Overview

This section describes how to develop Toil workflows using the Toil API, the batch system API, and the job store API.

Specifically, the developing Toil section documents the following:

• Developing a Workflow
  • Scripting quick start
  • Job basics
  • Invoking a workflow
  • Specifying arguments via the command line
  • Resuming a workflow
  • Functions and job functions
  • Workflows with multiple jobs
  • Dynamic job creation
  • Promises
  • Promised Requirements
  • FileID
  • Managing files within a workflow
    • Staging of files into the job store
  • Using Docker containers in Toil
  • Services
  • Checkpoints
  • Encapsulation
  • Depending on Toil
  • Best practices for Dockerizing Toil workflows
• Toil API
  • Job methods
  • Job.FileStore
  • Job.Runner
  • Toil
  • Job.Service
  • FunctionWrappingJob
  • JobFunctionWrappingJob
  • EncapsulatedJob
  • Promise
  • Exceptions
• Batch System API
  • Batch System Enivronmental Variables
  • Batch System API
• Job Store API