diff --git a/workflow/main.nf b/workflow/main.nf
index 6b59b778e7502c808743977a75c457f696bcfc23..4e9c50da22e13af3685c0682aa4e50767eaebed2 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -369,6 +369,7 @@ peaksDesign = experimentPeaks
 process consensusPeaks {
 
   publishDir "$outDir/${task.process}", mode: 'copy'
+  publishDir "$outDir/design", mode: 'copy',  pattern: '*.{csv|tsv}'
 
   input:
 
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index 99e290029f62ca5619f1b2b6f3cf59015259217f..17b1414b6236ee5cfda0d1c0694a988ecea237c9 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -239,6 +239,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
     # Remove temporary files
     os.remove(clipped_narrowpeak_fn)
     os.remove(rescaled_narrowpeak_fn)
+    os.remove(int_narrowpeak_fn)
 
 
 def main():