted)
      • NovaSeq X Series v1.3.0
        • Release Notes
        • Configuration
        • Manual Upgrade
      • NovaSeq X Series v1.2.1
        • Release Notes
      • NovaSeq X Series v1.2.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
      • NovaSeq X Series v1.1.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq X Series (On-Prem)
      • NovaSeq X Series On-Prem v1.0.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • References
      • Configure Multiple Identical netPathPrefixSearch Values
      • Configure Support for Samples Having Duplicate Names with Different Indexes
      • Illumina Instrument Sample Sheets
      • Terminology
  • Integration Toolkits
    • Lab Instrument Toolkit
      • Template File Generator
        • Creating Template Files
        • Template File Contents
        • Template File Generator Troubleshooting
      • Add Blank Lines
      • Convert CSV to Excel
      • Parse CSV
      • Name Matching XML Parser
      • Sample Placement Helper
    • Lab Logic Toolkit
      • Working with Lab Logic Toolkit
        • Data Collection Entities
        • Failing a Script
        • Mapping Field Types
        • Non-UDF/Custom Field Properties
        • Setting QC Flags
        • Setting Next Actions
        • Specifying Custom Fields
        • Working with Submitted Samples
        • Working with Containers
      • Lab Logic Toolkit Script Examples
        • Comparing Stop/Start Dates and Times with LLTK
      • Lab Logic Toolkit FAQ
  • Known Issues
    • Integration
      • Sample Sheet Generation Issue and CLPA Issues When Samples Have Been Assigned QC Flag Prior to Entering Steps
  • Security Bulletin
    • Investigation of OpenSSH vulnerability with Clarity LIMS
  • Resources
    • Third Party Software Information
  • Others
    • Revision History
Powered by GitBook
On this page
  • Compatibility
  • Prerequisites and Assumptions
  • Workflows, Protocols, and Steps
  • Step 1: Library Pooling (MiSeq v3.2)
  • Master Step Fields
  • Global Fields
  • Step 2: Denature and Dilute (MiSeq v3.2)
  • Master Step Fields
  • Global Fields
  • Step File Placeholders
  • Step 3: MiSeq Run (MiSeq v3.2)
  • Master Step Fields
  • Global Fields
  • Step File Placeholders
  • Sample Sheet Generation
  • Sequencing Results Parsing
  • Generated and Captured Files
  • Metadata
  • Primary Analysis Metrics
  • How It Works
  • Scripts and Files Installed
  • Properties Installed
  • Consumables Installed
  • Reagent Categories and Kits
  • Control Types
  • Container Types
  • Instrument Integration
  • Rules and Constraints

Was this helpful?

Export as PDF
  1. Instruments & Integrations
  2. MiSeq
  3. MiSeq v8.3.0

Configuration

PreviousInstallationNextUser Interaction, Validation and Troubleshooting

Last updated 4 months ago

Was this helpful?

The Illumina MiSeq Integration Package v8.3.0 supports the integration of Clarity LIMS to Illumina MiSeq Sequencing Systems.

The integration allows for automated tracking of an Illumina sequencing run in Clarity LIMS. This capability includes tracking sequencing run status, generating run report, and capturing and parsing run statistics. In addition, this integration provides automated generation of a sample sheet file for use with the MiSeq Control Software (MCS) and Local Run Manager (LRM).

For instructions on user interaction for each step, validating and troubleshooting the Illumina MiSeq Integration Package, refer to .

Compatibility

  • The MiSeq Sequencing v3.2 workflow is compatible with MiSeq Integration Package v8.2.0 and v8.3.0.

  • MiSeq Integration v8.2.0 and above is only required for MiSeq Control Software (MCS) v4.0. For MCS v3.1 or earlier, do not upgrade to MiSeq Integration v8.2.0 or above. This upgrade breaks the integration.

Prerequisites and Assumptions

Before samples are assigned to the MiSeq Sequencing v3.2 workflow, make sure that the following prerequisites are completed:

  • Samples have been accessioned into Clarity LIMS.

  • Samples have been run through QC and library prep.

  • Samples have been normalized, and the value is captured in a field called Normalized Molarity (nM).

For more information on sample accessioning, refer to Sample Accessioning and Upload and Modify Samples in the .

Samples can be assigned to the MiSeq Sequencing v3.2 workflow automatically using a routing script or manually from the Projects & Samples dashboard. Refer to Assign and Process Samples in the .

Workflows, Protocols, and Steps

The Illumina MiSeq Integration includes the MiSeq Sequencing v3.2 workflow, which contains a single protocol of the same name.

Step 1: Library Pooling (MiSeq v3.2)

In this step, the lab scientist manually places libraries into pools in the Clarity LIMS Placement screen.

Set Next Step - Advance Automation

This automation advances samples to the next step in the protocol. The automation is automatically triggered on exit of the Record Details screen.

The default command line is as follows.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-0extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
Validate Maximum Number of Samples Automation

This automation checks the maximum number of samples that is allowed in a single pool. The default maximum for Illumina MiSeq Control Software (MCS) is 1536 samples. The automation is automatically triggered on entry of the Pooling screen.

The default command line is as follows.

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 1536"

Master Step Fields

The following field is configured on the Library Pooling (MiSeq v3.2) master step. The field displays on the Record Details screen at run time.

Library Pooling (MiSeq v3.2) Master Step Field Configuration

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-down Items

Comment

Multiline Text

Global Fields

The following table lists the global fields that are displayed on the Queue and Ice Bucket screens of the Library Pooling (MiSeq v3.2) step. Most fields display in expanded view only.

Global Field Configuration (Submitted Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Application

Text Dropdown

Custom Entries

Presets

  • TruSeq mRNA sequencing

  • TruSeq DNA sequencing (large genome de novo)

  • TruSeq DNA sequencing (large genome re-seq)

  • TruSeq DNA sequencing (small genome de novo)

  • TruSeq DNA sequencing (small genome re-seq)

  • Nextera DNA sequencing

  • TruSeq Custom Amplicon sequencing

  • ChIP-sequencing

  • Exome sequencing

  • Mate pair sequencing

  • Small RNA sequencing

Pooling

Text Dropdown

Custom Entries

Presets

  • Yes

  • No

Read Length

Text

Sequencing Coverage

Text

Sequencing Method

Text Dropdown

Custom Entries

Presets

  • Single Read

  • Paired End Read

  • Indexed Single Read

  • Indexed Paired End Read

Global Field Configuration (Derived Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Normalized Molarity (nM)

Numeric

Decimal places displayed = 2

Step 2: Denature and Dilute (MiSeq v3.2)

In this step, pooled libraries are denatured and diluted, and then placed into the reagent cartridge loaded into the MiSeq instrument.

Validate Single Input Automation

This automation checks that there is only one pooled input in the step. The automation is automatically triggered when starting the step.

The default command line is as follows.

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"
Validate Run Setup and Generate MiSeq SampleSheet Automation

Select a button on the Record Details screen to trigger this automation.

Validation Rules

  • The Experiment Name custom field cannot exceed 40 characters.

  • The Experiment Name field can only contain letters, numbers, periods, nonconsecutive spaces, and the following special characters: `~!@#%-_}{.

  • If Starling is selected as the variant caller, the Export to gVCF field must be set to Yes.

  • If the Read 2 Cycles field is empty or 0, the following rules apply:

    • The Custom Primers field cannot have a selection that contains Read 2.

    • The Adapter Read 2 field cannot have a value.

    • The UMI - Read 2 Length field and the UMI - Read 2 Start From Cycle field cannot have values.

  • The UMI - Read 1 Length field and the UMI - Read 1 Start From Cycle field cannot be used independently.

  • The UMI - Read 2 Length field and the UMI - Read 2 Start From Cycle field cannot be used independently.

  • If the UMI - Read 2 Length field is greater than 0, the UMI - Read 1 Length field must be greater than 0.

  • The Adapter Read 1 and Adapter Read 2 fields can only contain ACGT+ characters. The adapter sequence cannot start or end with + or contain more than one +.

  • For DNA Enrichment analysis, if the Variant Caller value is Somatic, the Variant Frequency Percentage must be between 1 and 100.

  • For DNA Amplicon analysis, if the Variant Caller value is Somatic, the Variant Frequency Percentage field must contain a value between 0.05 and 30.

  • If the Aligner value is BWA or TruSeq Amplicon Aligner, an error occurs when the Workflow value is not equal to DNA Amplicon.

  • If the Aligner value is BWA-MEM or BWA-Backtrack Legacy, an error occurs when the Workflow value is equal to DNA Amplicon.

  • If the Variant Caller value is Starling or GATK, an error occurs when the Workflow value is equal to DNA Amplicon.

  • If the Variant Caller value is Somatic, an error occurs when the Workflow value is not equal to DNA Enrichment or DNA Amplicon.

  • If the Variant Caller value is Germline, an error occurs when the Workflow value is not equal to DNA Amplicon.

The default command line is as follows.

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 {udf:Validation Script 1} {udf:Validation Script 2}'\
-log {compoundOutputFileLuid3} \
-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} \
script:driver_file_generator \
-t /opt/gls/clarity/extensions/conf/driverfiletemplates/MiSeqSamplesheetv3.csv \
-o {compoundOutputFileLuid1}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid1} \
-l {compoundOutputFileLuid2}"

There is an 8000 character limit in the Oracle database used for the automation storage. Because of this character limit, the automation splits and saves the validation expressions to the Validation Script 1 and Validation Script 2. These fields are configured as master step fields.

Validation Script 1 Command Line

if (step.::Experiment Name::.length() > 40) { fail(::Experiment Name cannot exceed 40 characters.::) }; if (!step.::Experiment Name::.matches(::^(?!.*[ ]{2})[a-zA-Z0-9-_`.~!#@%{ }]+::)) { fail(::Experiment Name contains prohibited characters. Allowed characters are letters, numbers, periods, non-consecutive spaces and the following special characters: `~!@#%-_}{::) }; if (step.::Workflow:: == ::Resequencing:: && step.::Variant Caller:: == ::Starling:: && (!step.hasValue(::Export to gVCF::) || step.::Export to gVCF:: != ::Yes::)) { fail(::Export to gVCF must be set to Yes for Starling variant caller.::) }; if (step.::Workflow:: == ::DNA Enrichment:: && step.::Variant Caller:: == ::Somatic:: && (!step.hasValue(::Variant Frequency Percentage::) || step.::Variant Frequency Percentage:: > 100 || step.::Variant Frequency Percentage:: < 1)) { fail(::In the Variant Frequency Percentage field, please enter values between 1 and 100.::) }; if (step.::Workflow:: == ::DNA Amplicon:: && step.::Variant Caller:: == ::Somatic:: && (!step.hasValue(::Variant Frequency Percentage::) || step.::Variant Frequency Percentage:: > 30 || step.::Variant Frequency Percentage:: < 0.05)) { fail(::In the Variant Frequency Percentage field, please enter values between 0.05 and 30.::) }; if (!step.hasValue(::Read 2 Cycles::) || step.::Read 2 Cycles:: == 0) { if (step.::Custom Primers::.contains(::Read 2::)) { fail(::Custom Primers setting selected is invalid and can only be used in a Paired-End run.::) }; if (step.hasValue(::Adapter Read 2::)) { fail(::Adapter Read 2 is only applicable for a Paired-End run.::) }; if (step.hasValue(::UMI - Read 2 Length::) || step.hasValue(::UMI - Read 2 Start From Cycle::)) { fail(::UMI - Read 2 Length and UMI - Read 2 Start From Cycle are only applicable for a Paired-End run.::) }; }; if (step.hasValue(::UMI - Read 1 Length::) && !step.hasValue(::UMI - Read 1 Start From Cycle::)) { fail(::UMI - Read 1 Start From Cycle must be greater than 0 if UMI - Read 1 Length is greater than 0.::) }; if (!step.hasValue(::UMI - Read 1 Length::) && step.hasValue(::UMI - Read 1 Start From Cycle::)) { fail(::UMI - Read 1 Length must be greater than 0 if UMI - Read 1 Start From Cycle is greater than 0.::) }; if (step.hasValue(::UMI - Read 2 Length::) && !step.hasValue(::UMI - Read 2 Start From Cycle::)) { fail(::UMI - Read 2 Start From Cycle must be greater than 0 if UMI - Read 2 Length is greater than 0.::) }; if (!step.hasValue(::UMI - Read 2 Length::) && step.hasValue(::UMI - Read 2 Start From Cycle::)) { fail(::UMI - Read 2 Length must be greater than 0 if UMI - Read 2 Start From Cycle is greater than 0.::) }; if (!step.hasValue(::UMI - Read 1 Length::) && step.hasValue(::UMI - Read 2 Length::)) { fail(::UMI - Read 1 Length must be greater than 0 if UMI - Read 2 Length is greater than 0.::) }; if (step.hasValue(::Adapter Read 1::) && !step.::Adapter Read 1::.matches(::^[ACGT]+(\\+[ACGT]+){0,1}$::)) { fail(::Adapter Read 1 contains prohibited characters. Allowed characters are: ACGT+ and the adapter sequence cannot start or end with + or contain more than one +.::) }; if (step.hasValue(::Adapter Read 2::) && !step.::Adapter Read 2::.matches(::^[ACGT]+(\\+[ACGT]+){0,1}$::)) { fail(::Adapter Read 2 contains prohibited characters. Allowed characters are: ACGT+ and the adapter sequence cannot start or end with + or contain more than one +.::) };

Validation Script 2 Command Line

if ((step.::Aligner:: == ::BWA:: || step.::Aligner:: == ::TruSeq Amplicon Aligner::) && step.::Workflow:: != ::DNA Amplicon::) { fail(::Aligner field contains invalid value. Please refer to the \u005c\u0022Applicable analysis fields for the selected Workflow:\u005c\u0022 section for more information.::) }; if ((step.::Aligner:: == ::BWA-MEM:: || step.::Aligner:: == ::BWA-Backtrack Legacy::) && step.::Workflow:: == ::DNA Amplicon::) { fail(::Aligner field contains invalid value. Please refer to the \u005c\u0022Applicable analysis fields for the selected Workflow:\u005c\u0022 section for more information.::) }; if ((step.::Variant Caller:: == ::Starling:: || step.::Variant Caller:: == ::GATK::) && step.::Workflow:: == ::DNA Amplicon::) { fail(::Variant Caller field contains invalid value. Please refer to the \u005c\u0022Applicable analysis fields for the selected Workflow:\u005c\u0022 section for more information.::) }; if (step.::Variant Caller:: == ::Somatic:: && step.::Workflow:: != ::DNA Enrichment:: && step.::Workflow:: != ::DNA Amplicon::) { fail(::Variant Caller field contains invalid value. Please refer to the \u005c\u0022Applicable analysis fields for the selected Workflow:\u005c\u0022 section for more information.::) }; if (step.::Variant Caller:: == ::Germline:: && step.::Workflow:: != ::DNA Amplicon::) { fail(::Variant Caller field contains invalid value. Please refer to the \u005c\u0022Applicable analysis fields for the selected Workflow:\u005c\u0022 section for more information.::) }; step.::Indel-Realignment-Key:: = ::::; step.::Indel-Realignment-Value:: = ::::; step.::Aligner-Key:: = ::::; step.::Aligner-Value:: = ::::; step.::Variant-Caller-Value:: = ::::; if (step.::Workflow:: == ::DNA Amplicon::) { if (step.::Indel Realignment:: == ::Yes::) { step.::Indel-Realignment-Key:: = ::variantcallerrealignindels::; step.::Indel-Realignment-Value:: = ::1::; }; else if (step.::Indel Realignment:: == ::No::) { step.::Indel-Realignment-Key:: = ::variantcallerrealignindels::; step.::Indel-Realignment-Value:: = ::0::; }; if (step.::Aligner:: == ::TruSeq Amplicon Aligner::) { step.::Aligner-Key:: = ::aligner::; step.::Aligner-Value:: = ::Amplicon::; }; else if (step.::Aligner:: == ::BWA::) { step.::Aligner-Key:: = ::aligner::; step.::Aligner-Value:: = ::BWA::; }; }; if (step.::Workflow:: != ::DNA Amplicon::) { if (step.::Indel Realignment:: == ::Yes::) { step.::Indel-Realignment-Key:: = ::indelrealignment::; step.::Indel-Realignment-Value:: = ::GATK::; }; else if (step.::Indel Realignment:: == ::No::) { step.::Indel-Realignment-Key:: = ::indelrealignment::; step.::Indel-Realignment-Value:: = ::None::; }; if (step.::Aligner:: == ::BWA-Backtrack Legacy::) { step.::Aligner-Key:: = ::runbwaaln::; step.::Aligner-Value:: = ::1::; }; else if (step.::Aligner:: == ::BWA-MEM::) { step.::Aligner-Key:: = ::runbwaaln::; step.::Aligner-Value:: = ::0::; }; }; if (step.hasValue(::Variant Caller::)) { if (step.::Variant Caller:: == ::None::) { step.::Variant-Caller-Value:: = ::::; }; if (step.::Variant Caller:: == ::GATK::) { step.::Variant-Caller-Value:: = ::GATK::; }; else if (step.::Variant Caller:: == ::Starling::) { step.::Variant-Caller-Value:: = ::Starling::; }; else if (step.::Variant Caller:: == ::Germline::) { step.::Variant-Caller-Value:: = ::PiscesGermline::; }; else if (step.::Variant Caller:: == ::Somatic:: && step.::Workflow:: == ::DNA Amplicon::) { step.::Variant-Caller-Value:: = ::PiscesSomatic::; }; else if (step.::Variant Caller:: == ::Somatic:: && step.::Workflow:: != ::DNA Amplicon::) { step.::Variant-Caller-Value:: = ::Somatic::; }; }; if (step.hasValue(::Manifest::)) { step.::Manifest-Section:: = ::[Manifests]::; }; else { step.::Manifest-Section:: = ::::; }
Set Next Step - Advance Automation

This automation advances samples to the next step in the protocol. The automation is automatically triggered by exiting the Record Details screen.

The default command line is as follows.

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 {compoundOutputFileLuid3}"

Master Step Fields

Most fields configured on the Denature and Dilute (MiSeq v3.2) step display on the Record Details screen in the Step Data table.

These fields are manually populated at run time. The values are then used to generate the sample sheet.

Denature & Dilute (MiSeq v3.2) Master Step Field Configuration

Field Name

Field Type

Options

Additional Options and Drop-Down Items

Adapter Read 1

Text

Adapter Read 2

Text

Aligner

Text Dropdown

  • Presets

    • None (default)

    • BWA-MEM

    • BWA-Backtrack Legacy

    • BWA

    • TruSeq Amplicon Aligner

Aligner-Key

ℹ Used for sample sheet generation

Text

  • Read Only

  • Hidden

Aligner-Value

ℹ Used for sample sheet generation

Text

  • Read Only

Annotation

Text Dropdown

  • Presets

    • None (default)

    • RefSeq

    • Ensembl

Applicable analysis fields for the selected Workflow

Multiline Text

  • Read Only

ℹ Select a value from the drop-down list in the upper-right corner (below NEXT STEPS).

Comment

Multiline Text

Custom Primers

Text Dropdown

  • Presets

    • None (Default)

    • Read 1

    • Index

    • Read 2

    • Read 1, Index

    • Read 1, Index, Read 2

    • Read 1, Read 2

    • Index, Read 2

Description

Text

Experiment Name

Text

  • Required Field

Export to gVCF

Text Dropdown

  • Presets

    • None (default)

    • Yes

    • No

Flag PCR Duplicates

Text Dropdown

  • Presets

    • None (default)

    • Yes

    • No

Genome Folder

Text

Indel Realignment

Text Dropdown

  • Presets

    • None (default)

    • Yes

    • No

Indel Repeat Filter Cutoff

Text Dropdown

  • Presets

    • None (default)

    • Yes

    • No

Indel-Realignment-Key

ℹ Used for sample sheet generation

Text

  • Read Only

  • Hidden

Indel-Realignment-Value

ℹ Used for sample sheet generation

Text

  • Read Only

  • Hidden

Manifest

Text

Manifest Padding

Text Dropdown

  • Presets

    • None (default)

    • 0

    • 50

    • 100

    • 150

    • 200

    • 250

Manifest-Section

ℹ Used for sample sheet generation

Text

  • Read Only

  • Hidden

Picard HS Metric Reporting

Text Dropdown

  • Presets

    • None (default)

    • Yes

    • No

Read 1 Cycles

Numeric Dropdown

  • Required Field

  • Custom Entries

  • Presets

    • 251 (Default)

    • 151

    • 101

    • 76

    • 51

  • Range = 1–1000

  • Decimal places displayed = 0

Read 2 Cycles

Numeric Dropdown

  • Required Field

  • Custom Entries

  • Presets

    • 251 (Default)

    • 151

    • 101

    • 76

    • 51

  • Range = 0–1000

  • Decimal places displayed = 0

Read Stitching

Text Dropdown

  • Presets

    • None (default)

    • Yes

    • No

Reverse Complement

Text Dropdown

  • Presets

    • None (default)

    • Yes

    • No

UMI - Read 1 Length

Numeric

  • Minimum value: 1

UMI - Read 1 Start From Cycle

Numeric

  • Minimum value: 1

UMI - Read 2 Length

Numeric

  • Minimum value: 1

UMI - Read 2 Start From Cycle

Numeric

  • Minimum value: 1

Validation Script 1

ℹ Used for automation

Multiline Text

  • Required Field

  • Read Only

  • Hidden

Validation Script 2

ℹ Used for automation

Multiline Text

  • Required Field

  • Read Only

  • Hidden

Variant Caller

Text Dropdown

  • Presets

    • None (Default)

    • GATK

    • Germline

    • Somatic

    • Starling

Variant Caller Depth Filter

Numeric

  • Minimum value: 10

  • Maximum value: 10000

Variant Quality Filter

Numeric

  • Minimum value: 2

  • Maximum value: 1000

Variant Frequency Percentage

Numeric

  • Minimum value: 0.05

  • Maximum value: 100

  • Decimal places displayed = 2

Variant-Caller-Value

ℹ Used for sample sheet generation

Text

  • Read Only

  • Hidden

Workflow

Text Dropdown

  • Required Field

  • Presets

    • GenerateFASTQ

    • LibraryQC

    • Resequencing

    • DNA Enrichment

    • DNA Amplicon

Groups of Defaults

Resequencing
  • Workflow = Resequencing

  • Read 1 Cycles = 251

  • Custom Primers = None

  • Aligner = BWA-MEM

  • Annotation = None

  • Export to gVCF = No

  • Flag PCR Duplicates = Yes

  • Genome Folder = Required

  • Indel Realignment = No

  • Indel Repeat Filter Cutoff = None

  • Manifest = None

  • Manifest Padding = None

  • Picard HS Metric Reporting = None

  • Reverse Complement = None

  • Read Stitching = None

  • Variant Caller = GATK

  • Applicable analysis fields for the selected Workflow =

    • Aligner (BWA-Backtrack Legacy, BWA-MEM)

    • Export to gVCF

    • Flag PCR Duplicates

    • Genome Folder (fill in the folder path)

    • Indel Realignment

    • Variant Caller (Starling, GATK)

Library QC
  • Workflow = Library QC

  • Read 1 Cycles = 251

  • Custom Primers = None

  • Aligner = None

  • Annotation = None

  • Export to gVCF = None

  • Flag PCR Duplicates = Yes

  • Genome Folder = Required

  • Indel Realignment = None

  • Indel Repeat Filter Cutoff = None

  • Manifest = None

  • Manifest Padding = None

  • Picard HS Metric Reporting = None

  • Reverse Complement = None

  • Read Stitching = None

  • Variant Caller = None

  • Applicable analysis fields for the selected Workflow =

    • Flag PCR Duplicates

    • Genome Folder (fill in the folder path)

GenerateFastQ
  • Workflow = GenerateFastQ

  • Read 1 Cycles = 251

  • Custom Primers = None

  • Aligner = None

  • Annotation = None

  • Export to gVCF = None

  • Flag PCR Duplicates = None

  • Genome Folder = None

  • Indel Realignment = None

  • Indel Repeat Filter Cutoff = None

  • Manifest = None

  • Manifest Padding = None

  • Picard HS Metric Reporting = None

  • Reverse Complement = None

  • Read Stitching = None

  • Variant Caller = None

  • Applicable analysis fields for the selected Workflow = None

DNA Enrichment
  • Workflow = DNA Enrichment

  • Read 1 Cycles = 251

  • Custom Primers = None

  • Aligner = BWA-MEM

  • Annotation = None

  • Export to gVCF = None

  • Flag PCR Duplicates = Yes

  • Genome Folder = Required

  • Indel Realignment = Yes

  • Indel Repeat Filter Cutoff = None

  • Manifest = Required

  • Manifest Padding = 150

  • Picard HS Metric Reporting = No

  • Reverse Complement = None

  • Read Stitching = None

  • Variant Caller = Starling

  • Applicable analysis fields for the selected Workflow =

    • Aligner (BWA-Backtrack Legacy, BWA-MEM)

    • Flag PCR Duplicates

    • Genome Folder (fill in the folder path)

    • Indel Realignment

    • Indel Repeat Filter Cutoff (if Variant Caller is Somatic)

    • Manifest (fill in the file name)

    • Manifest Padding

    • Picard HS Metric Reporting

    • Variant Caller (Starling, Somatic, GATK)

    • Variant Frequency Percentage (if Variant Caller is Somatic)

DNA Amplicon
  • Workflow = DNA Amplicon

  • Read 1 Cycles = 251

  • Custom Primers = None

  • Aligner = BWA

  • Annotation = RefSeq

  • Export to gVCF = None

  • Flag PCR Duplicates = None

  • Genome Folder = Required

  • Indel Realignment = Yes

  • Indel Repeat Filter Cutoff = None

  • Manifest = Required

  • Manifest Padding = None

  • Picard HS Metric Reporting = None

  • Reverse Complement = None

  • Read Stitching = None

  • Variant Caller = Germline

  • Variant Caller Depth Filter = 10

  • Variant Quality Filter = 30

  • Applicable analysis fields for the selected Workflow =

    • Aligner (BWA, TruSeq Amplicon Aligner)

    • Annotation (RefSeq, Ensembl)

    • Genome Folder (fill in the folder path)

    • Indel Realignment

    • Manifest (fill in the file name)

    • Read stitching (if Aligner is TruSeq Amplicon Aligner)

    • Variant Caller (Germline, Somatic)

    • Variant Caller Depth Filter (10–10000)

    • Variant Frequency Percentage (if Variant Caller is Somatic)

    • Variant Quality Filter (2–1000)

Global Fields

The following table shows the global fields that are configured to display on the Queue, Ice Bucket, and Record Details screens of the Denature and Dilute (MiSeq v3.2) step:

The Submitted Sample field, Progress, (added from previous MiSeq workflow) is obsolete in MiSeq v3.2.

Global Field Configuration (Submitted Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Read Length

ℹ Displays on Queue & Ice Bucket screens

Text

Sequencing Method

ℹ Displays on Queue & Ice Bucket screens

Text Dropdown

  • Custom Entries

  • Presets

    • Single Read

    • Paired End Read

    • Indexed Single Read

    • Indexed Paired End Read

Global Field Configuration (Derived Sample)

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Final Loading Concentration

ℹ Displays on Record Details screen

Numeric Dropdown

  • Required Field

  • Custom Entries

  • Presets

    • 225

    • 400

  • Decimal places displayed = 0

Step File Placeholders

Placeholders for the following files are configured on the Record Details screen of the Denature and Dilute (MiSeq v3.2) step.

Lab Tracking Form
  • Manually uploaded

  • This item in Clarity LIMS allows the lab scientist to attach a lab-specific tracking form to the step manually.

MiSeq SampleSheet
  • Automatically attached

  • This CSV file is automatically generated by Clarity LIMS for use with the MiSeq system. The file can be opened as a text file or an Excel spreadsheet.

MiSeq SampleSheet Generation Log
  • Automatically attached

  • This log file is automatically generated by Clarity LIMS. The log file captures any errors that Clarity LIMS might encounter when generating the sample sheet.

Log File
  • Automatically attached

  • This log file is automatically generated by Clarity LIMS. The log file captures the status of the EvaluateDynamicExpression script that is invoked by the Set Next Step - Advance automation.

Step 3: MiSeq Run (MiSeq v3.2)

Set Next Step - Advance Automation

This automation advances samples to the next step in the protocol. The automation is automatically triggered by exiting the Record Details screen.

The default command line is as follows.

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 {compoundOutputFileLuid5}"

Master Step Fields

The following fields are configured on the MiSeq Run (MiSeq v3.2) step. These fields display on the Record Details screen at run time. The read-only fields are automatically populated at the end of the run.

MiSeq Run (MiSeq v3.2) Master Step Field Configuration

Field Name

Field Type

Options

Additional Options and Drop-Down Items

Chemistry

Text

Read Only

Comment

Multiline Text

Experiment Name

Text

Read Only

Finish Date

Date

Read Only

Flow Cell ID

Text

Read Only

Flow Cell Version

Text

Read Only

Index 1 Read Cycles

Numeric

Read Only

Decimal Places Displayed: 0

Index 2 Read Cycles

Numeric

Read Only

Decimal Places Displayed: 0

Output Folder

Text

Read Only

PR2 Bottle ID

Text

Read Only

Read 1 Cycles

Numeric

Read Only

Decimal Places Displayed: 0

Read 2 Cycles

Numeric

Read Only

Decimal Places Displayed: 0

Reagent Cartridge ID

Text

Read Only

Reagent Cartridge Part #

Text

Read Only

Run ID

Text

Read Only

Run Type

Text

Read Only

Status

Text

Read Only

Workflow

Text

Read Only

Global Fields

There are several sample and measurement global fields that are displayed on the Record Details screen of the MiSeq Run (MiSeq v3.2) step. These fields are autopopulated at the end of the sequencing run.

Step File Placeholders

Placeholders for the following files are configured on the Record Details screen of the MiSeq Run (MiSeq v3.2) step:

  • Illumina Run Report (automatically attached)

  • Link to Run Folder (automatically attached)

  • Run Parameters (automatically attached)

  • Run Info (automatically attached)

  • Lab Tracking Form (manually uploaded)

  • Log File (automatically attached)

Sample Sheet Generation

Sample sheet generation occurs in the Denature & Dilute (MiSeq v3.2) step. This step places samples on the container loaded in the system.

The default configuration provides only the Validate Run Setup and Generate MiSeq SampleSheet automation. This automation uses the Template File Generator (DriverFileGenerator.jar) and a template file to generate a CSV format file for use with the MiSeq Control Software (MCS).

The sample sheet content is determined by the fields on the Record Details screen of the step in the Step Data table. The values entered into these fields are used to populate the sample sheet.

To customize the template used to create the sample sheet, you can insert additional columns.

The following additional details are available:

Sequencing Results Parsing

The MiSeq Run (MiSeq v3.2) step records information for the flow cell lane and generates a report summarizing the results. In addition, run parameters, run info, and a link to the run folder are automatically captured.

Generated and Captured Files

The following table describes the run information files, reports, placeholders, and links that Clarity LIMS automatically generates or captures during a sequencing run:

Run Information Generated or Captured by MiSeq Run (MiSeq v3.2) Step

Item

Description

Run Info Run Parameters

  • These XML files are automatically captured by Clarity LIMS from the run folder of the system. They include the key run parameters that are parsed out into step custom fields in Clarity LIMS.

Link to Run Folder

  • This link is the path to the network run folder where the data that was captured from the system during the run is stored. The link is automatically generated by Clarity LIMS.

Illumina Run Report

  • This report provides key information about the run and the samples on the flow cell. The report is automatically generated by Clarity LIMS.

  • Information includes the flow cell ID, run directory location, and primary analysis metrics for the sequencing run. Information is summarized per flow cell lane for the entire run and individual reads for paired-end runs.

  • These metrics are compared against the per lane averages of the sequencing run. The per lane averages are calculated using metrics from the last five sequencing runs. Any values outside of one standard deviation are highlighted.

Lab Tracking Form

  • This item in Clarity LIMS allows you to manually attach a lab-specific tracking form to the step.

Metadata

The following list shows metadata that Clarity LIMS automatically captures from the Illumina sequencing software as part of a sequencing run. This information is gathered from various run result files and events.

  • Chemistry

  • Experiment Name (entered in software)

  • Finish Date (run completion date)

    • If the End Run event contains a date in the format YYYY-MM-DD, Finish Date is set to the date in the event file.

    • If the End Run event does not contain a date or the date is in the wrong format, Finish Date is set to the date when the event file is processed.

  • Flow Cell ID

  • Flow Cell Version

  • Index 1 Read Cycles (intended Index cycles)

  • Index 2 Read Cycles (intended Index cycles)

  • Output Folder (run folder root)

  • PR2 Bottle ID

  • Reagent Cartridge ID

  • Reagent Cartridge Part #

  • Read 1 Cycles

  • Read 2 Cycles

  • Run ID (the unique run ID)

  • Run Type

  • Status (current status of the sequencing run on the instrument)

  • Workflow

Primary Analysis Metrics

The following table lists the real-time analysis (RTA) primary analysis metrics Clarity LIMS automatically captures and records per read, for samples in each flow cell lane. These metrics are captured upon run completion and are stored as fields in the Sample Details table on the Record Details screen.

To see both per read and per lane metrics, expand the output.

RTA Primary Analysis Metrics Captured by MiSeq Run (MiSeq v3.2) Step

Per Read LIMS Field Name (Stored on derived sample/analyte input to the step)

Per Lane LIMS Field Name (Stored in measurement placeholders in the Sample Details table on the Record Details screen)

% Aligned R1

% Aligned R1

% Aligned R2

% Aligned R2

% Bases >=Q30 R1

% Bases >=Q30 R1

% Bases >=Q30 R2

% Bases >=Q30 R2

% Error Rate R1

% Error Rate R1

% Error Rate R2

% Error Rate R2

% Phasing R1

% Phasing R2

% Prephasing R1

% Prephasing R2

%PF R1

%PF R2

Cluster Density (K/mm^2) R1

Cluster Density (K/mm^2) R2

Intensity Cycle 1 R1

Intensity Cycle 1 R1

Intensity Cycle 1 R2

Intensity Cycle 1 R2

Reads PF (M) R1

Reads PF (M) R2

Yield PF (Gb) R1

Yield PF (Gb) R1

Yield PF (Gb) R2

Yield PF (Gb) R2

How It Works

  1. The sequencing service runs on the Clarity LIMS server. The service detects event files that instrument RTA produces as the run progresses. The event files let the service know where to find the run data.

  2. As the run data are written out and the End Run event is detected, the following events occur:

    • The data are matched to the step based on the reagent cartridge ID that was entered or scanned on the Denature and Dilute (MiSeq v3.2) step.

    • Read-only field values on the Record Details screen are populated accordingly.

  3. When the service has finished processing the end run event and updating the fields in Clarity LIMS, the sequencing service generates the report and attaches it to the step.

Scripts and Files Installed

This integration requires components installed with the Illumina Preset Protocols (IPP).

The Illumina MiSeq Integration Package v8.3.0 RPM installs the scripts and files listed in the following table.

Component

Location

Description

configure_extensions_miseq_sequencingservice-v8.sh

/opt/gls/clarity/config/

Script that installs the service properties in the database.

log4j.xml

/opt/gls/clarity/extensions/Illumina_MiSeq/v8/SequencingService/conf

File containing the settings for logging the sequencing jar.

miseq-sequencing-v8.jar

/opt/gls/clarity/extensions/Illumina_MiSeq/v8/SequencingService

Jar file containing API-based Clarity LIMS extensions used for capturing run results and report generation.

InterOp libraries

/opt/gls/clarity/extensions/Illumina_MiSeq/v8/lib

Illumina shared library for parsing InterOp data files.

MiSeqSamplesheetv3.csv

ℹ Installed by IPP

/opt/gls/clarity/extensions/conf/driverfiletemplates

Template file used for file generation.

Properties Installed

Consumables Installed

Reagent Categories and Kits

Reagent categories or label groups are installed with the IPP workflow configuration slices.

The MiSeq Reagent Kit is included in the Illumina MiSeq Integration.

Control Types

The PhiX v3 control type is included in the Illumina MiSeq Integration.

Container Types

The following container types are included in the Illumina MiSeq Integration:

  • MiSeq Reagent Cartridge

  • 96 well plate

  • Tube

All one-dimensional container types with both numeric rows and numeric columns are supported.

Instrument Integration

To make sure that the Illumina instrument warranty remains valid, the instrument integration must be performed and maintained by the Clarity LIMS Support team. To perform this integration, the Support team requires remote access to the system while it is idle.

The following steps are performed by the Clarity LIMS Support team when configuring the sequencing for use with the Illumina MiSeq Integration.

  1. Create a directory on the local computer to hold the batch files. These batch files write event files to the network attached storage (NAS) shares.

  2. Create a directory on the NAS to hold the event files.

  3. Modify Illumina software configuration files to call the batch files that create the event files.

  4. Update sequencing service default properties to match the specifics of the installation.

Rules and Constraints

The Illumina MiSeq Integration operates with the following constraints:

  • The reagent cartridge ID must be unique. There should not be multiple reagent cartridge containers in the system with the same name.

  • The reagent cartridge ID must be scanned as the reagent cartridge Container Name on the Denature & Dilute (MiSeq v3.2) step.

This automation validates the information entered on the Record Details screen, generates the sample sheet (refer to ), and attaches the sample sheet to the Denature and Dilute step.

For more information, refer to .

For details, refer to .

For a sample template that you can download and customize for the lab, refer to .

For instructions on customizing the template, refer to .

Refer to for the properties installed with Illumina MiSeq Integration v8.3.0.

MiSeq Integration v8.3.0 User Interaction, Validation and Troubleshooting
Clarity LIMS (Clarity & LabLink Reference Guide) documentation
Clarity LIMS (Clarity & LabLink Reference Guide) documentation
Illumina Instrument Sample Sheets (NGS v5.17 & later)
Creating Template Files
Sample Sheet Generation
Sequencing Results Parsing
Generated and Captured Files
Integration Properties Details