This is a Snakemake project template. The Snakefile is under workflow.

Slides describing and justifying the use of this template.

Please start by installing pixi which handles the environment of this Snakemake workflow.

You can then install the pixi environment by cloning this repository and running:

pixi install

pixi handles the execution of the Snakemake workflows:

pixi run snakemake ...

And if you want to run this Snakemake from another directory you can do so with:

pixi run --manifest-path /path/to/snakemake/pixi.toml snakemake ...

where you update /path/to/snakemake/pixi.toml to the path of the pixi.toml you cloned.

And in place of ... use all the normal Snakemake arguments for your workflow.