Update bug two

nf_core/components/install.py

@@ -58,10 +58,13 @@ def install(self, component: Union[str, Dict[str, str]], silent: bool = False) -
             self.modules_repo = ModulesRepo(remote_url, branch)
             component = component["name"]
 
-            if self.current_remote == self.modules_repo.remote_url and self.sha is not None:
-                self.current_sha = self.sha
-            else:
-                self.current_sha = None
+        if self.current_remote is None:
+            self.current_remote = self.modules_repo.remote_url
+
+        if self.current_remote == self.modules_repo.remote_url and self.sha is not None:
+            self.current_sha = self.sha
+        else:
+            self.current_sha = None
 
         if self.repo_type == "modules":
             log.error(f"You cannot install a {component} in a clone of nf-core/modules")

nf_core/components/update.py

@@ -1,5 +1,6 @@
 import logging
 import os
+import re
 import shutil
 import tempfile
 from pathlib import Path
@@ -41,6 +42,8 @@ def __init__(
         limit_output=False,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
+        self.current_remote = remote_url
+        self.branch = branch
         self.force = force
         self.prompt = prompt
         self.sha = sha
@@ -92,6 +95,13 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
         Returns:
             (bool): True if the update was successful, False otherwise.
         """
+        if isinstance(component, dict):
+            # Override modules_repo when the component to install is a dependency from a subworkflow.
+            remote_url = component.get("git_remote", self.current_remote)
+            branch = component.get("branch", self.branch)
+            self.modules_repo = ModulesRepo(remote_url, branch)
+            component = component["name"]
+
         self.component = component
         if updated is None:
             updated = []
@@ -868,7 +878,17 @@ def get_components_to_update(self, component):
         if self.component_type == "modules":
             # All subworkflow names in the installed_by section of a module are subworkflows using this module
             # We need to update them too
-            subworkflows_to_update = [subworkflow for subworkflow in installed_by if subworkflow != self.component_type]
+            git_remote = self.current_remote
+            for subworkflow in installed_by:
+                if subworkflow != component:
+                    for remote_url, content in mods_json["repos"].items():
+                        if (all_subworkflows := content.get("subworkflows")) is not None:
+                            for _, details in all_subworkflows.items():
+                                if subworkflow in details:
+                                    git_remote = remote_url
+                if subworkflow != self.component_type:
+                    subworkflows_to_update.append({"name": subworkflow, "git_remote": git_remote})
+
         elif self.component_type == "subworkflows":
             for repo, repo_content in mods_json["repos"].items():
                 for component_type, dir_content in repo_content.items():
@@ -879,9 +899,9 @@ def get_components_to_update(self, component):
                             # We need to update it too
                             if component in comp_content["installed_by"]:
                                 if component_type == "modules":
-                                    modules_to_update.append(comp)
+                                    modules_to_update.append({"name": comp, "git_remote": repo, "org_path": dir})
                                 elif component_type == "subworkflows":
-                                    subworkflows_to_update.append(comp)
+                                    subworkflows_to_update.append({"name": comp, "git_remote": repo, "org_path": dir})
 
         return modules_to_update, subworkflows_to_update
 
@@ -896,7 +916,7 @@ def update_linked_components(
         Update modules and subworkflows linked to the component being updated.
         """
         for s_update in subworkflows_to_update:
-            if s_update in updated:
+            if s_update["name"] in updated:
                 continue
             original_component_type, original_update_all = self._change_component_type("subworkflows")
             self.update(
@@ -908,7 +928,7 @@ def update_linked_components(
             self._reset_component_type(original_component_type, original_update_all)
 
         for m_update in modules_to_update:
-            if m_update in updated:
+            if m_update["name"] in updated:
                 continue
             original_component_type, original_update_all = self._change_component_type("modules")
             try:
@@ -931,28 +951,42 @@ def update_linked_components(
     def manage_changes_in_linked_components(self, component, modules_to_update, subworkflows_to_update):
         """Check for linked components added or removed in the new subworkflow version"""
         if self.component_type == "subworkflows":
-            subworkflow_directory = Path(self.directory, self.component_type, self.modules_repo.repo_path, component)
+            org_path_match = re.search(r"(?:https://|git@)[\w\.]+[:/](.*?)/", self.current_remote)
+            if org_path_match:
+                org_path = org_path_match.group(1)
+
+            subworkflow_directory = Path(self.directory, self.component_type, org_path, component)
             included_modules, included_subworkflows = get_components_to_install(subworkflow_directory)
             # If a module/subworkflow has been removed from the subworkflow
             for module in modules_to_update:
-                if module not in included_modules:
+                module = module["name"]
+                included_modules_names = [m["name"] for m in included_modules]
+                if module not in included_modules_names:
                     log.info(f"Removing module '{module}' which is not included in '{component}' anymore.")
                     remove_module_object = ComponentRemove("modules", self.directory)
                     remove_module_object.remove(module, removed_by=component)
             for subworkflow in subworkflows_to_update:
-                if subworkflow not in included_subworkflows:
+                subworkflow = subworkflow["name"]
+                included_subworkflow_names = [m["name"] for m in included_subworkflows]
+                if subworkflow not in included_subworkflow_names:
                     log.info(f"Removing subworkflow '{subworkflow}' which is not included in '{component}' anymore.")
                     remove_subworkflow_object = ComponentRemove("subworkflows", self.directory)
                     remove_subworkflow_object.remove(subworkflow, removed_by=component)
             # If a new module/subworkflow is included in the subworklfow and wasn't included before
             for module in included_modules:
-                if module not in modules_to_update:
-                    log.info(f"Installing newly included module '{module}' for '{component}'")
+                module_name = module["name"]
+                module["git_remote"] = module.get("git_remote", self.current_remote)
+                module["branch"] = module.get("branch", self.branch)
+                if module_name not in modules_to_update:
+                    log.info(f"Installing newly included module '{module_name}' for '{component}'")
                     install_module_object = ComponentInstall(self.directory, "modules", installed_by=component)
                     install_module_object.install(module, silent=True)
             for subworkflow in included_subworkflows:
-                if subworkflow not in subworkflows_to_update:
-                    log.info(f"Installing newly included subworkflow '{subworkflow}' for '{component}'")
+                subworkflow_name = subworkflow["name"]
+                subworkflow["git_remote"] = subworkflow.get("git_remote", self.current_remote)
+                subworkflow["branch"] = subworkflow.get("branch", self.branch)
+                if subworkflow_name not in subworkflows_to_update:
+                    log.info(f"Installing newly included subworkflow '{subworkflow_name}' for '{component}'")
                     install_subworkflow_object = ComponentInstall(
                         self.directory, "subworkflows", installed_by=component
                     )
@@ -971,3 +1005,5 @@ def _reset_component_type(self, original_component_type, original_update_all):
         self.component_type = original_component_type
         self.modules_json.pipeline_components = None
         self.update_all = original_update_all
+        if self.current_remote is None:
+            self.current_remote = self.modules_repo.remote_url

tests/subworkflows/test_update.py

@@ -15,7 +15,7 @@
 from nf_core.subworkflows.update import SubworkflowUpdate
 
 from ..test_subworkflows import TestSubworkflows
-from ..utils import CROSS_ORGANIZATION_BRANCH, CROSS_ORGANIZATION_URL, OLD_SUBWORKFLOWS_SHA, cmp_component
+from ..utils import CROSS_ORGANIZATION_URL, OLD_SUBWORKFLOWS_SHA, cmp_component
 
 
 class TestSubworkflowsUpdate(TestSubworkflows):
@@ -379,7 +379,6 @@ def test_update_subworkflow_across_orgs(self):
         install_obj = SubworkflowInstall(
             self.pipeline_dir,
             remote_url=CROSS_ORGANIZATION_URL,
-            branch=CROSS_ORGANIZATION_BRANCH,
             sha="b7dc6a4fcfdf780c9228b3abf6bd821b466c2f81",
         )
         # The fastq_trim_fastp_fastqc subworkflow contains the cross-org fastqc module, not the nf-core one
@@ -388,7 +387,6 @@ def test_update_subworkflow_across_orgs(self):
         update_obj = SubworkflowUpdate(
             self.pipeline_dir,
             remote_url=CROSS_ORGANIZATION_URL,
-            branch=CROSS_ORGANIZATION_BRANCH,
             update_all=False,
             update_deps=True,
             show_diff=False,