[TAVERNA-877] Parser for Common Workflow Language workflows

• Type: New Feature
• Status: To Do
• Priority: Minor
• Resolution: Unresolved
• Component/s: Taverna Language
• Labels: cwl gsoc2016
• Assignee: Unassigned
• Reporter: Stian Soiland-Reyes
• Created: 08/Jan/16 14:44
• Updated: 08/Feb/18 14:10

Description

Common Workflow Language
http://common-workflow-language.github.io/

..is an emerging standard for computational workflows with a focus on bioinformatics command line tools using Docker.

The semantics of CWL are inspired by Taverna's SCUFL2 model and the Wf4Ever wfdesc vocabulary.

A good first approximation for integration of CWL for Taverna would be to parse/read CWL workflows into the SCUFL2 model of Taverna Language.

Running CWL workflows can be achieved by interpreting CWL Tools (which are described in JSON) as a way to configure the Tool Activity with docker commands.

But this SCUFL2 reader can just represent the CWL configurations as-is.

There's an early Java SDK for CWL parsing just made, under development at https://github.com/common-workflow-language/cwljava/

Issue Links

• blocks: TAVERNA-878 Tool: Execute CWL Tool descriptions
• is part of: TAVERNA-900 GSOC: Add Common Workflow Language support to Taverna
• mentioned in: Page Loading...