Update README.md

README.md

@@ -13,18 +13,11 @@ cp -r /lustre/nobackup/WUR/ABGC/shared/pipelines_version2/population-mapping-ver
 ```
 conda activate /lustre/nobackup/WUR/ABGC/shared/pipelines_version2/envs/population-mapping-version2
 ```
-#### Create HPC config file:
-Necessary for snakemake to prepare and send jobs.
+#### Run the pipeline on the cluster:
+To run the pipeline, run the following command:
 ```
-mkdir -p ~/.config/snakemake/<name-of-pipeline>
-nano ~/.config/snakemake/<name-of-pipeline>/config.yaml
-```
-Include the following and save the file (ctr+x)
-```
-jobs: 10
-cluster: "sbatch -t 2-0:0:0 --mem=16000 -c8 --job-name={rule} --output=logs_slurm/{rule}_%j.out --error=logs_slurm/{rule}_%j.err"
+snakemake -j 8 --cluster-config cluster.yaml --cluster "sbatch --mem={cluster.mem} --time {cluster.time} --cpus-per-task {cluster.threads} --job-name={cluster.name} --output={cluster.output} --error={cluster.error}"
 
-use-conda: true
 ```