About this guide

This BioExcel Best Practice Guide outlines the development process for writing a workflow using the Common Workflow Language (CWL). It is intended to complement the other CWL guides which are already available, rather than replace them. Based on our experiences of working with the language, and associated tools, it highlights good practices to follow, features to use, and pitfalls to avoid when using CWL.

How to use this guide

This guide is structured with the intent of loosely following the development process of writing and using workflow tools, from sketching out the workflow from first principles, through to using the final workflow and capturing provenance from it. The guide can be read through in this manner, but is intended for you to dip into as needed through your development work, following the sections that you require at that point in time.

Contributions

Contributions to this guide are most welcome; the information contained within is based on our own (necessarily limited) experiences of using CWL, and it is always useful to get a wider input from other users for such a guide. Issues and error reports can be raised using the github issue tracker. Contributions can be made either via the issue tracker too, or by creating a fork of the github repository and then submitting a pull request with the new material.