move up code to be generalizable.

workflow/scripts/overlap_peaks.py

@@ -241,13 +241,13 @@ def main():
     # Find consenus overlap peaks for each experiment
 
     for experiment, df_experiment in design_peaks_df.groupby('experiment_id'):
+        replicated_peak, chr_peak = overlap(experiment, df_experiment)
         # 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:
-            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]