cookiecutter-smsk

cookiecutter boilerplate for smsk

What's this?

cookiecutter-smsk is a boilerplate folder hierarchy for snakemake.

Why?

It is a pain in the ass to start a snakemake workflow from scratch, so this boilerplate provides a skeleton with a Snakefile, some sub-snakefiles, test data and some scripts that work, and from there, modify it at your will.

How?

1. Install miniconda or the full Anaconda distribution.

2. Install snakemake: conda install -c bioconda snakemake.

3. Copy this template from GitHub:

cookiecutter gh:jlanga/cookiecutter-smsk

4. Fill the fields and you are set up.

5. Enter in the created folder and type snakemake --use-conda -j. Snakemake will download the required packages through conda and will execute the workflow in parallel.

References

• Snakemake. The workflow engine that saved my life. Written in Python3.
• conda. The package manager. The best thing that has happened in Bioinformatics in years.
• bioconda. Where all the Bioinformatics is.
• cookiecutter. The command line utility that manages these kinds of templates.
• smsk. The previous version of the template I was used until now.