LogoLogo
Illumina KnowledgeIllumina SupportSign In
  • Home
  • Start Here
  • Overview
    • Software Overview
    • What's New
    • FAQ
    • Technical Assistance
    • Release Notes
    • Data Model
    • Account Types
    • Professional Services
  • Automate
    • Data Automation Overview
    • Automatic Data Flow
    • Automatic Data Aggregation
      • Unlock Biosamples
      • Correct Aggregation
    • Request A Lab Requeue
    • Yield
    • Yield Examples
      • Example 1
      • Example 2
      • Example 3
    • Automate Lane QC
    • Manual QC
    • Statuses
  • Manage Data
    • Import Demo Data
    • Delete Data
    • Import Data Into Projects
      • FastQ Upload Requirements
    • Download Data
      • Download Individual Files
      • Download Datasets
      • Download Run Files
      • Download Project Files
      • Download Analysis Files
      • Download Samples
    • Copy Datasets
    • Transfer Ownership
    • Archival Storage
    • Automatic Data Deletion
  • Sequence
    • Sample Sheets
      • Mapping Sequencing Runs to Biosamples
    • Fix Indexes
    • Plan Runs
      • Plan a NextSeq 1000/2000 Run
        • Set up NextSeq 1000/2000 Secondary Analysis
        • Custom Noise Baseline File
      • Plan a NovaSeq X Series Run
        • Set up NovaSeq X Series Secondary Analysis
        • NovaSeq X Series Custom Reference File
      • Create a Custom Index Adapter Kit
      • Import samples
      • Requeue a Planned Run
      • Analysis Configuration Template
      • Prep Tab
        • Create Biological Samples
        • Import Biological Samples
        • Prep Libraries
        • Import Sample Libraries
        • Set Up a Custom Library Prep Kit
        • Pool Libraries
        • Plan Run Using Prep Tab
        • Neo Prep
          • Configure
          • Assign Wells
          • Review
  • Microarray
    • Getting Started
      • Troubleshooting iScan Integration
    • Analysis Setup
    • Data Management
  • Analyze
    • Analyze Data
    • Launching Apps
    • Analysis Workflows
    • Re-Launch Analysis
    • Auto Analysis QC
    • Basespace Apps
  • Collaborate
    • Sharing Data
    • Access Shared Data
    • Share with Collaborators
      • Share Analyses
      • Track Analysis Delivery Status
      • Share By Link
      • Share By Email
      • Manage Collaborator Access
      • Data Access After Share / Transfer
    • Workgroups
    • Manage Workgroups
      • Access Workgroups
      • Create a Workgroup and Assign Admins
      • Rename a Workgroup
      • Add Users to a Workgroup
      • Remove Users from a Workgroup
      • Add Admins to a Workgroup
      • Remove Admins from a Workgroup
      • Manage User Access
  • Manage Your Account
    • Change Password
    • iCredits and Billing
    • Generate Usage Reports
    • Manage Enterprise Domains
    • Global Regions
  • Developer Tools
    • Basespace API
    • Developer Tools
  • Files Used By Basespace
    • Biosample Workflow Files
    • BAM Files
    • FastQ Files
    • Quality Scores
    • VCF Files
    • gVCF Files
  • Data
    • View Data
      • View Runs
        • View Run Summary
        • View Run Biosamples
        • View Run Samples
        • View Run Charts
        • View Run Metrics
        • View Run Indexing QC
        • View Run Samplesheet
        • View Run Files
      • View Projects
      • View Analyses
      • View Biosamples
  • Projects
    • Create a Project
    • Edit Project Details
  • Runs
    • Fix Sample Sheet
    • Automated Run Zipping
  • Biosamples
    • Biosample Overview
    • Manage Biosamples
    • Biosample Workflow
      • Add Biosamples
      • Add Prep Requests
      • Add Analysis Workflows to an Existing Biosample
      • Schedule Multiple Analysis Workflows for a Biosample
      • Schedule Analysis Workflow - Multiple Biosamples
    • Associating Biosamples with Projects
  • Samples
    • Combine Samples
    • Copy Samples
  • Cmd Line Interfaces
    • Basespace CLI
      • Introduction to Basemount
  • Additional Resources
    • Additional Resources
      • Informatics Blog
      • Coverage Calculator
      • Support Bulletins
      • Training
      • Security Model
      • Data Streaming
      • AWS
  • Releases
    • Previous Releases
      • 2025
        • 7.33.0 - Shared BCL Convert Section
        • 7.32.0 - File Preview in Search
        • 7.31.0 - Usage Explorer
        • 7.30.0 - Prep Tab Deprecation
      • 2024
        • 7.29.0 - Improved Analysis Error Reporting
        • 7.28.0 - MiSeq i100 Support
        • 7.27.0 - App Store Upgrade
        • 7.26.0 - Prep Tab Obsolescence Notification
        • 7.25.0 - Project Column in the Analysis Files Tab
        • 7.24.0 - Requeue Improvements
        • 7.23.0 - BaseSpace CLI v1.6.0
        • 7.22.0 - Analysis Autolaunch for NovaSeq X Manual Mode Runs
        • 7.21.0 - Improved Look and Feel
        • 7.20.0 - Analysis List Improvements
        • 7.19.0 - Transfer of NovaSeq X Projects
        • 7.18.0 - Custom Kit Deletion
      • 2023
        • 7.17.0 - Deletion of Biosample Default Projects
        • 7.16.0 - Transfer of NovaSeq X Runs
        • 7.15.0 - Compatibility Filtering in Run Planning
        • 7.14.0 - Native App Engine Update
        • 7.13.0 - Sharing for NovaSeq X Runs and Analyses
        • 7.12.0 - Combined New and Classic Modes
        • 7.11.0 - NovaSeq X Analysis Requeue
        • 7.10.0 - NovaSeq X Analysis Autolaunch Improvements
        • 7.9.0 - Multi-Analysis Run Planning
        • 7.8.0 - Performance Improvements
      • 2022
        • 7.7.0 - NovaSeqX Support
        • 7.6.0 - Custom Configuration Files in Microarray Analysis Setup
        • 7.5.0 - Performance Enhancements
        • 7.4.0 - Run Planning Enhancements
        • 7.3.0 - Improve App Launch Performance
        • 7.2.0 - FastQ Generation and other Bug Fixes
        • 7.1.0 - FastQ Related Fixes and Performance Improvements
        • 7.0.0 - Datasets and Apps Performance
        • 6.19.0 - ICA Integration Enhancements
        • 6.18.0 - ICA Integration with BCL Convert
        • 6.17.0 - Preliminary ICA Integration
      • 2021
        • 6.16.0
        • 6.15.0
        • 6.14.0
        • 6.13.0
        • 6.12.0
        • 6.11.0
        • 6.10.0
        • 6.9.0
        • 6.8.0
        • 6.7.0
        • 6.6.0
        • 6.5.0
      • 2020
        • 6.4.0
        • 6.3.0
        • 6.2.0
        • 6.1.0
        • 6.0.0
        • 5.46.0
        • 5.45.0
        • 5.44.0
        • 5.43.0
        • 5.42.0
      • 2019
        • 5.41.0
        • 5.40.0
        • 5.39.0
        • 5.38.0
        • 5.37.0
        • 5.36.0
        • 5.35.0
        • 5.34.0
        • 5.33.0
        • 5.32.0
        • 5.31.0
        • 5.30.0
      • 2018
        • 5.29.0
        • 5.28.0
        • 5.27.0
        • 5.26.0
        • 5.25.0
        • 5.24.0
        • 5.23.0
        • 5.22.0
        • 5.21.1
        • 5.21.0
        • 5.20.0
        • 5.19.0
        • 5.18.0
        • 5.17.0
        • 5.16.0
        • 5.15.0
        • 5.14.0
        • 5.13.0
        • 5.12.0
        • 5.11.0
      • 2017
        • 5.10.0
        • 5.9.0
        • 5.8.0
        • 5.7.0
        • 5.6.0
        • 5.5.0
        • 5.4.0
        • 5.3.0
        • 5.2.0
        • 5.1.0
        • 5.0.0
        • 4.27.0
        • 4.26.0
        • 4.25.0
        • 4.24.0
        • 4.23.0
        • 4.22.0
        • 4.21.0
        • 4.20.0
        • 4.19.0
        • 4.18.0
        • 4.17.0
        • 4.16.0
        • 4.15.0
      • 2016
        • 4.14.0
        • 4.13.0
        • 4.12.0
        • 4.11.0
        • 4.10.0
        • 4.9.0
        • 4.8.0
        • 4.7.0
        • 4.6.0
        • 4.5.0
        • 4.4.0
        • 4.3.0
        • 4.2.0
        • 4.1.0
        • 4.0.4
        • 4.0.3
        • 4.0.2
        • 4.0.1
        • 4.0.0
      • 2015
        • 3.23.2
        • 3.23.1
        • 3.23.0 Issues
        • 3.23.0
        • 3.20.4
        • 3.20.3
        • 3.20.0
        • 3.19.1
        • 3.19.0
        • 3.18.0
        • 3.17.1
        • 3.17.0
        • 3.16.2
        • 3.16.0
        • 3.15.2
        • 3.15.1
    • Release notifications
Powered by GitBook
On this page
  • Create an Analysis Workflow
  • Modify an Analysis Workflow
  • Schedule Analysis Workflow to Automatically Launch
  • Cancel an Analysis

Was this helpful?

Export as PDF
  1. Analyze

Analysis Workflows

PreviousLaunching AppsNextRe-Launch Analysis

Last updated 1 year ago

Was this helpful?

Analysis workflows are packaged templates of BaseSpace Sequence Hub Apps with predefined settings and QC thresholds to support automation of running analyses. Use an analysis workflow to automatically launch the same app configurations on different biosamples in the project.

When you assign an analysis workflow using a biosample workflow file, the workflow status is listed as Pending. After data are received and conditional dependencies are met, the analysis is launched and the status is listed as Running.

Create an Analysis Workflow

For information about creating an Analysis Workflow for an existing app, using your own settings or QC thresholds with an existing BaseSpace Sequence Hub app, see the developer documentation at .

Modify an Analysis Workflow

Analysis Workflows can be modified by their owners or members of the workgroup in which the workflow was created. If you need to modify a workflow, Illumina recommends creating a new workflow and adding a version number to the workflow name.

Schedule Analysis Workflow to Automatically Launch

  1. Upload a Biosample Manifest with analysis workflows set for one or more biosamples. See .

  2. Sequence data for the biosample.

  3. BaseSpace Sequence Hub checks that dependencies are met, collects data sets associated with the biosample, and launches the analysis.

BaseSpace Sequence Hub excludes datasets that have been QC Failed or are linked to QC failed libraries, pools, or lanes.

Cancel an Analysis

  1. Select one or more analyses that are Running or Pending.

  2. Select the Status drop-down arrow, point to Cancel, and then select Analysis.

developer.basespace.illumina.com
Biosample Workflow