> 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.
Tool wrapper that use the repeat element include the GATK's depth of coverage
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