deltares_snakemake: Snakemake training Deltares

This repository contains material to discover Snakemake and its functionalities as a smart and reproducible workflow manager.

It uses Jupyter notebooks and requires a Python installation.

Two exercises are prepared around two workflows:

• a simple workflow for file manipulation in Windows: notebooks/1_first_workflow.ipynb
• a more advanced workflow with a simple weather generator and hydrological model: notebooks/2_rainfall_runoff_workflow.ipynb

Installation

Python and conda/mamba

You'll need Python 3.8 or greater and a package manager such as conda or mamba. These package managers help you to install (Python) packages and manage environments such that different installations do not conflict.

We recommend using the Mambaforge Python distribution. This installs Python and the mamba package manager. Miniforge and Miniconda will install Python and the conda package manager.

Download the content of deltares_snakemake repository

To run the exercices, you will need to download the content of the deltares_snakemake repository locally. You can either do a manual download and extract the content of the dowloaded ZIP folder or clone the repository locally:

git clone https://github.com/hcwinsemius/deltares_snakemake.git

Install the python dependencies in a separate Python environment

The last step is to install all the python dependencies required to run the notebooks, including of course snakemake. All required dependencies can be found in the environment.yml file.

First navigate into the deltares_snakemake folder (where the environment.yml file is located). Create a new snakeymakey environment using the environment.yml file (you can exchange mamba/conda in the exmaple below):

cd deltares_snakemake
mamba env create -f environment.yml

Running the exercises

We have prepared two iPython notebook examples to discover snakemake in the notebooks folder:

• 1_first_workflow.ipynb: a simple workflow for file manipulation in Windows to discover how to write and run a Snakefile, determine rule dependency and use a configuration file.
• 2_rainfall_runoff_workflow.ipynb: a more advanced workflow with a simple weather generator and hydrological model to discover generalization and parallelization in Snakemake with wildcards and Paramspace.

You can open and run the notebooks in Visual Studio Code or as a Jupyter notebook:

conda activate snakeymakey
cd notebooks
jupyter notebook