We have indexed a genome using the appropriate data manager, for GATK, and our reference is showing up and working for individual walkers in GATK 2.8.  When designing a workflow, however, the reference genome is not appearing as an option for many walkers, including indel realigner and realigner target creator.  It is appearing for haplotype caller.  Again outside of the workflow environment the indexed references show up for all walkers.  

Any thoughts on this issue?

Thanks!
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