Frequently Asked Questions
Questions that people ask often
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Which workflow execution engines support WDL? What is Cromwell?
Please see the getting started guide on execution for information about execution engines and Cromwell.For detailed information about Cromwell, check out Cromwell's documentation website.
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What do I need to set up to write and execute WDL workflows?
Below is a list of the basic requirements / things you need to get in order to run workflows written in WDL (using the Cromwell execution engine, because that's what we use), with installation instructions where necessary. Because we use GATK in m...
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How can I run different versions of Java on the same computer?
We sometimes need to be able to use multiple versions of Java on the same computer to run command-line tools that have different version requirements. At the time of writing, GATK requires an older version of Java (1.7), whereas Cromwell requires ...
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Can runtime parameter values be generated dynamically?
Say you have a task where the runtime requirements (like disk size and memory) can vary a lot depending on e.g. the size of the input files for a given run. To minimize costs, you want to be able to allocate those runtime parameters depending on w...
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