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Configure External Tool
Go to File | Settings | Tools | External Tools for Windows and Linux or WebStorm | Preferences | Tools | External Tools for OS X and click + to add a new tool. Let’s name it Prettify.
In Program set prettier
In Parameters set --write [other opts] $FilePathRelativeToProjectRoot$
In Working directory set $ProjectFileDir$
If on the other hand you have prettier installed locally, replace the Program with ./node_modules/.bin/prettier (on OS X and Linux) or .\node_modules\.bin\prettier.cmd (on Windows).
Configure Keymap
Now when you setup External Tool I guess you want to add hotkey for it. Go to File | Settings | Keymap for Windows and Linux WebStorm | Preferences | Keymap and type external tool name in search box.
See this documentation about configuring keyboard shortcuts.