The latest version of the paper “Sustainable data analysis with Snakemake” is out.

Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. Here, we analyze the properties needed for a data analysis to become reproducible, adaptable, and transparent. We show how the popular workflow management system Snakemake can be used to guarantee this, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.

In this latest version, we have clarified several claims in the readability analysis. Further, we have extended the description of the scheduling to also cover running Snakemake on cluster and cloud middleware. We have extended the description of the automatic code linting and formatting provided with Snakemake. Finally, we have extended the text to cover workflow modules, a new feature of Snakemake that allows to easily compose multiple external pipelines together, while being able to extend and modify them on the fly.