How to effectively manage increasingly complex enterprise computing environments is one of the hardest challenges that most organizations have to face in the era of cloud computing, big data and IoT. Advanced automation and orchestration systems are the most valuable solutions helping IT staff to handle large-scale cloud data centers. Containers are the new revolution in the cloud computing world, they are more lightweight than VMs, and can radically decrease both the start up time of instances and the processing and storage overhead with respect to traditional VMs. The aim of this paper is to provide a comprehensive description of cloud orchestration approaches with containers, analyzing current research efforts, existing solutions and presenting issues and challenges facing this topic.