The Common Workflow Language (CWL) is an open specification for describing command-line tools and workflows. CWL documents are used in many scientific disciplines to ensure that tools and workflows can be executed in a manner that is portable across workflow engines and computer systems. ToolJig facilitates creation of CWL tool descriptions, workflows, and input-object files for those tools. This video provides insight about ToolJig. This portion of ToolJig focuses on building workflows. Use this app if you wish to create tool descriptions.
Workflows created in ToolJig are compatible with v1.2 (or 1.0 or 1.1) of the CWL specification. You can see some example CWL workflows here. Our goal is support common use cases for research analyses. However, some options within the CWL specification are not supported; users should consult the specification if they wish to use other available features.
This app was created by the Piccolo lab. You can read our paper here. We are open to your feedback! Please submit an issue if you would like to report a bug or request a feature.
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The first step to creating a workflow is to upload CWL tool descriptions that will be used as steps within the workflow.
Here you can see which tool files have been uploaded. You can also remove () these files if you wish.
If you previously created a CWL workflow using ToolJig, you can upload it here and then edit it below. If you do not need to edit an existing CWL file, skip this step.
This section enables you to create a CWL workflow. Please fill in the information as requested below.
Please correct the following error(s):
Here you can define each step of the workflow.
Here you can see which steps have been added. You can also edit () or remove () steps if you wish.
Please correct the following error(s):
Please correct the following error(s):
First, you must install cwltool and Docker Engine. Then you can execute the following command, assuming the CWL file and input-object file are in your current working directory (if not, modify the command to point to the locations of these files). Alternatively, you can execute the tool using a variety of other engines.