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 or higher

• Docker

• Optional: cURL and git

Setup Instructions

You'll need to download:

• cromwell.jar

• 02_download_collection_files.wdl

Getting the Example Workflow

Download the worked examples repository using either method:

Clone with Git

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

Or Download and unzip the repository manually.

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/

Installing Cromwell

Download the latest Cromwell version:

Using cURL

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

Or download manually from the releases page and rename 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.

All commands should be run from the repository's root directory on your local machine.