I have a saved workflow involving a Map with Bowtie for Illumina step in which I want to map reads to the S cerevisiae reference genome sacCer3. This reference genome is an option when you normally run this step not in a workflow. When I edit or run this workflow I cannot select this option (it is not available) and it reverts back to the default arabidopsis genome. How do I get this sacCer3 option added when this step is edited in a workflow?
You need to re-edit your workflow.
choose the "Edit" option for your workflow, then, in the graphical display, select the "Map with Bowtie for Illumina" box and, in the configuration tab on the right, click on the downward arrow next to "Select a reference genome:".
Now choose the option "Set at runtime".