diff --git a/example/input/params.sh b/example/input/params.sh
index 877d77848491081a6553c31d384d28c0a125ad73..dd0055678018ff19e4e109a64ba8dcfc5ee725ed 100644
--- a/example/input/params.sh
+++ b/example/input/params.sh
@@ -12,7 +12,10 @@
 # Config file to use
 configFile="config.yaml"
 
-# Snakefile to use
+# Snakefile to use. use the path to your own snakefile from the Git repo that you cloned
+snakefile="/absolute/path/to/your/Snakefile"
+
+# Here, we used the main Snakefile in the project folder, for development purposes
 snakefile="/g/scb2/zaugg/carnold/Projects/AtacSeq/src/Snakefile"
 
 #######################
diff --git a/example/templates/params.sh b/example/templates/params.sh
index 2fee27d167c8fb1cf684c61797f41d4bad04fe0e..50e8e4fab764607e65e799c5eaf7dbb8cf1b2b45 100644
--- a/example/templates/params.sh
+++ b/example/templates/params.sh
@@ -12,8 +12,8 @@
 # Use the yaml format for the configFile now, which can contain comment lines and is therefore easier to use
 configFile="config.yaml"
 
-# Snakefile to use
-snakefile="/g/scb2/zaugg/carnold/Projects/AtacSeq/src/Snakefile"
+# Snakefile to use. use the path to your own snakefile from the Git repo that you cloned
+snakefile="/absolute/path/to/your/Snakefile"
 
 #######################
 # PERFORMANCE OPTIONS #
diff --git a/src/Snakefile b/src/Snakefile
index 96e3e09391d78adab1bd6663382f057b707c65e7..dc82b5d2aa12634c676f711978021b21e3635c9a 100755
--- a/src/Snakefile
+++ b/src/Snakefile
@@ -2140,26 +2140,27 @@ if annotatePeaks and doPeakCalling:
             mode = "individual"
         script: script_annoPeaks
 
-    use rule annotatePeaks_individual as annotatePeaks_consensus with:
-        input:
-            consensus_encode        = consensusPeaks_ENCODE,
-            consensus_stringent     = consensusPeaks_stringent,
-            consensus_nonStringent  = consensusPeaks_nonStringent
-        output:
-            annotation_consensus_encode = annotation_consensusPeaks_ENCODE,
-            annotation_consensus_stringent = annotation_consensusPeaks_stringent,
-            annotation_consensus_nonStringent = annotation_consensusPeaks_nonStringent
-        log:
-            expand('{dir}/annotatePeaks_consensus.R.log', dir = LOG_BENCHMARK_dir)
-        #singularity:
-        #    "shub://chrarnold/Singularity_images:atac_seq_r"
-        message:
-            "{ruleDisplayMessage} Annotating consensus peaks for all peak files with the script {script_annoPeaks}..."
-        params:
-            tabulateOutput = "true",
-            assemblyVersion = config["align"]["assemblyVersion"],
-            tssRegion = "-5000,5000",
-            mode = "consensus"
+    if nSamplesUnique > 1:
+        use rule annotatePeaks_individual as annotatePeaks_consensus with:
+            input:
+                consensus_encode        = consensusPeaks_ENCODE,
+                consensus_stringent     = consensusPeaks_stringent,
+                consensus_nonStringent  = consensusPeaks_nonStringent
+            output:
+                annotation_consensus_encode = annotation_consensusPeaks_ENCODE,
+                annotation_consensus_stringent = annotation_consensusPeaks_stringent,
+                annotation_consensus_nonStringent = annotation_consensusPeaks_nonStringent
+            log:
+                expand('{dir}/annotatePeaks_consensus.R.log', dir = LOG_BENCHMARK_dir)
+            #singularity:
+            #    "shub://chrarnold/Singularity_images:atac_seq_r"
+            message:
+                "{ruleDisplayMessage} Annotating consensus peaks for all peak files with the script {script_annoPeaks}..."
+            params:
+                tabulateOutput = "true",
+                assemblyVersion = config["align"]["assemblyVersion"],
+                tssRegion = "-5000,5000",
+                mode = "consensus"