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(howto) Set up an environment to test your workflows locally

KateNKateN Cambridge, MAMember, Broadie, Moderator admin
edited April 2018 in Tutorials

When creating WDL workflows, you can test on a local installation of the Cromwell execution engine prior to uploading and testing in FireCloud. Cromwell is the workflow execution service used to run and test WDL workflows.

Cromwell is a Java application which requires the Java 8 runtime environment. Install the Java 8 Developer Kit if you do not already have it. It is important to note that you should install the JDK, not the runtime environment or JRE.

You must also download Docker for Cromwell to work. Installation instructions can be found here.

After ensuring you have Java 8 installed on your laptop, download the latest Cromwell jar here.

To test that your environment works, try running the HelloWorld wdl below. You do not need an inputs file to run this workflow, and the output should be Hello World written in the stdout file.

workflow HelloWorld {

    call WriteGreeting
}

task WriteGreeting {

    command {
        echo "Hello World"
    }
    output {
        File outfile = stdout()
    }
}
Post edited by KateN on
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