Hi Jake,
So I'm looking for feedback and possibly advice. Ideally, we'd like to be able to run the entire pipeline, look at the results, possibly change a few parameters in some of the steps (e.g., minimum FDR cutoff) and rerun only what needs to be rerun. Galaxy workflows are easy to create, but don't seem to have the flexibility that we're looking for. Perhaps several workflows tied together would do the job (i.e., have separate workflows for the major parts of the analysis) which we could tie together (possible in galaxy?) into one uber-pipeline.
I'm a Galaxy developer who also uses Galaxy for NGS analyses; here are my opinions about workflows. First, separate workflows for major or time-consuming aspects of an analysis work well. Galaxy provides the ability to copy (clone) workflows, and I often copy a workflow and then add to it so that I have the simpler workflow and also the more complex workflow. This enables me to run either the simpler or the complex workflow. Often, I run the complex analysis initially and use the simpler workflows to rerun particular aspects of the analysis. I've talked with others that do something similar. What this means is that Galaxy needs to the ability to support embedded workflows. Making a change to the simple workflow currently requires manually propagating the changes to the more complex workflow, which is difficult and error-prone. Embedded/nested workflows are our on development list, but it's fairly far down the list right now because other issues are more pressing. Finally, Galaxy enables you to specify parameters that must be set at runtime, so it's possible to easily rerun Galaxy workflows with different parameter values. Best, J.