diff --git a/src/Snakefile b/src/Snakefile
index 02cba3b94de2f46e3e9b22fedd2941b199ebb645..98d10010e65364518b66d1545dcd32ae016a4ab4 100755
--- a/src/Snakefile
+++ b/src/Snakefile
@@ -668,8 +668,8 @@ if doPeakCalling:
         #                         peakType = ["narrow"])
         # allResultFiles.append(pooledPeaksNonStringent)
 
-#print(allResultFiles)
-#print('\n'.join(map(str, allResultFiles)))
+print(allResultFiles)
+print('\n'.join(map(str, allResultFiles)))
 
 #Sys.exit(0)
 
@@ -1798,10 +1798,14 @@ def getControlSample(filePrefix, addCommandLinePrefix):
     return ctrl_param
 
 def getAllInputFiles_macs(filePrefix):
-#
-    # For ATACSeq, no control sample
+
+    #print(controlSample)
+    bamFile = FINAL_OUTPUT_dir + "/" + filePrefix + ".bam"
+
+    # For ATACSeq, no control sample and only the BAM file
     if dataType != "ChIPseq":
-        return ""
+        inputFiles = [bamFile]
+        return inputFiles
 
     if mergeReplicates:
         sampleTableCol= "individual"
@@ -1817,8 +1821,7 @@ def getAllInputFiles_macs(filePrefix):
     sample_cur = re.search(samples_regex, file_base).group(0).replace(".merged","") # since the matching contains the merged suffix, we remove it here
     controlSample = samplesData["control_sampleName"][samplesData[sampleTableCol]==sample_cur].iloc[0]
 
-    #print(controlSample)
-    bamFile = FINAL_OUTPUT_dir + "/" + filePrefix + ".bam"
+
 
     if pandas.isnull(controlSample):
         inputFiles = [bamFile]
@@ -1826,6 +1829,8 @@ def getAllInputFiles_macs(filePrefix):
         controlFile = FINAL_OUTPUT_dir + "/" + controlSample + ".final.bam"
         inputFiles = [bamFile, controlFile]
 
+    print("Input files: " + inputFiles)
+
     return inputFiles
 
 # Runs for all bam files in the final output folder, also the replicated one