diff --git a/debian/patches/add_setup.py.patch b/debian/patches/add_setup.py.patch
index 8e84a52..994123f 100644
--- a/debian/patches/add_setup.py.patch
+++ b/debian/patches/add_setup.py.patch
@@ -1,9 +1,11 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Add setup.py
 Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40
+Index: ctdconverter/convert.py
+===================================================================
 --- ctdconverter.orig/convert.py
 +++ ctdconverter/convert.py
-@@ -8,7 +8,7 @@
+@@ -8,7 +8,7 @@ from argparse import RawDescriptionHelpF
  from common.exceptions import ApplicationException, ModelError
  
  __all__ = []
@@ -12,13 +14,15 @@
  __date__ = '2014-09-17'
  __updated__ = '2017-08-09'
  
-@@ -269,4 +269,4 @@
+@@ -269,4 +269,4 @@ def validate_and_prepare_common_argument
  
  
  if __name__ == "__main__":
 -    sys.exit(main())
 \ No newline at end of file
 +    sys.exit(main())
+Index: ctdconverter/setup.py
+===================================================================
 --- /dev/null
 +++ ctdconverter/setup.py
 @@ -0,0 +1,170 @@
diff --git a/debian/patches/correct_name b/debian/patches/correct_name
index a517c09..e92b980 100644
--- a/debian/patches/correct_name
+++ b/debian/patches/correct_name
@@ -1,8 +1,10 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: unify script name reporting
+Index: ctdconverter/convert.py
+===================================================================
 --- ctdconverter.orig/convert.py
 +++ ctdconverter/convert.py
-@@ -17,10 +17,11 @@
+@@ -17,10 +17,11 @@ program_build_date = str(__updated__)
  program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
  program_short_description = "CTDConverter - A project from the WorkflowConversion family " \
                                  "(https://github.com/WorkflowConversion/CTDConverter)"
@@ -15,7 +17,7 @@
  
  FORMAT can be either one of the supported output formats: cwl, galaxy.
  
-@@ -30,12 +31,12 @@
+@@ -30,12 +31,12 @@ documentation for each of the converters
  
  I - Parsing a single CTD file and convert it:
  
@@ -30,7 +32,7 @@
  
  
  III - Hardcoding parameters
-@@ -141,7 +142,7 @@
+@@ -141,7 +142,7 @@ III - Hardcoding parameters
  
        There are, for now, no CWL-specific parameters or options.
  
@@ -39,7 +41,7 @@
  
  program_license = '''%(short_description)s
  
-@@ -174,7 +175,8 @@
+@@ -174,7 +175,8 @@ def main(argv=None):
      # converter will register its own parameters after we've registered the basic ones... we have to do it old school
      if len(argv) < 2:
          utils.error("Not enough arguments provided")
diff --git a/debian/patches/py3_compat b/debian/patches/py3_compat
index 65ba38a..92473eb 100644
--- a/debian/patches/py3_compat
+++ b/debian/patches/py3_compat
@@ -1,8 +1,10 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: use `open` instead of `file`
+Index: ctdconverter/cwl/converter.py
+===================================================================
 --- ctdconverter.orig/cwl/converter.py
 +++ ctdconverter/cwl/converter.py
-@@ -72,7 +72,7 @@
+@@ -72,7 +72,7 @@ def convert_models(args, parsed_ctds):
  
          logger.info("Writing to %s" % utils.get_filename(output_file), 1)
  
@@ -11,7 +13,7 @@
          stream.write(CWL_SHEBANG + '\n\n')
          stream.write("# This CWL file was automatically generated using CTDConverter.\n")
          stream.write("# Visit https://github.com/WorkflowConversion/CTDConverter for more information.\n\n")
-@@ -103,6 +103,8 @@
+@@ -103,6 +103,8 @@ def convert_to_cwl(ctd_model, args):
          param_name = utils.extract_param_name(param)
          cwl_fixed_param_name = fix_param_name(param_name)
          hardcoded_value = args.parameter_hardcoder.get_hardcoded_value(param_name, ctd_model.name)
diff --git a/debian/patches/upgrade_deprecated_strip b/debian/patches/upgrade_deprecated_strip
index d39b370..89a0727 100644
--- a/debian/patches/upgrade_deprecated_strip
+++ b/debian/patches/upgrade_deprecated_strip
@@ -1,18 +1,18 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Upgrade deprecated using of string.strip()
+Index: ctdconverter/common/utils.py
+===================================================================
 --- ctdconverter.orig/common/utils.py
 +++ ctdconverter/common/utils.py
-@@ -4,8 +4,7 @@
+@@ -4,7 +4,6 @@ import ntpath
  import os
  
  from lxml import etree
 -from string import strip
--from logger import info, error, warning
-+from logger import info, error, warning
+ from logger import info, error, warning
  
  from common.exceptions import ApplicationException
- from CTDopts.CTDopts import CTDModel, ParameterGroup
-@@ -73,9 +72,9 @@
+@@ -73,9 +72,9 @@ def validate_argument_is_valid_path(args
      if member_value is not None:
          if isinstance(member_value, list):
              for file_name in member_value:
@@ -24,4 +24,3 @@
  
          for path_to_check in paths_to_check:
              validate_path_exists(path_to_check)
-