diff --git a/runme.sh b/runme.sh
index 099b64107b901bdd3339b289598c6dd2c5b05140..9344d47a26402deb39620cc62e3d4a38e6c932c3 100644
--- a/runme.sh
+++ b/runme.sh
@@ -15,6 +15,7 @@ conda install -c anaconda pandas
 conda install -c bioconda pysam
 
 #run the workflow:
+## DEPRECATED, follow the readme.md
 conda activate snakemake
 module load graalvm/ce-java8-20.0.0 fastqc
 module load samtools/1.10
@@ -28,8 +29,7 @@ module load MultiQC/1.9
 
 sbatch -q hubbioit -p hubbioit snakemake --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} -q hubbioit -p hubbioit" -j 300 --nolock
 
-
-# or without module: 
+#run the workflow without loading modules before (with --use-envmodules): 
 conda activate snakemake
 #check the pipeline:
 snakemake --use-envmodules -n