diff --git a/biobb_pmx/pmxbiobb/pmxanalyse.py b/biobb_pmx/pmxbiobb/pmxanalyse.py
index eb96a06..a0e5ca6 100755
--- a/biobb_pmx/pmxbiobb/pmxanalyse.py
+++ b/biobb_pmx/pmxbiobb/pmxanalyse.py
@@ -243,7 +243,8 @@ def launch(self) -> int:
         self.copy_to_host()
 
         self.tmp_files.extend(
-            [self.stage_io_dict.get("unique_dir", ""), list_a_dir, list_b_dir]
+            # [self.stage_io_dict.get("unique_dir", ""), list_a_dir, list_b_dir]
+            [list_a_dir, list_b_dir]
         )
         self.remove_tmp_files()
 
@@ -270,6 +271,8 @@ def pmxanalyse(
         properties=properties,
     ).launch()
 
+    pmxanalyse.__doc__ = Pmxanalyse.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
diff --git a/biobb_pmx/pmxbiobb/pmxatom_mapping.py b/biobb_pmx/pmxbiobb/pmxatom_mapping.py
index b47ab3a..733f4a5 100755
--- a/biobb_pmx/pmxbiobb/pmxatom_mapping.py
+++ b/biobb_pmx/pmxbiobb/pmxatom_mapping.py
@@ -266,7 +266,7 @@ def launch(self) -> int:
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -309,6 +309,8 @@ def pmxatom_mapping(
         **kwargs,
     ).launch()
 
+    pmxatom_mapping.__doc__ = Pmxatom_mapping.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
diff --git a/biobb_pmx/pmxbiobb/pmxcreate_top.py b/biobb_pmx/pmxbiobb/pmxcreate_top.py
index a91b617..51f538c 100755
--- a/biobb_pmx/pmxbiobb/pmxcreate_top.py
+++ b/biobb_pmx/pmxbiobb/pmxcreate_top.py
@@ -189,7 +189,8 @@ def launch(self) -> int:
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        self.tmp_files.extend([self.tmp_folder])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -214,6 +215,8 @@ def pmxcreate_top(
         **kwargs,
     ).launch()
 
+    pmxcreate_top.__doc__ = Pmxcreate_top.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
diff --git a/biobb_pmx/pmxbiobb/pmxgentop.py b/biobb_pmx/pmxbiobb/pmxgentop.py
index 1ad047e..2e41fb5 100755
--- a/biobb_pmx/pmxbiobb/pmxgentop.py
+++ b/biobb_pmx/pmxbiobb/pmxgentop.py
@@ -242,8 +242,8 @@ def launch(self) -> int:
             out_log=self.out_log,
         )
 
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), top_dir])
-        # self.remove_tmp_files()
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), top_dir, unique_dir_output_file])
+        self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
         return self.return_code
@@ -265,6 +265,8 @@ def pmxgentop(
         **kwargs,
     ).launch()
 
+    pmxgentop.__doc__ = Pmxgentop.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
diff --git a/biobb_pmx/pmxbiobb/pmxligand_hybrid.py b/biobb_pmx/pmxbiobb/pmxligand_hybrid.py
index 27e8b73..c2fa54b 100755
--- a/biobb_pmx/pmxbiobb/pmxligand_hybrid.py
+++ b/biobb_pmx/pmxbiobb/pmxligand_hybrid.py
@@ -243,7 +243,7 @@ def launch(self) -> int:
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -285,6 +285,8 @@ def pmxligand_hybrid(
         properties=properties,
     ).launch()
 
+    pmxligand_hybrid.__doc__ = Pmxligand_hybrid.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
diff --git a/biobb_pmx/pmxbiobb/pmxmerge_ff.py b/biobb_pmx/pmxbiobb/pmxmerge_ff.py
index bb92ce4..135e531 100755
--- a/biobb_pmx/pmxbiobb/pmxmerge_ff.py
+++ b/biobb_pmx/pmxbiobb/pmxmerge_ff.py
@@ -142,7 +142,8 @@ def launch(self) -> int:
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        self.tmp_files.extend([self.tmp_folder])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -165,6 +166,8 @@ def pmxmerge_ff(
         **kwargs,
     ).launch()
 
+    pmxmerge_ff.__doc__ = Pmxmerge_ff.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
diff --git a/biobb_pmx/pmxbiobb/pmxmutate.py b/biobb_pmx/pmxbiobb/pmxmutate.py
index f1ea0ef..32d3948 100755
--- a/biobb_pmx/pmxbiobb/pmxmutate.py
+++ b/biobb_pmx/pmxbiobb/pmxmutate.py
@@ -186,7 +186,8 @@ def launch(self) -> int:
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        self.tmp_files.extend([mutations_dir])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -211,6 +212,8 @@ def pmxmutate(
         **kwargs,
     ).launch()
 
+    pmxmutate.__doc__ = Pmxmutate.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""