Snakemake

Snakemake is a pythonic way of writing makefiles.

Snakemake works with distributions like anaconda to package and install dependencies. I recommend using Pyenv to keep things organized and separated out.

Links

Projects

Snakemake documentation: https://snakemake.readthedocs.io/en/stable/

Snakemake for Bioconda documentation: https://bioconda.github.io/recipes/snakemake/README.html

Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake

Examples

A SingleCell RNASeq pre-processing pipeline built on snakemake: https://github.com/Hoohm/dropSeqPipe/blob/master/Snakefile