We don't have a Trinity workflow available and I've looked through all
of the donated community tutorials and have not been able to find one
there, either. The Tool Shed has a newer feature that permits Workflow
sharing, but that also lacks a RNA-seq assembly->analysis workflow.
The closest I came was this post, over a year ago to the
firstname.lastname@example.org mailing list.
The general path outlined seems reasonable and is similar to what you
would find in the Trinity documentation:
Just to let you now, Jeremy (the wrapper author) let me know that the
Trinity wrapper in the Tool Shed may be slightly outdated compared to
the most recent binaries, so keep this in mind if you decide to use
Reviewing publications that make use of this tool is probably the best
approach. Or you could explore NGS hubs such as seqanswers.com to find
out what is available/being discussed.
Sorry that we could not help out more with this specific analysis,