snakemake-project

Example of a snakemake project

Installation

Download the repository from github

git clone https://github.com/Redmar-van-den-Berg/snakemake-project.git

Install and activate the conda environment.

conda env create --file environment.yml
conda activate snakemake-project

Settings

There are two ways configuration options are set, in decreasing order of priority.

1. Key-values pairs passed to snakemake using --config
2. In the specified --configfile.

Supported settings

The following settings are available for the pipeline.

Option	Type	Explanation
setting1	Required string	The first setting
setting2	Required settingsfile	A file with some settings
setting3	Required string	A third setting

Tests

You can run the tests that accompany this pipeline with the following commands

# Check if requirements are installed, and run linting on the Snakefile
pytest --kwd --tag sanity

# Test the pipeline settings in dry-run mode
pytest --kwd --tag dry-run

# Test the performance of the pipeline by running on the test data
pytest --kwd --tag integration