Use of Snakemake workflows in AWS Batch

Question

I wanted to ask the Snakemake community if anybody has had success implementing Snakemake workflows in AWS Batch.

Page 4 of a recent publication from Oct 2018 seems to suggest that Snakemake does not work on AWS as it cannot handle resource management. Here is the publication: Tibanna: software for scalable execution of portable pipelines on the cloud - https://www.biorxiv.org/content/early/2019/04/29/440974.full.pdf

Yes, the same paper does suggest the Snakemake works well with the Google Cloud Platform (GCP).

However, the Snakemake documentation states: "Snakemake 4.0 and later supports execution in the cloud via Kubernetes. This is independent of the cloud provider." - https://snakemake.readthedocs.io/en/stable/executable.html#cloud-support

Hence, I would like to know if anyone has implemented Snakemake with AWS Batch.

Also, while on this question, does anyone know of any github/bitbucket page that details the successful implementation of Snakemake with the GCP.

Thanks in advance.

Answer 1

This page details the use of Snakemake with cloud environments like GCP or AWS:

https://snakemake.readthedocs.io/en/stable/executing/cluster-cloud.html

AWS is actually available via Tibanna.