Update README.md

README.md

@@ -14,6 +14,8 @@ cp -r /lustre/nobackup/WUR/ABGC/shared/pipelines_version2/population-mapping-ver
 See installation instructions below. 
 
 #### Activate environmet:
+Since the pipelines can take a while to run, it’s best if you use a screen session. By using a screen session, Snakemake stays “active” in the shell while it’s running, there’s no risk of the connection going down and Snakemake stopping. `screen -S <name of session>` to start a new screen session and `screen -r <name of session` to reattach to the screen session. In the screen session activate the conda environment.
+
 ```
 conda activate /lustre/nobackup/WUR/ABGC/shared/pipelines_version2/envs/population-mapping-version2
 ```
@@ -22,6 +24,9 @@ conda activate /lustre/nobackup/WUR/ABGC/shared/pipelines_version2/envs/populati
 Configure your paths, but keep the variable names that are already in the config file. See below for more details.
 
 #### Run the pipeline on the cluster:
+First test the pipeline with a dry run: `snakemake -np`. This will show you the steps and commands that will be executed. Check the commands and file names to see if there’s any mistake. If all looks ok, you can now run your pipeline
+
+
 To run the pipeline, run the following command:
 ```
 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}"