From within the parent repo do
git submodule add [email protected]:iracooke/transcriptomes.git/wiki wiki
git commit -m "Adding wiki as submodule"
git pushMaking changes to the wiki and to the parent require separate git commit commands.
More helpful advice to be found here
https://web.archive.org/web/20180721003129/http://brendancleary.com/2013/03/08/including-a-github-wiki-in-a-repository-as-a-submodule/ courtesy of wayback machine