Fix output directories and file names.

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:
 

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():