This filter counts the words and characters in the body of a document (omitting metadata like titles and abstracts), including words in code. It should be more accurate than wc -w or wc -m run directly on a Markdown document, since wc will also count markup characters, like the # in front of an ATX header, or tags in HTML documents.

To run it, pandoc --lua-filter wordcount.lua myfile.md. The word count will be printed to stdout.