Merge pull request #1994 from mashehu/fix-install-command

Fix subworkflows install command

nf_core/modules/modules_json.py

@@ -784,6 +784,25 @@ def get_all_modules(self):
 
         return self.pipeline_modules
 
+    def get_all_components(self, component_type):
+        """
+        Retrieves all pipeline modules/subworkflows that are reported in the modules.json
+
+        Returns:
+            (dict[str, [(str, str)]]): Dictionary indexed with the repo urls, with a
+                                list of tuples (component_dir, components) as values
+        """
+        if self.modules_json is None:
+            self.load()
+        if self.pipeline_components is None:
+            self.pipeline_components = {}
+            for repo, repo_entry in self.modules_json.get("repos", {}).items():
+                if "modules" in repo_entry:
+                    for dir, modules in repo_entry[component_type].items():
+                        self.pipeline_components[repo] = [(dir, m) for m in modules]
+
+        return self.pipeline_modules
+
     def get_module_branch(self, module, repo_url, install_dir):
         """
         Gets the branch from which the module was installed

nf_core/modules/modules_repo.py

@@ -401,14 +401,15 @@ def get_component_git_log(self, component_name, component_type, depth=None):
         commits_new = [
             {"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_new
         ]
+        commits_old = []
         if component_type == "modules":
             # Grab commits also from previous modules structure
             component_path = os.path.join("modules", component_name)
             commits_old = self.repo.iter_commits(max_count=depth, paths=component_path)
             commits_old = [
                 {"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_old
             ]
-            commits = iter(commits_new + commits_old)
+        commits = iter(commits_new + commits_old)
         return commits
 
     def get_latest_component_version(self, component_name, component_type):

nf_core/subworkflows/install.py

@@ -91,7 +91,7 @@ def install(self, subworkflow, silent=False):
         log.debug(f"Installing subworkflow '{subworkflow}' at hash {version} from {self.modules_repo.remote_url}")
 
         # Download subworkflow files
-        if not self.install_subworkflow_files(subworkflow, version, self.modules_repo, install_folder):
+        if not self.install_component_files(subworkflow, version, self.modules_repo, install_folder):
             return False
 
         # Install included modules and subworkflows