dnaseq_slurm_cheo_ri.sh

#!/bin/bash
#SBATCH -A slurm
#SBATCH --partition=all
#SBATCH --job-name=crg2
#SBATCH --time=50:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4G
#SBATCH --output=%x-%j.out

SF="/srv/shared/pipelines/crg2/Snakefile"
CP="/srv/shared/conda_envs/crg2-conda/"
SLURM="/srv/shared/pipelines/crg2/slurm_profile/"
CONFIG="config_cheo_ri.yaml"

source /storage/modules/anaconda/2020.11/etc/profile.d/conda.sh
conda activate /srv/shared/conda_envs/snakemake_5.10.0/

snakemake --use-conda -s ${SF} --cores 4 --conda-prefix ${CP} --configfile ${CONFIG} --profile ${SLURM}