I’ve disovered that this issue is related to tools rather than workflows, and 
specifically with tools that produce dataset collections on output.  In the 
"job.finish()" method, metadata that includes the input dataset’s dbkey setting 
is generated correctly for output datasets that are not part of a collection, 
but the dbkey (and possibly other metadata attributes) are lost if the output 
dataset is part of a collection.  I’m still digging to find how setting 
metadata for output dataset collections is handled differently than regular 
output datasets.

> On Jan 22, 2016, at 2:34 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello Galaxians,
> I’m running Galaxy 15.10 and running workflows that include tools that 
> require reference genomes (e.g. Extract Genomic DNA).  I set the dbkey for 
> the input dataset and it is retained for some tools, but not others.  Running 
> the workflow multiple times, it looks like the dbekey is lost at different 
> tool points in the workflow.  Is this a known issue or is there some setting 
> I’ve missed.  I’ve seen where the output dattype can be set for each tool, 
> but not the dbkey.  This is a problem because any tools that require a dbkey 
> downstream result in errors.
> I was running the dev branch for a while, but workflow bugs in that branch 
> forced me to revert back to 15.10.
> I’ve searched biostar and the mail lists, but haven’t seen an answer for this 
> specific issue, although there are several related threads from the past.  
> Sorry if it’s been answered and I missed it.
> Thanks very much for any help you can provide,
> Greg Von Kuster

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