Cromwell

Cromwell is the original execution engine for WDL and can be run in either server or local command line mode. A majority of Cromwell users today run their workflows in Terra, using Docker and workflows in the WDL format, however, Cromwell supports various other backends and workflows.

Below will outline how to run the 02_download_collection_files workflow in the WDL format locally using Cromwell and Docker.

Prerequisites

• java 8+

• Docker

• (Optional) cURL

• (Optional) git

Getting Started

The following software and workflow are required and will be downloaded, installed, and used as part of this tutorial:

• cromwell.jar

• 02_download_collection_files.wdl

Download the worked examples repository by one of the following methods.

1. Clone with Git

git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git

or

1. Download and Unzip

It is assumed that all commands will be run from the root directory of this repository on your local machine. From the directory where you’ve downloaded the examples repository.

cd dnastack-client-library-worked-examples/

Download the latest version of Cromwell by one of the following methods.

1. Using cURL

curl -o cromwell.jar -L https://github.com/broadinstitute/cromwell/releases/download/64/cromwell-64.jar

or

1. Download from the releases page to the current directory and rename the file to cromwell.jar.

Running the workflow

To run the workflow:

java -jar cromwell.jar run ./examples/wdl/02_download_collection_files.wdl

Output files can be found in the directory cromwell-executions/download_first_ten_files/<workflow id>/call-download_files/execution/out/ where <workflow id> corresponds to ID given by cromwell.