First, create a new rule as follows (command from https://scalacenter.github.io/scalafix/docs/developers/setup.html):
sbt new scalacenter/scalafix.g8 --repo="Repository Name"
To run the rule against some codebase:
scalafix -r file:scalafix/rules/src/main/scala/fix/YourRule.scala your/code/base/
YourRule.scala is the rule you developed and
your/code/base is the code base you are running the rule against.