AWS EC2 user data docker system prune before start ecs task - amazon-web-services

Question

I have followed the below code from the AWS to start a ECS task when the EC2 instance launches. This works great.
However my containers only run for a few minutes(max ten) then once finished the EC# is shutdown using a cloudwatch rule.
The problem I am find is that due to the instances shutting down straight after the task is finished the auto clean up of the docker containers doesn't happen resulting in the EC2 instance getting full up stopping other tasks to fail. I have tried the lower the time between clean up but it still can be a bit flaky.
Next idea was to add docker system prune -a -f to the user data of the EC2 instance but it doesnt seem to get ran. I think its because I am putting it in the wrong part of the user data, I have searched through the docs for this but cant find anything to help.
Question where can I put the docker prune command in the user data to ensure that at each launch the prune command is ran?
--==BOUNDARY==
Content-Type: text/x-shellscript; charset="us-ascii"
#!/bin/bash
# Specify the cluster that the container instance should register into
cluster=your_cluster_name
# Write the cluster configuration variable to the ecs.config file
# (add any other configuration variables here also)
echo ECS_CLUSTER=$cluster >> /etc/ecs/ecs.config
# Install the AWS CLI and the jq JSON parser
yum install -y aws-cli jq
--==BOUNDARY==
Content-Type: text/upstart-job; charset="us-ascii"
#upstart-job
description "Amazon EC2 Container Service (start task on instance boot)"
author "Amazon Web Services"
start on started ecs
script
exec 2>>/var/log/ecs/ecs-start-task.log
set -x
until curl -s http://localhost:51678/v1/metadata
do
sleep 1
done
# Grab the container instance ARN and AWS region from instance metadata
instance_arn=$(curl -s http://localhost:51678/v1/metadata | jq -r '. | .ContainerInstanceArn' | awk -F/ '{print $NF}' )
cluster=$(curl -s http://localhost:51678/v1/metadata | jq -r '. | .Cluster' | awk -F/ '{print $NF}' )
region=$(curl -s http://localhost:51678/v1/metadata | jq -r '. | .ContainerInstanceArn' | awk -F: '{print $4}')
# Specify the task definition to run at launch
task_definition=my_task_def
# Run the AWS CLI start-task command to start your task on this container instance
aws ecs start-task --cluster $cluster --task-definition $task_definition --container-instances $instance_arn --started-by $instance_arn --region $region
end script
--==BOUNDARY==--

Answer 1

I hadn't considered terminated then creating a new instance.
I use cloud formation currently to create EC2.
What's the best workflow for terminating an EC2 after the task definition has completed then on schedule create a new one registering it to the ECS cluster?
Cloud watch scheduled rule to start lambda that creates EC2 then registers to cluster?