sm3

Simple Snakemake example

This repo is intended as an easy-to-use starting point for making a quick reproducible bioinformatics analysis using Snakemake.

Usage

1. Clone the repo to create your analysis folder

git clone git@github.com:ctmrbio/sm3 my_analysis

2. Modify the Snakefile according to your needs. Add rules to produce output files and add desired final output files to the all rule.
3. Define the environment required to run the rules in workflows/envs/conda.yaml.
4. Create an input directory and put your input files there (a symlink usually works fine).

Running

Run the workflow locally:

snakemake --use-conda --jobs 10

Run the workflow using Slurm on Gandalf:

snakemake --use-conda --profile profiles/ctmr_gandalf

Example

git clone git@github.com:ctmrbio/sm3
cd sm3
ln -s example_input input
snakemake --use-conda --jobs 1