Snakemake and Jupyter Notebooks

[s-canchi]

Can you describe when workflows like Snakemake are better to use than Jupyter notebooks?

[marisalim]

Jupyter notebooks are great for interactive analysis, but may be too slow for longer processes that take more than a few minutes to complete. In those cases, you may prefer to run your analyses with snakemake workflows on a high performance computer cluster or on the cloud (i.e., AWS, Google). The outputs of those workflows can be further explored interactively and shared with Jupyter notebooks!