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My request is I want to create a dashboard to monitor all the initiatives in my company and see if there's any is delayed, I can use this JQL(Duedate < now() and status !=done) to filter those "delayed" initiatives, can I custom a filed to indicate this status? Means this custom field can be defined by JQL
Welcome to the Atlassian community.
Can you explain why you want to note an item is overdue using a custom field when you can get that list of issues already with the JQL statement?
You certainly can do what you want by using an Automation Rule to execute the JQL to find the issues and then set the custom field. But it seems like an unnecessary extra step.