Move logic ahead of redo for blacklist.

workflow/scripts/overlap_peaks.py

@@ -242,14 +242,15 @@ def main():
 
     for experiment, df_experiment in design_peaks_df.groupby('experiment_id'):
         replicated_peak, chr_peak = overlap(experiment, df_experiment)
+        design_diff.loc[design_diff.experiment_id == experiment, "peak"] = replicated_peak
+        design_anno.loc[experiment] = [experiment, chr_peak]
+
         # Remove blacklist regions; if blacklist = True
         if blacklist and os.path.exists(blacklist):
             bl_peaks, bl_chr_peak = blacklist_peaks(experiment, blacklist)
             design_diff.loc[design_diff.experiment_id == experiment, "peak"] = bl_peaks
             design_anno.loc[design_anno.Condition == experiment, "Peaks"] = bl_chr_peak
-        else:
-            design_diff.loc[design_diff.experiment_id == experiment, "peak"] = replicated_peak
-            design_anno.loc[experiment] = [experiment, chr_peak]
+
 
     # Write out file
     design_diff.columns = ['SampleID',