I talked about this in the colophon of the piece, but perhaps you'd like an example? This is Pandoc Markdown--basically Markdown, a little bit of YAML front matter, a smattering of inline LaTeX, and some very small shell scripts. Here's the the build scripts and a little bit of fronttmatter if you'd like to do the same:
https://gist.github.com/aphyr/6f0cd6910ccfe2cd7828d1ade2eac5...