wdl

About WDL

The Workflow Description Language (WDL) is a workflow specification language. Workflow written in WDL can be executed with cromwell or Toil(experimental).

Training material and documentation

• WDL tutorials
• WDL documentation

Community-developed workflows in snakemake

BioWDL contains a collection of community developed pipelines written in WDL.

Running the proof of concept WDL pipeline

1. Install cromwell by following the instructions here
2. Install the files from this repo locally
   • example.wdl is the workflow specification
   • wdl_input.json is the input data - change this file to point to your desired paths
   • options.json allows you to specify extra options for cromwell, such as an output directory. More information here
3. Run the pipeline with the following command:
   • java -jar path/to/cromwell-53.1.jar run example.wdl --inputs wdl_input.json -o options.json

Notes and Contribution

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

How to cite WDL

Voss K, Gentry J and Van der Auwera G. Full-stack genomics pipelining with GATK4 + WDL + Cromwell (version 1; not peer reviewed). F1000Research 2017, 6(ISCB Comm J):1379 (poster) (doi: 10.7490/f1000research.1114631.1)