I changed the workflow to use my own uploaded reference file, not the built-in index, but judging from the nomenclature I suspect I may have to process (index?) the reference file first into a format usable by the pileup generation tool. However I do not see how I can do that.
Galaxy should do this automatically. At least it did it for me yesterday (admittedly using SOLiD data instead of Illumina.
I still recommend manually running each step instead of relying on a workflow.