This is a master thesis written with Markdown. The purpose of this was to create a workflow that allows me to easily add meaning to the content thanks to the markdown syntax, while save time for doing the layout. The features are extended thanks to atom packages (links below) : dynamic footnotes and zotero citations.

Thanks to pandoc, the markdown file can be converted to many formats, including pdf, html and icml (for indesign).

When you import the icml file in indesign, the text can be very easily styled, because every markdown component is associated with a paragraph style (headers, lists, blockquotes, footnotes...), and the emphasis are associated with character styles. The footnotes remain dynamic, they are inserted at the bottom of the text block.

• atom
• atom packages : Markdown Preview Plus, Markdown footnotes, Zotero Markdown citations, Zotero picker.
• Zotero

• Pandoc
• XeLaTeX

• You can use all the markdown syntaxes supported by Pandoc. Markdown cheatsheet.
• You can also add some latex commands such as \newpage.

pandoc thesis.md --pdf-engine=xelatex --variable urlcolor=blue --bibliography citations-thesis.bib -o thesis.pdf

• thesis.md is the input file.
• thesis.pdf is the output file.
• citations-thesis.bib is the bib file created with Zotero. Zotero needs to be open at the time of converting. The bibliography is parsed at the end of the file.
• --pdf-engine can also be wkhtml, but wkhtml needs to be installed on the computer first.
• --variable urlcolor=blue for coloring the hyperlinks un blue

pandoc -s thesis.md --bibliography citations-thesis.bib --toc -o html/index.html

• '-s' is for 'standalone', it's used to produce a valid HTML file with a doctype, head, body etc.
• '--toc' is for 'table of content'

pandoc --lua-filter=page-break-for-indesign.lua -s -f markdown -t icml --bibliography citations-thesis.bib -o thesis.icml thesis.md

• --bibliography citations-thesis.bib is for creating the bibliography automatically. If you don't use a bibtex file, just remove it.
• --lua-filter=page-break-for-indesign.lua is a filter intended to help the conversion of some latex commands to indesign features. Thanks to that filter :
  • \newpage put the following content at the next page. More infos here.
  • \cleardoublepage put the following content at the next right (odd) page.

File > Place (Fichier > Importer), then maj + click at the top left of the first page (not gabarit). The page have to be empty, the block will be created automatically.

• How to simply convert to icml
• Pandoc documentation on lua filters
• InDesign CS5 IDML Language Specification