As an Agile enthusiast and Scrum Master in previous gigs, I like looking at the overall approach as a series of experiments to see what resonates with your team. Incrementally apply changes and see if doing so helps your team. Here's some things, based upon tool.
JIra:
1. Really watch when you stop the old sprint/start the new sprint. This will affect all the reports you have.
2. Jira really likes it when you assign your stories to the sprint before you start that sprint. Again, it's part of keeping the reports in line.
3. If your team does Planning Poker, take a look at Marketplace apps that allow your team to do it remotely.
4. This is me because I steal borrow from Kanban, but I set up both a Kanban board and Scrum board on my project. The Kanban board gives me visualization to bottlenecks through the Cumulative Flow Diagram.
Confluence:
1. EXCELLENT way of creating/storing your team charter/working agreement and retrospectives.
2. For your retros, you can create Jira issues to put in your backlog for your action items using the Jira macro.
I'm sure others have more tips. Good luck!
I really like the idea of experimentation especially if the team isn't already tuned into scrum or Jira.
The main one for me is that Jira Scrum boards are built to support Scrum and only Scrum. If you're doing Scrum by the book, then Jira works great, and it supports most of the variations you see within it (estimates on any numbers you want, more rigid workflows than "can move it anywhere I feel like", breaking stories into bits for the team to be able to see which bit they need to do, etc)
But if you're a little off-piste, you may have to think very carefully about how you configure it. If you don't have multifunctional scrum teams, or your team has to accept unplanned work into sprints, for example.
For the other Atlassian tools, there's not much to say other than Confluence is a great place to record Sprint Reviews and Retrospectives.
Beyond the obvious use of Jira to track the work in your backlog and sprint, here are other Atlassian tools and how I've seen them used in scrum:
I like the format @Alice M used so I'll use the same and chime in here. Here are the other Atlassian tools I use and how I use them in Agile:
We did a retro this week using the Better Retros template in Confluence. It's really cool! It lets you comment anonymously / privately and then group similar comments, and then capture action items. Highly recommend!
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