Check if you are on the front page with is_front_page(). The home page (in WordPress the page with the latest posts) can be checked with is_home().
You can add this to the header.php between <head> and </head>:
<?php
if ( is_front_page() )
echo '<link rel="canonical" href="' . home_url( "https://wordpress.stackexchange.com/" ) . '" />';
?>