add cluster command lines

README.md

@@ -86,10 +86,18 @@ Execute the workflow locally via
 
 `snakemake --use-singularity --singularity-args "-B '/home/login/'" --cores $N`
 
-using $N cores or run it in a cluster environment via
+using $N cores or run it in a cluster environment via this standard command line :
 
 `snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
 
+Or specifically on Slurm cluster:
+
+`sbatch snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores $SLURM_JOB_CPUS_PER_NODE`
+
+or on SGE cluster:
+
+`snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "qsub -cwd -V -b y -l h_vmem={cluster.ram} -pe [PE] {threads}" -j 200 --nolock --cores 1`
+
 
 Visualize how the rules are connected via