I use Emacs Org mode for this project (and everything else). Here's how I set up my (org-babel) notebooks to publish into a Jekyll site.

1 Using Org to publish html

(require 'ox-publish)
(setq org-publish-project-alist
      '(

        ("org-notebooks"
         :base-directory "~/statistics/projects/march_madness/notebooks/"
         :base-extension "org"
         :publishing-directory "~/statistics/projects/march_madness/docs/"
         :recursive t
         :publishing-function org-html-publish-to-html
         :headline-levels 4
         :html-extension "html"
         :body-only t ;; only export section between <body> </body>
         )

        ("org-static"
         :base-directory "~/statistics/projects/march_madness/notebooks/"
         :base-extension "css\\|js\\|png\\|jpg\\|gif\\|pdf\\|mp3\\|ogg\\|swf"
         :publishing-directory "~/statistics/projects/march_madness/docs/"
         :recursive t
         :publishing-function org-publish-attachment
         )

        ("org" :components ("org-notebooks" "org-static"))

      ))