pass repo_path

nf-core · mirpedrol · Dec 2, 2025 · Dec 2, 2025 · Dec 2, 2025 · Dec 2, 2025
commit b8004aa0d2c6ac8559169711dc390d08400f46f2
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
@@ -171,7 +171,7 @@ def install(self, component: str | dict[str, str], silent: bool = False) -> bool
         # Regenerate container configuration files for the pipeline when modules are installed
         if self.component_type == "modules":
             try:
-                ContainerConfigs(self.directory).generate_container_configs()
+                ContainerConfigs(self.directory, self.modules_repo.repo_path).generate_container_configs()
             except UserWarning as e:
                 log.warning(f"Could not regenerate container configuration files: {e}")
 

diff --git a/nf_core/components/remove.py b/nf_core/components/remove.py
@@ -176,7 +176,7 @@ def remove(self, component, repo_url=None, repo_path=None, removed_by=None, remo
             # Regenerate container configuration files for the pipeline when modules are removed
             if self.component_type == "modules":
                 try:
-                    ContainerConfigs(self.directory).generate_container_configs()
+                    ContainerConfigs(self.directory, repo_path).generate_container_configs()
                 except UserWarning as e:
                     log.warning(f"Could not regenerate container configuration files: {e}")
 

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
@@ -303,7 +303,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 # Regenerate container configuration files for the pipeline when modules are updated
                 if self.component_type == "modules":
                     try:
-                        ContainerConfigs(self.directory).generate_container_configs()
+                        ContainerConfigs(self.directory, modules_repo.repo_path).generate_container_configs()
                     except UserWarning as e:
                         log.warning(f"Could not regenerate container configuration files: {e}")
                 recursive_update = True

diff --git a/nf_core/pipelines/containers_utils.py b/nf_core/pipelines/containers_utils.py
@@ -14,13 +14,16 @@ class ContainerConfigs:
 
     Args:
         workflow_directory (str | Path): The directory containing the workflow files.
+        org (str): Organisation path.
     """
 
     def __init__(
         self,
         workflow_directory: str | Path = ".",
+        org: str = "nf-core",
     ):
         self.workflow_directory = Path(workflow_directory)
+        self.org: str = org
 
     def generate_container_configs(self) -> None:
         """Generate the container configuration files for a pipeline."""
@@ -97,7 +100,7 @@ def generate_all_container_configs(self, default_config: str) -> None:
                 module_path = Path(module_name.lower())
 
             try:
-                with open(self.workflow_directory / "modules" / module_path / "meta.yml") as fh:
+                with open(self.workflow_directory / "modules" / module_path / self.org / "meta.yml") as fh:
                     meta = yaml.safe_load(fh)
             except FileNotFoundError:
                 log.warning(f"Could not find meta.yml for {module_name}")