To specify a canonical url on posts for this site, I added the following snippet to the default.hbs file.

{{#post}}<link rel="canonical" href="{{url absolute="true"}}" />{{/post}}

This grabs the absolute url of the actual post which results in something like this

<link rel="canonical" href="http://codybonney.com/specifying-a-canonical-url-in-a-template-on-the-ghost-blogging-platform/" />