Merge pull request #2771 from mirpedrol/extra-module-file

Modules: patch: handle file not found when it is an added file to a module

CHANGELOG.md

@@ -22,6 +22,7 @@
 ### Modules
 
 - Handle dirty local module repos by force checkout of commits and branches if needed ([#2734](https://github.com/nf-core/tools/pull/2734))
+- Patch: handle file not found when it is an added file to a module ([#2771](https://github.com/nf-core/tools/pull/2771))
 - Handle symlinks when migrating pytest ([#2770](https://github.com/nf-core/tools/pull/2770))
 - Add `--profile` parameter to nf-test command ([#2767](https://github.com/nf-core/tools/pull/2767))
 

nf_core/modules/modules_differ.py

@@ -447,8 +447,12 @@ def try_apply_patch(module, repo_path, patch_path, module_dir, reverse=False):
             log.debug(f"Applying patch to {file}")
             fn = Path(file).relative_to(module_relpath)
             file_path = module_dir / fn
-            with open(file_path) as fh:
-                file_lines = fh.readlines()
+            try:
+                with open(file_path) as fh:
+                    file_lines = fh.readlines()
+            except FileNotFoundError:
+                # The file was added with the patch
+                file_lines = [""]
             patched_new_lines = ModulesDiffer.try_apply_single_patch(file_lines, patch, reverse=reverse)
             new_files[str(fn)] = patched_new_lines
         return new_files