Hi again,

I'm trying to set up a workflow for Galaxy (6799:40f1816d6857), but I can't
seem to find a way to make a workflow that invokes another workflow. It seems
like this wouldn't be unreasonable, since workflows have defined inputs and

There might be another way to accomplish what I'm trying to ultimately do,
though. We have a set of analyses and conversions, and want to assemble a
workflow that goes through a long series of steps. The workflow can roughly be
organized into three parts. Once the workflow is finished, we might want to
rerun the third or second and third parts after modifiying some of the
intermediate files.

It seems like this might also be accomplished by somehow marking that some
input files should be substituted instead of using the outputs of some of the
steps in the workflow.

Anyway, I've been unable to find a simple way of doing this..

I could make each part of the workflow a tool, but if I also wanted to expose
the tools used in each part, I would be duplicating those invocations and
increasing the maintenance burden.

I could also make separate workflows for parts 1+2+3, 2+3, and 3, but that
would also be duplicating work and increasing the maintenance burden.

I could also make this three completely separate workflows, but that would mean
that the user would have to remember to run each of these separately. Each part
can take a very long time, so it would be useful to have this set up so that a
user can start from the first part on a Friday and have the output from the
third part available on Monday.

Thanks in advance for any help,

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