Nice! 
If you want to get started using Snakemake, I highly recommend it. It has a wonderful learning curve, making it easy to automate easy tasks, then slowly adds complexity to automake complex tasks.
There's the excellent snakemake tutorial, and this 5-step Qiime2 pipeline I made that trains a sklearn classifier
EDIT: One of the best parts about Snakemake + Qiime2 is that you can build fully automated pipelines AND you still have the detailed provenance baked into each Qiime2 artifact produced. So even as you distribute results or proceed with downstream analysis outside of your Snakemake pipeline, the full provenance is preserved. 
