I created two stories; one has sub-tasks, the other one doesn't. I assigned both stories to a sprint, and clicked on the Active Sprints page. I found that I can move the story without the sub-tasks across columns, as expected.
For the story with the sub-tasks, I can only move the sub-tasks, not the story itself. I guess that would be fine in theory if at least moving all of the sub-tasks to Done would turn the story itself to Done, but that's not happening either (though I created custom statuses, if that may have something to do with it).
Am I just missing something, or is this how JIRA is supposed to work?
First of you have probably configured your scrum board to use stories as swimlanes, which would explain the fact that you cannot move the second story as it's being displayed as a swimlane instead of a ticket (it's sub tasks are displayed as tickets that are part of this Story/Swimlane)
If you want to get a pop-up requesting to move your story to done you'll need to create a transition to the done/closed status from whichever status the story can be in, that should allow JIRA Agile to prompt you if you want to close the Story once all subtasks have been closed.
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