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.
The following software and workflow are required and will be downloaded, installed, and used as part of this tutorial:
Download the worked examples repository by one of the following methods.
- Clone with Git
git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git
- Or 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.
Download the latest version of Cromwell by one of the following methods.
- Using cURL:
curl -o cromwell.jar -L https://github.com/broadinstitute/cromwell/releases/download/64/cromwell-64.jar
- Or download from the releases page to the current directory and rename the file to
Running the workflow
To run the workflow:
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.