adding instructions for running workflow

README.md

@@ -62,4 +62,14 @@ conda activate clusterTutorial
 ```
 8. Before running any jobs on the cluster, don't forget to change the `ACCOUNT` and `EMAIL` fields in the [cluster profile configuration](config/cluster.json) and the [cluster submission script](code/clusterSnakemake.pbs).
 
+9. Run the Snakemake workflow. **Note**: If you wish to rerun the workflow after having it successfully complete, use the `--forcerun` or the `--forceall` flags or just delete the `results/` directory.
+    - To run it locally on the login node:
+    ```
+    snakemake
+    ```
+    - To run it on the cluster:
+    ```
+    snakemake --profile config/pbs-torque/ --latency 20
+    ```
+
 See the [`conda` documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/index.html) for more information.