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we trying to create an automation rule when a PR is merged, but we want to transition the issues to DONE only when the PR were merge to the Master branch
^ You may also want to include a check that there are no other Pull requests open. You can do this using a JQL condition.
key = {{issue.key}} AND development[pullrequests].open = 0
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Instead of using an automation rule, why not use a workflow trigger instead? This is what workflow triggers are intended for, to transition issues when something happens in your development tool. Have a look at Configure workflow triggers for more information.
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