A simple Snakemake file consists of several rules and Python functions to execute workflows. With large workflows, however, the enter pipeline file can be cumbersome and difficult to maintain. Snakemake has a recommended structure to simplify large scale workflows by seperating it into common rule and function files.

The Snakemake structure was obtained from the snakemake deployment documentation.

├── README.md
├── workflow
│   ├── envs
|   │   └── environment.yaml
│   ├── rules
|   │   └── common.smk
|   │   └── defaults.smk
|   │   └── rule.smk
│   ├── scripts
|   │   ├── script1.py
|   │   └── script2.R
|   └── Snakefile
└── config
    ├── config.yaml
    └── some-sheet.tsv

Install the latest version of cookiecutter if you have not already.

pip install cookiecutter

Generate the snakemake project using cookiecutter:

cookiecutter https://github.com/simpsonlab/cookiecutter-snakemake.git

Several items will be requested which will be used to complete the template files and directories:

name [project]: project_name
author [Author Name]: Simpson Lab
institute [Institute Name]: The Ontario Insitute for Cancer Research
year [2020]:

A directory with the name project_name will be created and default files and sub-directories will be constructed as described above.

The initial boilerplate setup was influenced by (https://github.com/audreyfeldroy/cookiecutter-pypackage).

MIT