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README.md

About Toil

Toil is a scalable, efficient, cross-platform pipeline management system written entirely in Python and designed around the principles of functional programming. https://toil.ucsc-cgl.org/

Training material and documentation

https://toil.readthedocs.io/en/latest/

Tutorial for using Toil Python API for workflows https://toil.readthedocs.io/en/latest/developingWorkflows/developing.html

Tutorial for using Toil with WDL https://toil.readthedocs.io/en/latest/running/wdl.html

Tutorial for using Toil with CWL https://toil.readthedocs.io/en/latest/running/cwl.html

Community-developed workflows in Toil

Add description and links to community-developed pipelines.

Running the proof of concept Toil pipeline

General

  1. Install Toil by following the instructions listed here

  2. Install Docker by following the instructions listed here Docker isn't a necessity however we offer the option of using docker to increase the portability of the workflows

WDL

  1. Install the files under toil/wdl locally
    • example.wdl is the workflow specification
    • wdl_input.json is the input data, change this file to point to desired paths
  2. Run the pipeline with the following command: toil-wdl-runner example.wdl wdl_input.json

CWL

  1. Install the files under toil/cwl locally
    • example.cwl is the workflow specification
    • fastqc.cwl is a command line tool used by the workflow
    • salmonIndex.cwl is a command line tool used by the workflow
    • salmonQuant.cwl is a command line tool used by the workflow
    • cwl_input.yaml is the input data, change this file to point to desired paths
  2. Run the pipeline with the following command: toil-cwl-runner example.cwl cwl_input.yaml

Python

  1. Install the files under toil/python locally
    • draft.py is both workflow specification and input, modify for desired file paths
  2. Run the pipeline with the following command: python3 draft.py file:my-job-store

Notes and Contribution

This pipeline is a minimal example of using Toil. We welcome contributions to the documentation and workflow, please create an issue or submit a pull request!

How to cite Toil

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