Merge pull request #920 from KevinMenden/path-fix-triage-2

Path fix triage 2
nf-core · Mar 19, 2021 · 5e032b4 · 5e032b4
2 parents ccd9ef1 + e0c22bb
commit 5e032b4
Showing 1 changed file with 8 additions and 4 deletions.
diff --git a/nf_core/modules/lint.py b/nf_core/modules/lint.py
@@ -235,6 +235,10 @@ def get_installed_modules(self):
         # Get nf-core modules
         if os.path.exists(nfcore_modules_dir):
             for m in sorted([m for m in os.listdir(nfcore_modules_dir) if not m == "lib"]):
+                if not os.path.isdir(os.path.join(nfcore_modules_dir, m)):
+                    raise ModuleLintException(
+                        f"File found in '{nfcore_modules_dir}': '{m}'! This directly should only contain module directories."
+                    )
                 m_content = os.listdir(os.path.join(nfcore_modules_dir, m))
                 # Not a module, but contains sub-modules
                 if not "main.nf" in m_content:
@@ -289,8 +293,8 @@ def format_result(test_results, table):
                 last_modname = mod.module_name
                 table.add_row(
                     Markdown(f"{mod.module_name}"),
-                    Markdown(f"{result[1]}"),
                     os.path.relpath(result[2], self.dir),
+                    Markdown(f"{result[1]}"),
                     style=row_style,
                 )
             return table
@@ -307,8 +311,8 @@ def _s(some_list):
             )
             table = Table(style="green", box=rich.box.ROUNDED)
             table.add_column("Module name", width=max_mod_name_len)
-            table.add_column("Test message", no_wrap=True)
             table.add_column("File path", no_wrap=True)
+            table.add_column("Test message")
             table = format_result(self.passed, table)
             console.print(table)
 
@@ -321,8 +325,8 @@ def _s(some_list):
             )
             table = Table(style="yellow", box=rich.box.ROUNDED)
             table.add_column("Module name", width=max_mod_name_len)
-            table.add_column("Test message", no_wrap=True)
             table.add_column("File path", no_wrap=True)
+            table.add_column("Test message")
             table = format_result(self.warned, table)
             console.print(table)
 
@@ -333,8 +337,8 @@ def _s(some_list):
             )
             table = Table(style="red", box=rich.box.ROUNDED)
             table.add_column("Module name", width=max_mod_name_len)
-            table.add_column("Test message", no_wrap=True)
             table.add_column("File path", no_wrap=True)
+            table.add_column("Test message")
             table = format_result(self.failed, table)
             console.print(table)