Drafting Manuscripts with Pandoc

Why Pandoc

Pandoc works seamlessly with markdown files, converting them to a desired format—HTML, Docx, or PDF. We can leverage that with Obsidian’s enhanced functionality to plan, write, and edit manuscripts.

Check out Pandoc’s markdown for a more detailed guide.

Using Pandoc in Obsidian

Prerequisites

• Install Pandoc and a TeX distribution (needed to install pdflatex) on your machine. (I recommend MikTeX for Windows users.)
• Install pdflatex in MikTeX

Method 1: Pandoc Plugin

• Install the Pandoc plugin in Obsidian (available in community plugins).
• Find the absolute path to Pandoc by running which pandoc on Mac/Linux or Get-Command pandoc in Powershell on Windows.
• Copy & paste the path in the Pandoc plugin settings.
• Copy & paste the absolute path to PDFLaTeX (run which pdflatex on Mac/Linux; Get-Command pdflatex on Windows).
• Copy & paste the absolute path to your export folder (for example: C:\Users\<YOUR_USERNAME>\Documents).

Pandoc offers a wide range of commands and functionalities. In the extra arguments section, adding --citeproc and --bibliography=C:\Users\<YOUR_USERNAME>\path_to_bib_file.bib creates bibliographic entries and sorts them under a “Bibliography” heading.

We can also define the .bib file in the front matter.

bibliography: 

Method 2.1: Command Line

If the plugin feels too limiting, the command line provides extended functionality that might suit your use case.

pandoc -f markdown -t pdf "input.md" -o "output.pdf" --citeproc --bibliography "absolute/path/to/.bib"

Method 2.2: With Shell Commands (Recommended)

Optionally, we can create a command to run via the Shell Commands plugin.

I’ve been a big air-conditioner* of Overleaf to write project reports and papers due to the ease it offers STEM students. Aside collaborative purposes, I now use Pandoc instead. The best part is being able to do all this right from my note-taking app.

* (air-conditioner = fan; Get it? I’ll leave now.)