Is it possible to have a custom template/workflow to manage a project that follows Waterfall methodology and use JIRA for managing such projects?
Is there a plugin or way to customize the default flow?
Wow, it is really hard to believe that someone is still using the Waterfall model... Anyway I guess you can just have separate projects for each step of the model:
So for example if your project is called X then you can have:
as projects in JIRA. Then create consecutive issues for all tasks.
As a summary I'd like to strongly encourage shifting away from the Waterfall model in Software Development. Things have changed a lot for the last 10-15 years - not mentioning that the Waterfall is much older than that period.
Modern agile (or not) methodologies provide a far better view of the iteration process in Software Development.
Yes switching may be hard initially (depending on the size of the company and what not) but the implications after are far more advantageous. You will experience a ton of optimizations and the most important factor - more communication with the client means a happier client!