custom-template.php

<?php 
// First we remove all the shortcodes from the post body
add_action('the_content', 'strip_shortcodes');

get_template_part('header');
?>

    <div id="main-container" class="container">
        <div class="row">
            <div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
                <?php get_template_part('content'); ?>
            </div>
            <div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
                <?php
                // Now we take only the shortcodes from the post body and print their output here, in a separate DOM element
                global $post;
                $pattern = get_shortcode_regex();
                preg_match_all('/'.$pattern.'/s', $post->post_content, $matches);
                if(is_array($matches[0])){
                    foreach($matches[0] as $shortcode){
                        echo do_shortcode($shortcode);
                    }
                }
                ?>
            </div>
        </div>
    </div>

<?php get_template_part('footer'); ?>