Containerize Pipeline

[slsevilla]

Describe what enhancement you'd like to see.
In order to 1) deploy unit testing via GitHub actions and to 2) allow the pipeline to be deployed outside of our HPC (Biowulf) the pipeline should be containerized at the rule level. This will include:

• identifying publicly available containers per tool to utilize within the pipeline
• creating .yaml files for each of those tools
• adding conda expressions to each rule that utilizes one such container
• adding a check for whether the pipeline is being run on our HPC (Biowulf) or externally

Notes

• https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#running-jobs-in-containers
• https://www.biostars.org/p/335903/