"Common Workflow Language" explained in 64 seconds
Channel: Common Workflow Language
Date: 2017-06-28

In many scientific fields (such as bioinformatics, medical imaging, and astronomy) large quantities of data need to be analyzed.

This can involve large-scale and repetitive processes in long pipelines of different tools — referred to as workflows.

it can be very time-consuming to run the data through all these different tools by hand and convert outputs to various formats to make them compatible with the next step.

Workflow management systems are designed to alleviate this problem by allowing these workflows to be expressed formally
and providing infrastructure to set up, execute, and monitor them.

This formal expression of workflows allows for scientists to easily share and reuse them.

Crucially they can also be used to verify results of computation for published work.

However there are many competing [ways] for describing workflows which is a barrier to this aim.

Currently there are over a hundred different data analysis workflow systems with no interoperability between them.

The need has arisen to have a single common standard and so the "Common Workflow Language" project was created: An open standard designed to express workflows and their tooling in groups of YAML structured text files.

http://www.commonwl.org
https://www.commonwl.org/user_guide/
https://bcbio-nextgen.readthedocs.io
https://view.commonwl.org/workflows/github.com/common-workflow-language/workflows/tree/920c6be/workflows/lobSTR/lobSTR-workflow.cwl
https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems

Video from "CWLViewer", https://www.youtube.com/watch?v=_yjhVTmvxLU by Mark Robinson, Stian Soiland-Reyes, Carole Goble /  BioExcel Center of Excellence for Computational Biomolecular Research