Hi, I've noticed something odd with creating workflows recently, which I think is a new issue, and I'm just wondering if I'm doing something wrong or whether it's a bug. If I run a history using a mapping step (this happens with either BWA or Tophat) and then use the cog icon to 'Extract workflow', in the extracted workflow, the reference genome to use always switches to the first genome listed on that server (on http://usegalaxy.org for example, it resets it to Arabidopsis lyrata).
I can set it back to my target genome using the workflow editor, but surely the correct behaviour should be to default either to the original genome specified in the history, or to require the genome to be provided at runtime, and not to silently switch to the alphabetically first reference genome?
I'm sure that this didn't use to be the case, so is there a configuration issue that I've not noticed, or is it a recent feature/bug of the extract workflow function? Thanks.
P.S. I've set up a very simple test case on useGalaxy.com - history https://usegalaxy.org/u/mark-crowe/h/workflow-test. If you import the history and use 'extract workflow', you'll see in the workflow editor that the reference genome switches from sacCer2 (in the history) to Arabidopsis lyrata (in the workflow).
