FieldPathogenomics

Contents:

• Introduction
  • The Luigi Workflow Manager
  • General Set-up
  • Next Steps
• Getting Started
  • Setting up a local develop environment
  • Starting the Scheduler
  • Connecting to the Scheduler
  • Pulling
  • Releasing
• Writing a new task
  • Slurm Executable Task
  • Slurm Task
  • Notebook Tasks
  • Database Tasks
  • Committed Tasks
• Using ScatterGather
• Protocols
  • Generating a new callset
  • Generating a new tree
• Output Data
• Pipelines
  • Library Pipeline
  • Callset Pipeline
  • Tree Pipeline
  • Transcripts Pipeline
• Databases
  • Sample Metadata Table
  • Alignments Statistics Table
• API Documentation

Indices and tables

• Index
• Module Index
• Search Page