Hey hey @Matt_Kizaric1!
This is basically how docker itself is designed to operate - disposable containers don’t persist data, unless you ask them to! It sounds like maybe you aren’t mounting a volume while running the docker container - that will certainly make things difficult in terms of persistence. As well, you can run things in interactive and TTY mode - at that point its basically like you are running the command natively (check out our simple example in the docs):
demux.qza # This is local, on my host laptop
# Volume mounting with -v, run QIIME 2 in a docker container
$ docker run -t -i -v $(pwd):/data qiime2/core:2018.6 qiime demux summarize --i-data demux.qza --o-visualization demux.qzv
demux.qza demux.qzv # still local!
# TTY/interactive mode with -t -i
$ docker run -t -i -v $(pwd):/data qiime2/core:2018.6 bash
$ # you are now inside the container
All of this and much more can be found in the
docker run docs, in case you want to see more!
Now with that said, maybe I misunderstood your question, or you are just generally curious - the
Dockerfile for this image can be found here, one of the great things about docker is that you can layer your own functionality on to our image using your own Dockerfile, no need to let us get in your way! Anyway, have fun and keep us posted!