Introduction

This repo contains some code and data to demonstrate how to work with snakemake.

SSH tunneling

ssh -L 8215:localhost:8890 yourname@your.target.server

Submit jobs to Slurm

Put the following content to ~/.config/snakemake/{profile_name}/config.yaml

jobs: 60
cluster: "sbatch --nodes=1 --mem={resources.mem} --time={resources.time}"
use-conda: true
default-resources: [time="00:10:00", mem="15G"]

You can submit jobs to Slurm with snakemake using the following command

snakemake {command} --profile {profile_name}