Idea #4035
Updated by Tom Clegg 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) based on 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 Curoverse beta account. Hopefully Seven Bridges and/or Galaxy do the same thing for use in the diagnostics suite. their platforms so we can show actual portability between at least two platforms. This should For this proof of concept story I think we can do this entirely with a crunch script and not require any changes to Arvados features.