A repository for converting YesWorkflow models in to CWL

CWL tool:

• The Common Workflow Language (CWL)(https://github.com/common-workflow-language/), is a way to describe command line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard.

YesWorkflow:

The yw-prototypes repository contains early implementations of YesWorkflow(https://github.com/yesworkflow-org/yw-prototypes), an approach to modeling conventional scripts and programs as scientific workflows.

Differences between the models.

1. Execution Language Vs Modeling
2. No Provenance Vs Provenance
3. Flexibility

Installing CWL:

• Please follow the steps for installing CWL (https://github.com/common-workflow-language/cwltool).

Installing YW2CWL parser. Using Github (requires installation of git)

• Install git from https://git-scm.com/downloads
• Open your command line tool (CMD for windows and terminal for Mac or Linux)
• Go to a directory where you would like to clone the repository
• Run git clone https://github.com/idaks/cwl_modeling.git

Executing yw2cwl.py

• The script yw2cwl.py takes yesworkflow model facts file as input.
• Run the following command from command prompt

$ python yw2cwl.py  

• Enter the YW model filename:

Enter the YW model filename:  **get_itrdb_data/get_itrdb_data.P**

• The CWL files will be created in the example_sql/get_itrdb_data folder.
• Verify the CWL workflow file using the cwl-runner tool.

Creating CWL graph.

• Once the CWL workflow file is created.
• Use http://view.commonwl.org for generating the CWL graph, using the github link for the workflow file.