For the
initial trinity de novo assembly, I took Jeremy's initial workflow and
tweaked it to work with the latest release - and submitted it to the
galaxy tool shed.
Excellent. I'll remove my old Trinity wrapper from our code base and point people to your wrapper.
There are some complexities here, such as not knowing ahead of time
how many different samples are to be processed - so this needs to be
determined dynamically, which impacts the overall complexity of the
total workflow. Is this possible in Galaxy, and if so, are there
examples I can work from?
Take a look at the repeat element; it enables a user to specify a number of inputs to a tool.