About this course

This course will provide a brief introduction to the Common Workflow Language (CWL) and help you get started with the CWL reference implementation cwltool, as well as giving you a taster of the implementation Toil using the BioExcel Cloud Portal. At the end of this session, you will be able to:

• Write workflows in CWL and execute them
• Execute workflows with Docker containers
• Make your own tool descriptions in CWL
• Share and reuse workflow and tool descriptions with the CWL community
• Follow best practice guidelines for writing CWL

Please note the following is not covered in the course:

• This course will not teach you how to design a scientifically valid bioinformatics pipeline
  • Bioinformatics tools/workflows may be used as examples, alongside generic UNIX tools
• This course will not explain how to set up other CWL implementations (e.g. Galaxy or CWLEXEC for LSF)
  •  You will be shown how to install the reference implementation cwltool, and cloud support in toil will be demonstrated
  • The strengths and pitfalls of the different engine choices will be covered in brief
• This course will not detail how to use particular compute/cloud infrastructure
  • Cloud computing may be used as example
• This course will not provide support for rewriting your existing pipeline to CWL
  • Instructors will assist attendees with tutorial lessons

Prerequisites

No prior knowledge of workflows, CWL or Python is required.

A basic understanding of the command line (UNIX shell as on Linux/OS X) is advised; guidance will also be provided for Windows users.  

Experience with writing JSON or textual scripts in any programming/scripting language is advised, e.g. understanding of quotes, indentation, blocks; however a full introduction to the CWL syntax in YAML will be provided.

No prior knowledge of bioinformatics is required.