diff --git a/nf_core/lint.py b/nf_core/lint.py
index 07bd28bcd..44ad3673d 100644
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -104,7 +104,7 @@ def pf(file_path):
                 files = [files]
             if any([os.path.isfile(pf(f)) for f in files]):
                 self.passed.append((1, "File found: {}".format(files)))
-                self.files.append(f)
+                self.files.extend(files)
             else:
                 self.failed.append((1, "File not found: {}".format(files)))
 
@@ -114,7 +114,7 @@ def pf(file_path):
                 files = [files]
             if any([os.path.isfile(pf(f)) for f in files]):
                 self.passed.append((1, "File found: {}".format(files)))
-                self.files.append(f)
+                self.files.extend(files)
             else:
                 self.warned.append((1, "File not found: {}".format(files)))
 
@@ -210,7 +210,8 @@ def check_config_vars(self):
             raise AssertionError("`nextflow config` returned non-zero error code: %s,\n   %s", e.returncode, e.output)
         else:
             for l in nfconfig_raw.splitlines():
-                k, v = l.split(' = ', 1)
+                ul = l.decode()
+                k, v = ul.split(' = ', 1)
                 self.config[k] = v
             for cf in config_fail:
                 if cf in self.config.keys():
@@ -269,7 +270,7 @@ def check_readme(self):
             nf_config_version = self.config.get('params.nf_required_version').strip('\'"')
             try:
                 assert nf_badge_version == nf_config_version
-            except AssertionError, KeyError:
+            except (AssertionError, KeyError):
                 self.failed.append((6, "README Nextflow minimum version badge does not match config. Badge: '{}', Config: '{}'".format(nf_badge_version, nf_config_version)))
             else:
                 self.passed.append((6, "README Nextflow minimum version badge matched config. Badge: '{}', Config: '{}'".format(nf_badge_version, nf_config_version)))