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Couldn't find a solution after a quick google so thought i'd pop a quick post on here.

Trying to remove a automatically added rel=canonical link (which is added by Wordpress SEO plugin - by Yoast).

I actually want google to crawl each of the different subs even though it may not move away from the parent page.

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rel="canonical" has nothing to do with crawling. It has to do with indexing and prevents the same page from indexing twice or more.

Anyway, if you still want to do this you can do it by adding this code to your functions.php:

add_filter( 'wpseo_canonical', '__return_false' );

Source: https://yoast.com/wordpress/plugins/seo/api/

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