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Wednesday, June 29 • 12:00pm - 12:20pm
Planemo – A Scientific Workflow SDK

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John Chilton, Galaxy Project
Aysam Guerler, Galaxy Project
Galaxy Team, Galaxy Project 

A novel approach to building, refining, and running scientific workflows leveraging Galaxy through Planemo will be presented. The Galaxy workflow editor and workflow extraction interface are great tools enabling any Galaxy user to easily build workflows. However, tool authors using Planemo and sophisticated bioinformaticians may prefer driving workflow development through their existing tool chains such as programming text editors, command-line testing, and revision control. The approach presented leverages YAML-based workflow descriptions as plain files allowing exactly this.

The approach will be used as a lens to highlight these workflows formats (Format 2 Galaxy workflows and Common Workflow Language (CWL) workflows) as well as important highlights from the myriad of recent Galaxy workflow enhancements that have made them dramatically more usable, powerful, and performant.

Available today, Format 2 Galaxy workflows map directly to existing Galaxy tool and workflow concepts and are described in a very concise and readable YAML format. CWL specifications for tools and workflows are developed in an open fashion by many organizations with the aim of creating truly portable descriptions. The execution of CWL workflows in Galaxy is being actively worked on and progress will be discussed.

Underlying all of this is core Galaxy enhancements that will be demonstrated. The user interface for workflows has been overhauled and improved. Additionally, workflows now allow nesting, labels, non-data inputs, implicit connections between steps, and many new operations over collections - greatly increasing the expressive power of Galaxy workflows. Finally, recent performance enhancements allow Galaxy workflows to scale to thousands of datasets.

avatar for John Chilton

John Chilton

Galaxy Project, Penn State University

Attendees (25)