Pandoc is great software for converting among file formats, such as text, markdown, HTML, PDF, etc.

Example:

    pandoc in.md -o out.html -V pagetitle="My Title" --to=html5 --template="my.html" --css "my.css"

The example converts a markdown file to HTML, using a given title, a template file, and a stylesheet file.

The pipeline is also well implemented with Haskell, which is good for writing your own fast functional transformations.