Community-led specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments

The Common Workflow Language (CWL) is a community-led specification to express portable workflow and tool descriptions, which can be executed by multiple leading workflow engine implementations. Unlike previous standardisation attempts, CWL has taken a pragmatic approach and focused on what most workflow systems are able to do: Execute command line tools and pass files around in a top-to-bottom pipeline. At the heart of CWL workflows are the tool descriptions. A command line is described, with parameters, input and output files, in a YAML format so they can be shared across workflows and linked to from registries like ELIXIR’s bio.tools. These are then combined and wired together in a second YAML file to form a workflow template, which can be executed on any of the supported implementations, repeatedly and on different platforms by specifying input files and workflow parameters. The CWL User Guide gives a gentle introduction to the language, while the more detailed CWL specifications formalize CWL concepts so they can be implemented by the different workflow systems.

The eScience Lab have participated in the CWL project since its early days, contributing with our workflow and reproducibility expertise from Apache Taverna, Research Objects and myExperiment. The CWL Viewer, developed by the eScience Lab with support from BioExcel, provides a graphical visualization of CWL workflows.

References

Mark Robinson, Stian Soiland-Reyes, Michael R Crusoe, Carole Goble (2017): CWL Viewer: The Common Workflow Language viewer [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1075 (poster) https://doi.org/10.7490/f1000research.1114375.1

Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić (editors), Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes, Luka Stojanovic (2016): Common Workflow Language, v1.0. Specification, Common Workflow Language working group. https://w3id.org/cwl/v1.0/ https://doi.org/10.6084/m9.figshare.3115156.v2