There are 2 ways that issues can be moved automatically to "In Progress" if you use the default settings (in Settings->Columns) for your Waffle project.

  1. If you push a branch that contains an issue number in the branch name - that issue will move to "In Progress". (You can disable this by moving the "Work Started" action in Settings->Columns to "Backlog".)
  2. If you create a pull request that has either GitHub's closing keywords (closes, fixes, resolves) or Waffle's connect keywords (connects, connects to, connected to) followed by the issue number. This will cause the issue to move "In Progress" and can also be disabled by moving the "New Collaborator PRs" action in Settings->Columns to the Backlog.
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