After a pull command, I ended up with a conflict in a file, which I fixed by manually editing the file (search for the <<< signs). The merge is fine and therefore tried to commit the file again but got this error:
fatal: cannot do a partial commit during a merge.
git commit -a my_filename
did not work, instead use
git commit -i my_filename
From the git documentation, the -i should be used to conclude a conflicted merge.