add_shortcode('custom_popup_container','custom_popup_container');
function custom_popup_container($atts, $content = '') {

    $content = do_shortcode($content);
    $output = '';
    $output = '<a class="btn with-icon btn-default open-popup-link" href=""><i class="icon-desktop"></i>Open pop-up</a>';
    $output .= '<div id="show-in-popup" class="mfp-hide">';
    $output .= $content;
    $output .= '</div>';

    return $output;
}

/* The JS */

<script>
        jQuery('.open-popup-link').magnificPopup({
            items: {
                src: '#show-in-popup',
                type: 'inline',
            },
            preloader: false,
            mainClass: 'kleo-mfp-zoom',
        });
</script>