Supported Languages

Overview

In the realm of bioinformatics and computational analysis, workflow languages play a pivotal role in orchestrating complex processes.

WDL (Workflow Description Language)

Workbench offers native support for WDL. Workflow Description Language (WDL, pronounced ‘widdle’). WDL is an open, community-driven workflow language stewarded by the OpenWDL organization. WDL is a popular choice among bioinformatics professionals for defining and executing complex workflows. Its structured syntax and capabilities make it a preferred option for many who are looking to design robust and reproducible pipelines.

Example of WDL:

task echoString {
    input {
        String message
    }

    command {
        echo ${message}
    }

    output {
        String echoedMessage = read_string(stdout())
    }

    runtime {
        docker: "ubuntu:latest"
    }
}

workflow SimpleWorkflow {
    input {
        String inputMessage
    }

    call echoString {
        input: message = inputMessage
    }

    output {
        String outputMessage = echoString.echoedMessage
    }
}

When you run this workflow with an input message, it will create a task that simply echoes that message.

Conclusion

Choosing the right workflow language is crucial for seamless execution and scalability. Workbench, with its support for WDL, ensures that its users can leverage one of the industry's leading workflow languages.