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
Getting Started
Running Toil
Developing Toil Workflows
- Developing a Workflow
- Scripting Quick Start
- Job Basics
- Invoking a Workflow
- Specifying Commandline Arguments
- Resuming a Workflow
- Functions and Job Functions
- Workflows with Multiple Jobs
- Dynamic Job Creation
- Promises
- Promised Requirements
- FileID
- Managing files within a workflow
- Using Docker Containers in Toil
- Services
- Checkpoints
- Encapsulation
- Depending on Toil
- Best Practices for Dockerizing Toil Workflows
- Toil Class API
- Job Store API
- Toil Job API
- Job Methods API
- Job.Runner API
- job.fileStore API
- Batch System API
- Job.Service API
- Exceptions API
Contributing to Toil
Appendices
