This merge request adds the tools **assemblystats**, **filter_spades_repeats**, and **flash**. I then add a workflow in `workflows/AssemblyAnnotation/0.2/assembly-annotation.ga` which corresponds roughly to the **SOP: Spades assemblies with FLASH v1.2** and **Prokka Workflow v1.0**. The differences being I combine both into one workflow, and I remove the **bundle** tools since for IRIDA I'm only running one assembly per workflow.
I also updated the install instructions for how to install all tools and I've put them all on http://irida.corefacility.ca/galaxy-shed which is publicly available.
Let me know if all these changes make sense (there's a lot of changes since I added all those tool scripts).
See merge request !2