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I have defined my project with 2-week sprint in JIRA but when looking at the plan in Portfolio, Portfolio seems to overwrite this with a 6-week sprint length except for my currently ongoing sprint.
I read the hint to start up all the sprints in JIRA, but that really creates a mess in JIRA to make the plan look nice in Portfolio. Can't I have the best of both worlds?
In your Portfolio setting make sure that it's set up as a Scrum based plan and then you should be able to set up your Sprint length to your desired 2 weeks.
This guide should be able to help: https://confluence.atlassian.com/jiraportfolioserver/scheduling-settings-715263133.html
Hope this helps,