Fix logic if paired-end and single replicate.

workflow/scripts/pool_and_psuedoreplicate.py

@@ -204,6 +204,7 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
         pool_control_tmp = bedpe_to_tagalign(pool_control, "pool_control")
         pool_control = pool_control_tmp
 
+
     # Duplicate rows and update for pool and psuedoreplicates and update tagAlign with single end data
     experiment_id = design_df.at[0, 'experiment_id']
     replicate_files = design_df.tag_align.unique()
@@ -237,9 +238,9 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
     else:
         pool_experiment_se = pool_experiment
 
-        # Check controls against cutoff_ratio
-        # if so replace with pool_control
-        # unless single control was used
+    # Check controls against cutoff_ratio
+    # if so replace with pool_control
+    # unless single control was used
     if not single_control:
         path_to_pool_control = cwd + '/' + pool_control
         if control_df.values.max() > cutoff_ratio:
@@ -267,7 +268,10 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
                                                             path_to_control
 
     else:
-        path_to_pool_control = pool_control
+        if paired:
+            path_to_pool_control = cwd + '/' + pool_control
+        else:
+            path_to_pool_control = pool_control
         design_new_df['control_tag_align'] = path_to_pool_control
 
     # Add in pseudo replicates