jjjermiah / snakemake-pixi-template

A basic template to get started with Snakemake using Pixi

snakemake-pixi-template

This is a template repository for snakemake workflow with pixi as a package manager. It is based on the pixi.

Idea

Traditionally, I would use Conda to create my environments and manage my packages. However the added step of making sure my environment.yml file is up to date is a bit of a hassle.

conda env create -f environment.yml -n snakemake
conda activate snakemake

Instead, I can use pixi to manage my packages and create a pixi.lock file that will be used to create the environment.

pixi install

This makes sure that the lock is synchronized and version controlled.

Usage

To add packages to the default environment:

pixi add pandas

To run a command in the environment

pixi run snakemake --dryrun

Enter into the environment

pixi shell

# Exit the environment using "exit"

Pixi Tasks

Pixi also allows defining tasks for common tasks. This is done in the pyproject.toml file.

[tool.pixi.tasks]
dryrun = "snakemake --dry-run"
snake = "snakemake --cores 1"

This allows me to run pixi run dryrun to see what snakemake would do and pixi run snake to run snakemake.

A common task I like to do is creating the dags regularly and including them in my README. This can then be automated with the task.

dag = "snakemake -F --dag | dot -Tsvg > resources/dag.svg"
rulegraph = "snakemake -F --rulegraph | dot -Tsvg > resources/rulegraph.svg"
filegraph = "snakemake -F --filegraph | dot -Tsvg > resources/filegraph.svg"
graphs = { depends_on = ["dag", "rulegraph", "filegraph"] }

Running pixi run graphs will create the three graphs and save them in the resources folder. This way, they are automatically updated below in this README.

DAG

Rulegraph

Filegraph