Toil Documentation¶

Toil is an open-source pure-Python workflow engine that lets people write better pipelines.

Check out our website for a comprehensive list of Toil’s features and read our paper to learn what Toil can do in the real world. Please subscribe to our low-volume announce mailing list and feel free to also join us on GitHub and Gitter.

If using Toil for your research, please cite

Vivian, J., Rao, A. A., Nothaft, F. A., Ketchum, C., Armstrong, J., Novak, A., … Paten, B. (2017). Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology, 35(4), 314–316. http://doi.org/10.1038/nbt.3772

Common Workflow Language (CWL)

CWL in Toil
Running CWL Workflows

Workflow Description Language (WDL)

WDL in Toil
Running WDL with Toil
- Toil WDL Runner Options
- Managing Workflow Logs
Developing a WDL Workflow
WDL Conformance Testing

Advanced Toil Usage

Introduction
Commandline Options
Toil Utilities
Toil Debugging
Running in the Cloud
- Managing a Cluster of Virtual Machines (Provisioning)
  - Toil Cluster Utilities
- Storage (Toil jobStore)
Cloud Platforms
HPC Environments
- Running on Slurm
  - Slurm Tips
- Standard Output/Error from Batch System Jobs
Workflow Execution Service (WES)

Contributing to Toil

Running Tests
Developing with Docker
- Making Your Own Toil Docker Image
- Running a Cluster Locally
Maintainer’s Guidelines
Pull Request Checklists
- Reviewing Pull Requests
- Merging Pull Requests

Appendices

Toil Architecture
Minimum AWS IAM permissions
Auto-Deployment
Environment Variables
API Reference
- toil
  - Subpackages