From efba8908fe56edbfd31eac4bc71fbcbfc2e80f9d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 3 Nov 2022 11:53:05 +0100
Subject: [PATCH 1/2] add get_all_components to modules_json

---
 nf_core/modules/modules_json.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index b1f1ab3ca8..96a62dd2ef 100644
--- a/nf_core/modules/modules_json.py
+++ b/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

From d50d6a18d8aa9f78d4e9a8839c0863e4718494b5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 3 Nov 2022 12:05:05 +0100
Subject: [PATCH 2/2] small fixes for sw install

---
 nf_core/modules/modules_repo.py | 3 ++-
 nf_core/subworkflows/install.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 1c242b4764..d0a831c933 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -401,6 +401,7 @@ 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)
@@ -408,7 +409,7 @@ def get_component_git_log(self, component_name, component_type, depth=None):
             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):
diff --git a/nf_core/subworkflows/install.py b/nf_core/subworkflows/install.py
index a5f0c63dcb..439cf187b7 100644
--- a/nf_core/subworkflows/install.py
+++ b/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