We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
nf-core modules install is asking for two files
### Description of the bug

nf-core modules install is asking for two files: main.nf and nextflow.config. I think this is not necessary, since one can use a different naming convention for both files.

https://github.com/nf-core/modules/issues/2272

I think this can be just a warning since you can decide to install the modules outside a nf-core pipeline


### Command used and terminal output

_No response_

### System information

_No response_

--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `nf_core/modules/modules_command.py`
Content:
```
1 import logging
2 import os
3 import shutil
4 from pathlib import Path
5 
6 import yaml
7 
8 import nf_core.modules.module_utils
9 import nf_core.utils
10 
11 from .modules_json import ModulesJson
12 from .modules_repo import ModulesRepo
13 
14 log = logging.getLogger(__name__)
15 
16 
17 class ModuleCommand:
18     """
19     Base class for the 'nf-core modules' commands
20     """
21 
22     def __init__(self, dir, remote_url=None, branch=None, no_pull=False, hide_progress=False):
23         """
24         Initialise the ModulesCommand object
25         """
26         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
27         self.hide_progress = hide_progress
28         self.dir = dir
29         self.default_modules_path = Path("modules", "nf-core")
30         self.default_tests_path = Path("tests", "modules", "nf-core")
31         try:
32             if self.dir:
33                 self.dir, self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)
34             else:
35                 self.repo_type = None
36         except LookupError as e:
37             raise UserWarning(e)
38 
39     def get_modules_clone_modules(self):
40         """
41         Get the modules available in a clone of nf-core/modules
42         """
43         module_base_path = Path(self.dir, self.default_modules_path)
44         return [
45             str(Path(dir).relative_to(module_base_path))
46             for dir, _, files in os.walk(module_base_path)
47             if "main.nf" in files
48         ]
49 
50     def get_local_modules(self):
51         """
52         Get the local modules in a pipeline
53         """
54         local_module_dir = Path(self.dir, "modules", "local")
55         return [str(path.relative_to(local_module_dir)) for path in local_module_dir.iterdir() if path.suffix == ".nf"]
56 
57     def has_valid_directory(self):
58         """Check that we were given a pipeline or clone of nf-core/modules"""
59         if self.repo_type == "modules":
60             return True
61         if self.dir is None or not os.path.exists(self.dir):
62             log.error(f"Could not find pipeline: {self.dir}")
63             return False
64         main_nf = os.path.join(self.dir, "main.nf")
65         nf_config = os.path.join(self.dir, "nextflow.config")
66         if not os.path.exists(main_nf) and not os.path.exists(nf_config):
67             raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
68         return True
69 
70     def has_modules_file(self):
71         """Checks whether a module.json file has been created and creates one if it is missing"""
72         modules_json_path = os.path.join(self.dir, "modules.json")
73         if not os.path.exists(modules_json_path):
74             log.info("Creating missing 'module.json' file.")
75             ModulesJson(self.dir).create()
76 
77     def clear_module_dir(self, module_name, module_dir):
78         """Removes all files in the module directory"""
79         try:
80             shutil.rmtree(module_dir)
81             # Try cleaning up empty parent if tool/subtool and tool/ is empty
82             if module_name.count("/") > 0:
83                 parent_dir = os.path.dirname(module_dir)
84                 try:
85                     os.rmdir(parent_dir)
86                 except OSError:
87                     log.debug(f"Parent directory not empty: '{parent_dir}'")
88                 else:
89                     log.debug(f"Deleted orphan tool directory: '{parent_dir}'")
90             log.debug(f"Successfully removed {module_name} module")
91             return True
92         except OSError as e:
93             log.error(f"Could not remove module: {e}")
94             return False
95 
96     def modules_from_repo(self, install_dir):
97         """
98         Gets the modules installed from a certain repository
99 
100         Args:
101             install_dir (str): The name of the directory where modules are installed
102 
103         Returns:
104             [str]: The names of the modules
105         """
106         repo_dir = Path(self.dir, "modules", install_dir)
107         if not repo_dir.exists():
108             raise LookupError(f"Nothing installed from {install_dir} in pipeline")
109 
110         return [
111             str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files
112         ]
113 
114     def install_module_files(self, module_name, module_version, modules_repo, install_dir):
115         """
116         Installs a module into the given directory
117 
118         Args:
119             module_name (str): The name of the module
120             module_version (str): Git SHA for the version of the module to be installed
121             modules_repo (ModulesRepo): A correctly configured ModulesRepo object
122             install_dir (str): The path to where the module should be installed (should be the 'modules/' dir of the pipeline)
123 
124         Returns:
125             (bool): Whether the operation was successful of not
126         """
127         return modules_repo.install_module(module_name, install_dir, module_version)
128 
129     def load_lint_config(self):
130         """Parse a pipeline lint config file.
131 
132         Look for a file called either `.nf-core-lint.yml` or
133         `.nf-core-lint.yaml` in the pipeline root directory and parse it.
134         (`.yml` takes precedence).
135 
136         Add parsed config to the `self.lint_config` class attribute.
137         """
138         config_fn = os.path.join(self.dir, ".nf-core-lint.yml")
139 
140         # Pick up the file if it's .yaml instead of .yml
141         if not os.path.isfile(config_fn):
142             config_fn = os.path.join(self.dir, ".nf-core-lint.yaml")
143 
144         # Load the YAML
145         try:
146             with open(config_fn, "r") as fh:
147                 self.lint_config = yaml.safe_load(fh)
148         except FileNotFoundError:
149             log.debug(f"No lint config file found: {config_fn}")
150 
151     def check_modules_structure(self):
152         """
153         Check that the structure of the modules directory in a pipeline is the correct one:
154             modules/nf-core/TOOL/SUBTOOL
155 
156         Prior to nf-core/tools release 2.6 the directory structure had an additional level of nesting:
157             modules/nf-core/modules/TOOL/SUBTOOL
158         """
159         if self.repo_type == "pipeline":
160             wrong_location_modules = []
161             for directory, _, files in os.walk(Path(self.dir, "modules")):
162                 if "main.nf" in files:
163                     module_path = Path(directory).relative_to(Path(self.dir, "modules"))
164                     parts = module_path.parts
165                     # Check that there are modules installed directly under the 'modules' directory
166                     if parts[1] == "modules":
167                         wrong_location_modules.append(module_path)
168             # If there are modules installed in the wrong location
169             if len(wrong_location_modules) > 0:
170                 log.info("The modules folder structure is outdated. Reinstalling modules.")
171                 # Remove the local copy of the modules repository
172                 log.info(f"Updating '{self.modules_repo.local_repo_dir}'")
173                 self.modules_repo.setup_local_repo(
174                     self.modules_repo.remote_url, self.modules_repo.branch, self.hide_progress
175                 )
176                 # Move wrong modules to the right directory
177                 for module in wrong_location_modules:
178                     modules_dir = Path("modules").resolve()
179                     module_name = str(Path(*module.parts[2:]))
180                     correct_dir = Path(modules_dir, self.modules_repo.repo_path, Path(module_name))
181                     wrong_dir = Path(modules_dir, module)
182                     shutil.move(wrong_dir, correct_dir)
183                     log.info(f"Moved {wrong_dir} to {correct_dir}.")
184                     # Check if a path file exists
185                     patch_path = correct_dir / Path(module_name + ".diff")
186                     self.check_patch_paths(patch_path, module_name)
187                 shutil.rmtree(Path(self.dir, "modules", self.modules_repo.repo_path, "modules"))
188                 # Regenerate modules.json file
189                 modules_json = ModulesJson(self.dir)
190                 modules_json.check_up_to_date()
191 
192     def check_patch_paths(self, patch_path, module_name):
193         """
194         Check that paths in patch files are updated to the new modules path
195         """
196         if patch_path.exists():
197             log.info(f"Modules {module_name} contains a patch file.")
198             rewrite = False
199             with open(patch_path, "r") as fh:
200                 lines = fh.readlines()
201                 for index, line in enumerate(lines):
202                     # Check if there are old paths in the patch file and replace
203                     if f"modules/{self.modules_repo.repo_path}/modules/{module_name}/" in line:
204                         rewrite = True
205                         lines[index] = line.replace(
206                             f"modules/{self.modules_repo.repo_path}/modules/{module_name}/",
207                             f"modules/{self.modules_repo.repo_path}/{module_name}/",
208                         )
209             if rewrite:
210                 log.info(f"Updating paths in {patch_path}")
211                 with open(patch_path, "w") as fh:
212                     for line in lines:
213                         fh.write(line)
214                 # Update path in modules.json if the file is in the correct format
215                 modules_json = ModulesJson(self.dir)
216                 modules_json.load()
217                 if modules_json.has_git_url_and_modules():
218                     modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
219                         self.modules_repo.repo_path
220                     ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve()))
221                 modules_json.dump()
222
```
--- END FILES ---

Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.

Here is an example:

```diff
diff --git a/examples/server_async.py b/examples/server_async.py
--- a/examples/server_async.py
+++ b/examples/server_async.py
@@ -313,4 +313,4 @@
 
 
 if __name__ == "__main__":
-    asyncio.run(run_async_server("."), debug=True)
+    asyncio.run(run_async_server(), debug=True)
diff --git a/examples/server_sync.py b/examples/server_sync.py
--- a/examples/server_sync.py
+++ b/examples/server_sync.py
@@ -313,5 +313,5 @@
 
 
 if __name__ == "__main__":
-    server = run_sync_server(".")
+    server = run_sync_server()
     server.shutdown()

```

diff --git a/nf_core/modules/modules_command.py b/nf_core/modules/modules_command.py
--- a/nf_core/modules/modules_command.py
+++ b/nf_core/modules/modules_command.py
@@ -64,7 +64,9 @@
         main_nf = os.path.join(self.dir, "main.nf")
         nf_config = os.path.join(self.dir, "nextflow.config")
         if not os.path.exists(main_nf) and not os.path.exists(nf_config):
-            raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
+            if Path(self.dir).resolve().parts[-1].startswith("nf-core"):
+                raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
+            log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
         return True
 
     def has_modules_file(self):

{"golden_diff": "diff --git a/nf_core/modules/modules_command.py b/nf_core/modules/modules_command.py\n--- a/nf_core/modules/modules_command.py\n+++ b/nf_core/modules/modules_command.py\n@@ -64,7 +64,9 @@\n         main_nf = os.path.join(self.dir, \"main.nf\")\n         nf_config = os.path.join(self.dir, \"nextflow.config\")\n         if not os.path.exists(main_nf) and not os.path.exists(nf_config):\n-            raise UserWarning(f\"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'\")\n+            if Path(self.dir).resolve().parts[-1].startswith(\"nf-core\"):\n+                raise UserWarning(f\"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'\")\n+            log.warning(f\"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'\")\n         return True\n \n     def has_modules_file(self):\n", "issue": "nf-core modules install is asking for two files\n### Description of the bug\n\nnf-core modules install is asking for two files: main.nf and nextflow.config. I think this is not necessary, since one can use a different naming convention for both files.\r\n\r\nhttps://github.com/nf-core/modules/issues/2272\r\n\r\nI think this can be just a warning since you can decide to install the modules outside a nf-core pipeline\r\n\n\n### Command used and terminal output\n\n_No response_\n\n### System information\n\n_No response_\n", "before_files": [{"content": "import logging\nimport os\nimport shutil\nfrom pathlib import Path\n\nimport yaml\n\nimport nf_core.modules.module_utils\nimport nf_core.utils\n\nfrom .modules_json import ModulesJson\nfrom .modules_repo import ModulesRepo\n\nlog = logging.getLogger(__name__)\n\n\nclass ModuleCommand:\n    \"\"\"\n    Base class for the 'nf-core modules' commands\n    \"\"\"\n\n    def __init__(self, dir, remote_url=None, branch=None, no_pull=False, hide_progress=False):\n        \"\"\"\n        Initialise the ModulesCommand object\n        \"\"\"\n        self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)\n        self.hide_progress = hide_progress\n        self.dir = dir\n        self.default_modules_path = Path(\"modules\", \"nf-core\")\n        self.default_tests_path = Path(\"tests\", \"modules\", \"nf-core\")\n        try:\n            if self.dir:\n                self.dir, self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)\n            else:\n                self.repo_type = None\n        except LookupError as e:\n            raise UserWarning(e)\n\n    def get_modules_clone_modules(self):\n        \"\"\"\n        Get the modules available in a clone of nf-core/modules\n        \"\"\"\n        module_base_path = Path(self.dir, self.default_modules_path)\n        return [\n            str(Path(dir).relative_to(module_base_path))\n            for dir, _, files in os.walk(module_base_path)\n            if \"main.nf\" in files\n        ]\n\n    def get_local_modules(self):\n        \"\"\"\n        Get the local modules in a pipeline\n        \"\"\"\n        local_module_dir = Path(self.dir, \"modules\", \"local\")\n        return [str(path.relative_to(local_module_dir)) for path in local_module_dir.iterdir() if path.suffix == \".nf\"]\n\n    def has_valid_directory(self):\n        \"\"\"Check that we were given a pipeline or clone of nf-core/modules\"\"\"\n        if self.repo_type == \"modules\":\n            return True\n        if self.dir is None or not os.path.exists(self.dir):\n            log.error(f\"Could not find pipeline: {self.dir}\")\n            return False\n        main_nf = os.path.join(self.dir, \"main.nf\")\n        nf_config = os.path.join(self.dir, \"nextflow.config\")\n        if not os.path.exists(main_nf) and not os.path.exists(nf_config):\n            raise UserWarning(f\"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'\")\n        return True\n\n    def has_modules_file(self):\n        \"\"\"Checks whether a module.json file has been created and creates one if it is missing\"\"\"\n        modules_json_path = os.path.join(self.dir, \"modules.json\")\n        if not os.path.exists(modules_json_path):\n            log.info(\"Creating missing 'module.json' file.\")\n            ModulesJson(self.dir).create()\n\n    def clear_module_dir(self, module_name, module_dir):\n        \"\"\"Removes all files in the module directory\"\"\"\n        try:\n            shutil.rmtree(module_dir)\n            # Try cleaning up empty parent if tool/subtool and tool/ is empty\n            if module_name.count(\"/\") > 0:\n                parent_dir = os.path.dirname(module_dir)\n                try:\n                    os.rmdir(parent_dir)\n                except OSError:\n                    log.debug(f\"Parent directory not empty: '{parent_dir}'\")\n                else:\n                    log.debug(f\"Deleted orphan tool directory: '{parent_dir}'\")\n            log.debug(f\"Successfully removed {module_name} module\")\n            return True\n        except OSError as e:\n            log.error(f\"Could not remove module: {e}\")\n            return False\n\n    def modules_from_repo(self, install_dir):\n        \"\"\"\n        Gets the modules installed from a certain repository\n\n        Args:\n            install_dir (str): The name of the directory where modules are installed\n\n        Returns:\n            [str]: The names of the modules\n        \"\"\"\n        repo_dir = Path(self.dir, \"modules\", install_dir)\n        if not repo_dir.exists():\n            raise LookupError(f\"Nothing installed from {install_dir} in pipeline\")\n\n        return [\n            str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if \"main.nf\" in files\n        ]\n\n    def install_module_files(self, module_name, module_version, modules_repo, install_dir):\n        \"\"\"\n        Installs a module into the given directory\n\n        Args:\n            module_name (str): The name of the module\n            module_version (str): Git SHA for the version of the module to be installed\n            modules_repo (ModulesRepo): A correctly configured ModulesRepo object\n            install_dir (str): The path to where the module should be installed (should be the 'modules/' dir of the pipeline)\n\n        Returns:\n            (bool): Whether the operation was successful of not\n        \"\"\"\n        return modules_repo.install_module(module_name, install_dir, module_version)\n\n    def load_lint_config(self):\n        \"\"\"Parse a pipeline lint config file.\n\n        Look for a file called either `.nf-core-lint.yml` or\n        `.nf-core-lint.yaml` in the pipeline root directory and parse it.\n        (`.yml` takes precedence).\n\n        Add parsed config to the `self.lint_config` class attribute.\n        \"\"\"\n        config_fn = os.path.join(self.dir, \".nf-core-lint.yml\")\n\n        # Pick up the file if it's .yaml instead of .yml\n        if not os.path.isfile(config_fn):\n            config_fn = os.path.join(self.dir, \".nf-core-lint.yaml\")\n\n        # Load the YAML\n        try:\n            with open(config_fn, \"r\") as fh:\n                self.lint_config = yaml.safe_load(fh)\n        except FileNotFoundError:\n            log.debug(f\"No lint config file found: {config_fn}\")\n\n    def check_modules_structure(self):\n        \"\"\"\n        Check that the structure of the modules directory in a pipeline is the correct one:\n            modules/nf-core/TOOL/SUBTOOL\n\n        Prior to nf-core/tools release 2.6 the directory structure had an additional level of nesting:\n            modules/nf-core/modules/TOOL/SUBTOOL\n        \"\"\"\n        if self.repo_type == \"pipeline\":\n            wrong_location_modules = []\n            for directory, _, files in os.walk(Path(self.dir, \"modules\")):\n                if \"main.nf\" in files:\n                    module_path = Path(directory).relative_to(Path(self.dir, \"modules\"))\n                    parts = module_path.parts\n                    # Check that there are modules installed directly under the 'modules' directory\n                    if parts[1] == \"modules\":\n                        wrong_location_modules.append(module_path)\n            # If there are modules installed in the wrong location\n            if len(wrong_location_modules) > 0:\n                log.info(\"The modules folder structure is outdated. Reinstalling modules.\")\n                # Remove the local copy of the modules repository\n                log.info(f\"Updating '{self.modules_repo.local_repo_dir}'\")\n                self.modules_repo.setup_local_repo(\n                    self.modules_repo.remote_url, self.modules_repo.branch, self.hide_progress\n                )\n                # Move wrong modules to the right directory\n                for module in wrong_location_modules:\n                    modules_dir = Path(\"modules\").resolve()\n                    module_name = str(Path(*module.parts[2:]))\n                    correct_dir = Path(modules_dir, self.modules_repo.repo_path, Path(module_name))\n                    wrong_dir = Path(modules_dir, module)\n                    shutil.move(wrong_dir, correct_dir)\n                    log.info(f\"Moved {wrong_dir} to {correct_dir}.\")\n                    # Check if a path file exists\n                    patch_path = correct_dir / Path(module_name + \".diff\")\n                    self.check_patch_paths(patch_path, module_name)\n                shutil.rmtree(Path(self.dir, \"modules\", self.modules_repo.repo_path, \"modules\"))\n                # Regenerate modules.json file\n                modules_json = ModulesJson(self.dir)\n                modules_json.check_up_to_date()\n\n    def check_patch_paths(self, patch_path, module_name):\n        \"\"\"\n        Check that paths in patch files are updated to the new modules path\n        \"\"\"\n        if patch_path.exists():\n            log.info(f\"Modules {module_name} contains a patch file.\")\n            rewrite = False\n            with open(patch_path, \"r\") as fh:\n                lines = fh.readlines()\n                for index, line in enumerate(lines):\n                    # Check if there are old paths in the patch file and replace\n                    if f\"modules/{self.modules_repo.repo_path}/modules/{module_name}/\" in line:\n                        rewrite = True\n                        lines[index] = line.replace(\n                            f\"modules/{self.modules_repo.repo_path}/modules/{module_name}/\",\n                            f\"modules/{self.modules_repo.repo_path}/{module_name}/\",\n                        )\n            if rewrite:\n                log.info(f\"Updating paths in {patch_path}\")\n                with open(patch_path, \"w\") as fh:\n                    for line in lines:\n                        fh.write(line)\n                # Update path in modules.json if the file is in the correct format\n                modules_json = ModulesJson(self.dir)\n                modules_json.load()\n                if modules_json.has_git_url_and_modules():\n                    modules_json.modules_json[\"repos\"][self.modules_repo.remote_url][\"modules\"][\n                        self.modules_repo.repo_path\n                    ][module_name][\"patch\"] = str(patch_path.relative_to(Path(self.dir).resolve()))\n                modules_json.dump()\n", "path": "nf_core/modules/modules_command.py"}], "after_files": [{"content": "import logging\nimport os\nimport shutil\nfrom pathlib import Path\n\nimport yaml\n\nimport nf_core.modules.module_utils\nimport nf_core.utils\n\nfrom .modules_json import ModulesJson\nfrom .modules_repo import ModulesRepo\n\nlog = logging.getLogger(__name__)\n\n\nclass ModuleCommand:\n    \"\"\"\n    Base class for the 'nf-core modules' commands\n    \"\"\"\n\n    def __init__(self, dir, remote_url=None, branch=None, no_pull=False, hide_progress=False):\n        \"\"\"\n        Initialise the ModulesCommand object\n        \"\"\"\n        self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)\n        self.hide_progress = hide_progress\n        self.dir = dir\n        self.default_modules_path = Path(\"modules\", \"nf-core\")\n        self.default_tests_path = Path(\"tests\", \"modules\", \"nf-core\")\n        try:\n            if self.dir:\n                self.dir, self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)\n            else:\n                self.repo_type = None\n        except LookupError as e:\n            raise UserWarning(e)\n\n    def get_modules_clone_modules(self):\n        \"\"\"\n        Get the modules available in a clone of nf-core/modules\n        \"\"\"\n        module_base_path = Path(self.dir, self.default_modules_path)\n        return [\n            str(Path(dir).relative_to(module_base_path))\n            for dir, _, files in os.walk(module_base_path)\n            if \"main.nf\" in files\n        ]\n\n    def get_local_modules(self):\n        \"\"\"\n        Get the local modules in a pipeline\n        \"\"\"\n        local_module_dir = Path(self.dir, \"modules\", \"local\")\n        return [str(path.relative_to(local_module_dir)) for path in local_module_dir.iterdir() if path.suffix == \".nf\"]\n\n    def has_valid_directory(self):\n        \"\"\"Check that we were given a pipeline or clone of nf-core/modules\"\"\"\n        if self.repo_type == \"modules\":\n            return True\n        if self.dir is None or not os.path.exists(self.dir):\n            log.error(f\"Could not find pipeline: {self.dir}\")\n            return False\n        main_nf = os.path.join(self.dir, \"main.nf\")\n        nf_config = os.path.join(self.dir, \"nextflow.config\")\n        if not os.path.exists(main_nf) and not os.path.exists(nf_config):\n            if Path(self.dir).resolve().parts[-1].startswith(\"nf-core\"):\n                raise UserWarning(f\"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'\")\n            log.warning(f\"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'\")\n        return True\n\n    def has_modules_file(self):\n        \"\"\"Checks whether a module.json file has been created and creates one if it is missing\"\"\"\n        modules_json_path = os.path.join(self.dir, \"modules.json\")\n        if not os.path.exists(modules_json_path):\n            log.info(\"Creating missing 'module.json' file.\")\n            ModulesJson(self.dir).create()\n\n    def clear_module_dir(self, module_name, module_dir):\n        \"\"\"Removes all files in the module directory\"\"\"\n        try:\n            shutil.rmtree(module_dir)\n            # Try cleaning up empty parent if tool/subtool and tool/ is empty\n            if module_name.count(\"/\") > 0:\n                parent_dir = os.path.dirname(module_dir)\n                try:\n                    os.rmdir(parent_dir)\n                except OSError:\n                    log.debug(f\"Parent directory not empty: '{parent_dir}'\")\n                else:\n                    log.debug(f\"Deleted orphan tool directory: '{parent_dir}'\")\n            log.debug(f\"Successfully removed {module_name} module\")\n            return True\n        except OSError as e:\n            log.error(f\"Could not remove module: {e}\")\n            return False\n\n    def modules_from_repo(self, install_dir):\n        \"\"\"\n        Gets the modules installed from a certain repository\n\n        Args:\n            install_dir (str): The name of the directory where modules are installed\n\n        Returns:\n            [str]: The names of the modules\n        \"\"\"\n        repo_dir = Path(self.dir, \"modules\", install_dir)\n        if not repo_dir.exists():\n            raise LookupError(f\"Nothing installed from {install_dir} in pipeline\")\n\n        return [\n            str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if \"main.nf\" in files\n        ]\n\n    def install_module_files(self, module_name, module_version, modules_repo, install_dir):\n        \"\"\"\n        Installs a module into the given directory\n\n        Args:\n            module_name (str): The name of the module\n            module_version (str): Git SHA for the version of the module to be installed\n            modules_repo (ModulesRepo): A correctly configured ModulesRepo object\n            install_dir (str): The path to where the module should be installed (should be the 'modules/' dir of the pipeline)\n\n        Returns:\n            (bool): Whether the operation was successful of not\n        \"\"\"\n        return modules_repo.install_module(module_name, install_dir, module_version)\n\n    def load_lint_config(self):\n        \"\"\"Parse a pipeline lint config file.\n\n        Look for a file called either `.nf-core-lint.yml` or\n        `.nf-core-lint.yaml` in the pipeline root directory and parse it.\n        (`.yml` takes precedence).\n\n        Add parsed config to the `self.lint_config` class attribute.\n        \"\"\"\n        config_fn = os.path.join(self.dir, \".nf-core-lint.yml\")\n\n        # Pick up the file if it's .yaml instead of .yml\n        if not os.path.isfile(config_fn):\n            config_fn = os.path.join(self.dir, \".nf-core-lint.yaml\")\n\n        # Load the YAML\n        try:\n            with open(config_fn, \"r\") as fh:\n                self.lint_config = yaml.safe_load(fh)\n        except FileNotFoundError:\n            log.debug(f\"No lint config file found: {config_fn}\")\n\n    def check_modules_structure(self):\n        \"\"\"\n        Check that the structure of the modules directory in a pipeline is the correct one:\n            modules/nf-core/TOOL/SUBTOOL\n\n        Prior to nf-core/tools release 2.6 the directory structure had an additional level of nesting:\n            modules/nf-core/modules/TOOL/SUBTOOL\n        \"\"\"\n        if self.repo_type == \"pipeline\":\n            wrong_location_modules = []\n            for directory, _, files in os.walk(Path(self.dir, \"modules\")):\n                if \"main.nf\" in files:\n                    module_path = Path(directory).relative_to(Path(self.dir, \"modules\"))\n                    parts = module_path.parts\n                    # Check that there are modules installed directly under the 'modules' directory\n                    if parts[1] == \"modules\":\n                        wrong_location_modules.append(module_path)\n            # If there are modules installed in the wrong location\n            if len(wrong_location_modules) > 0:\n                log.info(\"The modules folder structure is outdated. Reinstalling modules.\")\n                # Remove the local copy of the modules repository\n                log.info(f\"Updating '{self.modules_repo.local_repo_dir}'\")\n                self.modules_repo.setup_local_repo(\n                    self.modules_repo.remote_url, self.modules_repo.branch, self.hide_progress\n                )\n                # Move wrong modules to the right directory\n                for module in wrong_location_modules:\n                    modules_dir = Path(\"modules\").resolve()\n                    module_name = str(Path(*module.parts[2:]))\n                    correct_dir = Path(modules_dir, self.modules_repo.repo_path, Path(module_name))\n                    wrong_dir = Path(modules_dir, module)\n                    shutil.move(wrong_dir, correct_dir)\n                    log.info(f\"Moved {wrong_dir} to {correct_dir}.\")\n                    # Check if a path file exists\n                    patch_path = correct_dir / Path(module_name + \".diff\")\n                    self.check_patch_paths(patch_path, module_name)\n                shutil.rmtree(Path(self.dir, \"modules\", self.modules_repo.repo_path, \"modules\"))\n                # Regenerate modules.json file\n                modules_json = ModulesJson(self.dir)\n                modules_json.check_up_to_date()\n\n    def check_patch_paths(self, patch_path, module_name):\n        \"\"\"\n        Check that paths in patch files are updated to the new modules path\n        \"\"\"\n        if patch_path.exists():\n            log.info(f\"Modules {module_name} contains a patch file.\")\n            rewrite = False\n            with open(patch_path, \"r\") as fh:\n                lines = fh.readlines()\n                for index, line in enumerate(lines):\n                    # Check if there are old paths in the patch file and replace\n                    if f\"modules/{self.modules_repo.repo_path}/modules/{module_name}/\" in line:\n                        rewrite = True\n                        lines[index] = line.replace(\n                            f\"modules/{self.modules_repo.repo_path}/modules/{module_name}/\",\n                            f\"modules/{self.modules_repo.repo_path}/{module_name}/\",\n                        )\n            if rewrite:\n                log.info(f\"Updating paths in {patch_path}\")\n                with open(patch_path, \"w\") as fh:\n                    for line in lines:\n                        fh.write(line)\n                # Update path in modules.json if the file is in the correct format\n                modules_json = ModulesJson(self.dir)\n                modules_json.load()\n                if modules_json.has_git_url_and_modules():\n                    modules_json.modules_json[\"repos\"][self.modules_repo.remote_url][\"modules\"][\n                        self.modules_repo.repo_path\n                    ][module_name][\"patch\"] = str(patch_path.relative_to(Path(self.dir).resolve()))\n                modules_json.dump()\n", "path": "nf_core/modules/modules_command.py"}]}