Refactor Snakefiles to support distinct analysis directories

[genehack]

Aside: might be nice to extract a set of instructions from doing this; could be added to the pathogen repo guide.

[genehack]

Removing this from the scope of work for #7, as I'm not sure there's full consensus on the "right" way forward here, and because it feels like copypastaing the path resolution method into many repos would not be a great path forward.