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Idea #4035

Updated by Peter Amstutz over 9 years ago

The "common-workflow-language working group":https://groups.google.com/forum/#!forum/common-workflow-language is working on a tool description language and pipeline framework so that pipelines can be portable across various platforms such as Galaxy, Seven Bridges, and Arvados. 

 The first step is to implement proof of concept support: 
 # Review and contribute as necessary to the "reference implementation":https://github.com/rabix/experiments and "specification documents":https://github.com/rabix/common-workflow-language 
 # Implement a runner crunch script (similar to, but distinct from, run-command) which uses the reference implementation, accepts the tool description language and job inputs, generates a command line, runs the tool, and collects the outputs. 
 # Write a tutorial on how to try out the tool description language using Arvados. Provide an example specification document for a common tool like bwa-aln or bwa-index. 
 # Write a fast-running test case suitable for use in the diagnostics suite. 

 This should not require any changes to Arvados features. 

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