The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language.

Documentation

Snakemake home
Snakemake documentation home

Slurm scripts

Please refer to the Snakemake documentation on the format of the Snakemake input file.
By default, the input file is named Snakefile, snakefile, workflow/Snakefile or workflow/snakefile.

#!/bin/bash
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=8
module load snakemake
module load bwa
module load samtools
snakemake --cores ${SLURM_NTASKS} 

CCBR has written a tutorial written for Biowulf but that be adapted for FRCE. The only change comes in the section titled Utilize cluster for rules. One of the parameters the tutorial sets is --gres=lscratch:200. Do not use this line in the cluster command given.