Hello @Adam_Hillier
Glad to learn you are proceeding with your project! 
There are a few primary places to source workflows for Galaxy.
IWC – Production quality workflows
These are curated, so if you can find what you need here, that would be preferred! Each has been optimized for large batch stream processing. This catalog is newer and growing and has stricter community standards.
Galaxy Hub – Public Workflows
This is the “meta” search. You’ll find workflows from the GTN trainings, WorkflowHub, and the Public Workflows available from the communities at the UseGalaxy* servers.
A workflow from either can be customized further, too. I would be pretty common to break out an analysis like yours into two or three distinct module workflows. Then scientists could run them separately or nest as subworkflows into a single master workflow that does everything with a bit more customization (reference data preparation, intermediate file offloading, workflow reports).
I didn’t find an IWC workflow for eDNA specifically and one of the training quality workflows from the GTN is probably too simple for your needs (no clustering). The other, using Obitools, will work best at one of the “Available at these Galaxies” servers for now – UseGalaxy.eu would be a good choice. 
- Hands-on: Metabarcoding/eDNA through Obitools / Metabarcoding/eDNA through Obitools / Ecology
- Note that the training version of workflows may have disconnected steps (on purpose!) and this one does. But, you’ll probably want to be starting at step 4 anyway since you already have your fastq reads prepared. I would suggest deleting the training initial steps, adding in your collection input, then connect.
Hope this helps to get things started!