Shamelessly taken from https://github.com/jasonrudolph/toggle-markdown-task, but I added the option for a [~] checkmark, which I use to show a task is in progress.
Provides a command to toggle completion of tasks in GitHub-flavored Markdown files.
Using apm:
apm install toggle-markdown-task-with-ongoing
Or search for toggle-markdown-task-with-ongoing in the Atom Settings UI.
To get the most out of this package, you'll want to use a keyboard shortcut for toggling Markdown tasks. This package does not provide a keyboard shortcut by default, but you can easily define your own. For example, if you wanted to use Control-D (as shown in the demo above), you'd add the following mapping to your ~/.atom/keymap.cson file:
'atom-workspace atom-text-editor:not(.mini)':
'ctrl-d': 'toggle-markdown-task:toggle'