iiinova — where your digital self keeps evolving

Damien Mannion @djmannion.net · 07/09/2026

This work was done in collaboration with Mar Quiroga (@mariadelmarq.bsky.social), Jacob Paul (@jacobmpaul.bsky.social), and Marta Garrido. Note that we are only users of Snakemake, which was created and developed by Johannes Köster and team (snakemake.readthedocs.io/en/stable/pr...).

snakemake.readthedocs.io

Credits | Snakemake 9.26.1 documentation

012

Damien Mannion @djmannion.net · 07/09/2026

This supports reproducibility (execution of a complete workflow), efficiency (parallelisation and partial re-execution), understandability (a common framework for workflow steps), and flexibility (steps describable in different languages, adaptable to different computation and storage providers).

111

Damien Mannion @djmannion.net · 07/09/2026

Broadly, using Snakemake involves writing a set of 'rules' that capture how data is processed in a workflow. The rules are written in YAML/Python and describe how outputs are produced from inputs given a mechanism (e.g., a script or command running in a container), parameters, and resources.

Diagram of a Snakemake workflow, consisting of multiple steps that each have inputs, mechanism, resources, parameters, and outputs. The steps exist within a context that has configuration, custom Python functions and variables, and Snakemake helper functions.

111

Damien Mannion @djmannion.net · 07/09/2026

Snakemake (#snakemake) is established software for workflow management in scientific data processing. In this paper, we describe the use of Snakemake in a neuroimaging context: "Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager" (doi.org/10.1007/s004...)

doi.org

Client Challenge

111

Damien Mannion @djmannion.net · 04/05/2026

Our manuscript on the Snakemake workflow manager in neuroimaging now has an accompanying website that provides a detailed worked example of the implementation of an fMRI processing workflow: unimelbmdap.github.io/neuroimaging...

unimelbmdap.github.io

Snakemake in neuroimaging: a worked example

This is a detailed worked example of how the workflow manager Snakemake can be used to specify and execute workflows for processing and analysing neuroimaging data. The accompanying manuscript, Orc...

011

Damien Mannion @djmannion.net · 17/02/2026

We have found the workflow manager 'Snakemake' to be very useful for fMRI data processing and analysis. In this paper, we describe how Snakemake can be applied in a neuroimaging context.

272

Damien Mannion @djmannion.net · 11/02/2026

My Matlab is a bit rusty, but using `surf` maybe? gist.github.com/djmannion/19...

000