add source even if the module/subworkflow is already installed

nf_core/components/components_install.py

@@ -100,4 +100,4 @@ def clean_modules_json(component, component_type, modules_repo, modules_json):
                         f"Removing {component_type[:-1]} '{modules_repo.repo_path}/{component}' from repo '{repo_to_remove}' from modules.json"
                     )
                     modules_json.remove_entry(component, repo_to_remove, modules_repo.repo_path)
-                    break
+                    return

nf_core/modules/install.py

@@ -73,6 +73,11 @@ def install(self, module, silent=False):
         if not nf_core.components.components_install.check_component_installed(
             self.component_type, module, current_version, module_dir, self.modules_repo, self.force, self.prompt
         ):
+            log.debug(
+                f"Module is already installed and force is not set.\nAdding the new installation source {self.installed_by} for module {module} to 'modules.json' without installing the module."
+            )
+            modules_json.load()
+            modules_json.update(self.modules_repo, module, current_version, self.installed_by)
             return False
 
         version = nf_core.components.components_install.get_version(

nf_core/subworkflows/install.py

@@ -79,6 +79,11 @@ def install(self, subworkflow, silent=False):
             self.force,
             self.prompt,
         ):
+            log.debug(
+                f"Subworkflow is already installed and force is not set.\nAdding the new installation source {self.installed_by} for subworkflow {subworkflow} to 'modules.json' without installing the subworkflow."
+            )
+            modules_json.load()
+            modules_json.update(self.modules_repo, subworkflow, current_version, self.installed_by)
             return False
 
         version = nf_core.components.components_install.get_version(
@@ -89,7 +94,13 @@ def install(self, subworkflow, silent=False):
 
         # Remove subworkflow if force is set and component is installed
         if self.force and nf_core.components.components_install.check_component_installed(
-            self.component_type, subworkflow, current_version, subworkflow_dir, self.modules_repo, self.force
+            self.component_type,
+            subworkflow,
+            current_version,
+            subworkflow_dir,
+            self.modules_repo,
+            self.force,
+            self.prompt,
         ):
             log.info(f"Removing installed version of '{self.modules_repo.repo_path}/{subworkflow}'")
             self.clear_component_dir(subworkflow, subworkflow_dir)