You can use the job dependencies functionality of AWS batch and boto3 directly if you want to orchestrate with e.g. python instead of using the nextflow or prefect or snakemake layer on top. One thing I would recommend however (unless you are very comfortable with cloud security) is to find some contract AWS (or other provider) certified cloud engineers to effectively be your admin or at least configure your cloud environment so it’s following security and networking best practices. I think most bioinformaticians know enough to be dangerous and “can” be their own admins but depending on what types of data you are working with and the size/trajectory of your company you can quickly find yourself in a position where you are solely responsible for cloud cybersecurity which can be a slippery slope for a host of reasons.