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• Introduction
• Installing the Analysis Automation Server Plugin
• Running analysis automation
  • Configuring user for running analysis automation service
  • Starting and stopping analysis automation service
  • Monitoring analysis automation service
    • Viewing job status and errors
    • Resetting submission statistics
• Configuring analysis automation
  • Managing automation configurations
    • Adding automation configuration
    • Editing automation configuration
    • Deleting automation configuration
    • Multi-configuration operations
    • Importing and exporting configurations
  • Concept definitions
    • Definition of sample completion
    • Definition of sample grouping
    • Definition of wildcards
    • Definition of placeholders
  • Configuration settings
    • Description
    • Enabled
    • Sequencer type
    • Sequencer folder
    • Workflow matcher
    • Sample completion
    • Sample sheet
    • Sample detection delay
    • Filename pattern
    • Files to ignore
    • Workflow
    • Sample types
    • Output folder
    • Export folder
    • Batch folder
    • Output prefix
    • Execution environment
    • Grid preset
    • File system location
    • Cloud preset
    • S3 bucket
• Troubleshooting
  • Accessing log file
  • Issues
    • Samples produced by sequencer were not submitted for analysis
    • Server cannot check if sequencer is done writing sample file to disk
• System requirements
  • Linux and macOS
    • Support for checking if sequencer is done writing sample file to disk
  • Windows
    • Path length limit

Concept definitions

The following sections provide definitions of concepts relevant for configuring automation for an analysis workflow.

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Subsections

• Definition of sample completion
• Definition of sample grouping
• Definition of wildcards
• Definition of placeholders

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