Merge branch '31-BlacklistRegions' of...

Merge branch '31-BlacklistRegions' of git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis into 31-BlacklistRegions

workflow/scripts/overlap_peaks.py

@@ -40,7 +40,8 @@ def get_args():
 
     parser.add_argument('-b', '--blacklist',
                         help="Bed file of blacklisted regions to remove",
-                        required=False)
+                        required=False,
+                        default="None")
 
     args = parser.parse_args()
     return args
@@ -198,7 +199,7 @@ def main():
     args = get_args()
     design = args.design
     files = args.files
-    blacklist = args.files
+    blacklist = args.blacklist
 
     # Create a file handler
     handler = logging.FileHandler('consensus_peaks.log')
@@ -230,7 +231,7 @@ def main():
     design_diff.to_csv("design_exQC.tsv", header=True, sep='\t', index=False)
 
     # Remove blacklist regions; if blacklist = True
-    if blacklist:
+    if os.path.exists(blacklist):
         for experiment, df_experiment in design_peaks_df.groupby('experiment_id'):
             bl_peaks = blacklist_peaks(experiment, blacklist)