diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 6c37eed940ca89f71ebd3c49a2dae042f94d5b05..25cc444d53ca995a957acb51e38e2633a25e1c44 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -267,7 +267,7 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
                                                             path_to_control
 
     else:
-        path_to_pool_control = cwd + '/' +  pool_control
+        path_to_pool_control = pool_control
         design_new_df['control_tag_align'] = path_to_pool_control
 
     # Add in pseudo replicates
@@ -306,7 +306,7 @@ def main():
     design_df = pd.read_csv(design, sep='\t')
 
     # Get current directory to build paths
-    cwd = os.getcwd() 
+    cwd = os.getcwd()
 
     # Check Number of replicates and replicates
     no_reps = check_replicates(design_df)