I have posted this question before and did not receive any responses. Let me try to articulate the issue more effectively this time. I have 200 samples (specifically from 200 different coyotes). I am trying to detect SNPs in the MHC gene. I have created a workflow in galaxy and would like to be able to use this to automate all of the steps required. At the end I would like all of the data to be compiled in one vcf file listed by sample name. The problem is I cannot find a way to have each sample maintain it's unique sample name through the workflow without manually entering this at some point. Any ideas?