feat: Install subworkflows with modules from different remotes

nf_core/components/components_utils.py

@@ -1,10 +1,11 @@
 import logging
 import re
 from pathlib import Path
-from typing import TYPE_CHECKING, List, Optional, Tuple, Union
+from typing import TYPE_CHECKING, Dict, List, Optional, Tuple, Union
 
 import questionary
 import rich.prompt
+import yaml
 
 if TYPE_CHECKING:
     from nf_core.modules.modules_repo import ModulesRepo
@@ -142,12 +143,15 @@ def prompt_component_version_sha(
     return git_sha
 
 
-def get_components_to_install(subworkflow_dir: Union[str, Path]) -> Tuple[List[str], List[str]]:
+def get_components_to_install(
+    subworkflow_dir: Union[str, Path],
+) -> Tuple[List[Dict[str, Optional[str]]], List[Dict[str, Optional[str]]]]:
     """
     Parse the subworkflow main.nf file to retrieve all imported modules and subworkflows.
     """
-    modules = []
-    subworkflows = []
+    modules: Dict[str, Dict[str, Optional[str]]] = {}
+    subworkflows: Dict[str, Dict[str, Optional[str]]] = {}
+
     with open(Path(subworkflow_dir, "main.nf")) as fh:
         for line in fh:
             regex = re.compile(
@@ -158,7 +162,40 @@ def get_components_to_install(subworkflow_dir: Union[str, Path]) -> Tuple[List[s
                 name, link = match.groups()
                 if link.startswith("../../../"):
                     name_split = name.lower().split("_")
-                    modules.append("/".join(name_split))
+                    component_name = "/".join(name_split)
+                    component_dict: Dict[str, Optional[str]] = {
+                        "name": component_name,
+                    }
+                    modules[component_name] = component_dict
                 elif link.startswith("../"):
-                    subworkflows.append(name.lower())
-    return modules, subworkflows
+                    component_name = name.lower()
+                    component_dict = {"name": component_name}
+                    subworkflows[component_name] = component_dict
+
+    if (sw_meta := Path(subworkflow_dir, "meta.yml")).exists():
+        with open(sw_meta) as fh:
+            meta = yaml.safe_load(fh)
+            if "components" in meta:
+                components = meta["components"]
+                for component in components:
+                    if isinstance(component, dict):
+                        component_name = list(component.keys())[0].lower()
+                        git_remote = component[component_name]["git_remote"]
+                        org_path_match = re.search(r"(?:https://|git@)[\w\.]+[:/](.*?)/", git_remote)
+                        if org_path_match:
+                            org_path = org_path_match.group(1)
+                        else:
+                            raise UserWarning(
+                                f"The organisation path of {component_name} could not be established from '{git_remote}'"
+                            )
+                        current_comp_dict = subworkflows if component_name in subworkflows else modules
+
+                        component_dict = {
+                            "org_path": org_path,
+                            "git_remote": git_remote,
+                            "branch": component[component_name].get("branch"),
+                        }
+
+                        current_comp_dict[component_name].update(component_dict)
+
+    return list(modules.values()), list(subworkflows.values())

nf_core/components/install.py

@@ -1,7 +1,7 @@
 import logging
 import os
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import Dict, List, Optional, Union
 
 import questionary
 from rich import print
@@ -20,6 +20,7 @@
     prompt_component_version_sha,
 )
 from nf_core.modules.modules_json import ModulesJson
+from nf_core.modules.modules_repo import ModulesRepo
 
 log = logging.getLogger(__name__)
 
@@ -38,6 +39,8 @@ def __init__(
         installed_by: Optional[List[str]] = None,
     ):
         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
@@ -46,7 +49,14 @@ def __init__(
         else:
             self.installed_by = [self.component_type]
 
-    def install(self, component: str, silent: bool = False) -> bool:
+    def install(self, component: Union[str, Dict[str, str]], silent: bool = False) -> bool:
+        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"]
+
         if self.repo_type == "modules":
             log.error(f"You cannot install a {component} in a clone of nf-core/modules")
             return False

nf_core/modules/modules_json.py

@@ -674,7 +674,7 @@ def check_up_to_date(self):
             dump_modules_json = True
             for repo, subworkflows in subworkflows_dict.items():
                 for org, subworkflow in subworkflows:
-                    self.recreate_dependencies(repo, org, subworkflow)
+                    self.recreate_dependencies(repo, org, {"name": subworkflow})
         self.pipeline_components = original_pipeline_components
 
         if dump_modules_json:
@@ -1249,20 +1249,27 @@ def recreate_dependencies(self, repo, org, subworkflow):
         i.e., no module or subworkflow has been installed by the user in the meantime
         """
 
-        sw_path = Path(self.subworkflows_dir, org, subworkflow)
+        sw_name = subworkflow["name"]
+        sw_path = Path(self.subworkflows_dir, org, sw_name)
         dep_mods, dep_subwfs = get_components_to_install(sw_path)
         assert self.modules_json is not None  # mypy
         for dep_mod in dep_mods:
-            installed_by = self.modules_json["repos"][repo]["modules"][org][dep_mod]["installed_by"]
+            name = dep_mod["name"]
+            current_repo = dep_mod.get("git_remote", repo)
+            current_org = dep_mod.get("org_path", org)
+            installed_by = self.modules_json["repos"][current_repo]["modules"][current_org][name]["installed_by"]
             if installed_by == ["modules"]:
                 self.modules_json["repos"][repo]["modules"][org][dep_mod]["installed_by"] = []
-            if subworkflow not in installed_by:
-                self.modules_json["repos"][repo]["modules"][org][dep_mod]["installed_by"].append(subworkflow)
+            if sw_name not in installed_by:
+                self.modules_json["repos"][repo]["modules"][org][dep_mod]["installed_by"].append(sw_name)
 
         for dep_subwf in dep_subwfs:
-            installed_by = self.modules_json["repos"][repo]["subworkflows"][org][dep_subwf]["installed_by"]
+            name = dep_subwf["name"]
+            current_repo = dep_subwf.get("git_remote", repo)
+            current_org = dep_subwf.get("org_path", org)
+            installed_by = self.modules_json["repos"][current_repo]["subworkflows"][current_org][name]["installed_by"]
             if installed_by == ["subworkflows"]:
                 self.modules_json["repos"][repo]["subworkflows"][org][dep_subwf]["installed_by"] = []
-            if subworkflow not in installed_by:
-                self.modules_json["repos"][repo]["subworkflows"][org][dep_subwf]["installed_by"].append(subworkflow)
+            if sw_name not in installed_by:
+                self.modules_json["repos"][repo]["subworkflows"][org][dep_subwf]["installed_by"].append(sw_name)
             self.recreate_dependencies(repo, org, dep_subwf)

nf_core/subworkflows/lint/meta_yml.py

@@ -93,6 +93,7 @@ def meta_yml(subworkflow_lint_object, subworkflow):
         included_components = (
             included_components[0] + included_components[1]
         )  # join included modules and included subworkflows in a single list
+        included_components = [component["name"] for component in included_components]
         if "components" in meta_yaml:
             meta_components = [x for x in meta_yaml["components"]]
             for component in set(included_components):

tests/subworkflows/test_install.py

@@ -7,6 +7,8 @@
 
 from ..test_subworkflows import TestSubworkflows
 from ..utils import (
+    CROSS_ORGANIZATION_BRANCH,
+    CROSS_ORGANIZATION_URL,
     GITLAB_BRANCH_TEST_BRANCH,
     GITLAB_REPO,
     GITLAB_SUBWORKFLOWS_BRANCH,
@@ -83,6 +85,20 @@ def test_subworkflows_install_different_branch_fail(self):
             install_obj.install("bam_stats_samtools")
             assert "Subworkflow 'bam_stats_samtools' not found in available subworkflows" in str(excinfo.value)
 
+    def test_subworkflows_install_across_organizations(self):
+        """Test installing a subworkflow with modules from different organizations"""
+        install_obj = SubworkflowInstall(
+            self.pipeline_dir, remote_url=CROSS_ORGANIZATION_URL, branch=CROSS_ORGANIZATION_BRANCH
+        )
+        # The hic_bwamem2 subworkflow contains modules from different organizations
+        install_obj.install("get_genome_annotation")
+        # Verify that the installed_by entry was added correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        mod_json = modules_json.get_modules_json()
+        assert mod_json["repos"][CROSS_ORGANIZATION_URL]["modules"]["jvfe"]["wget"]["installed_by"] == [
+            "get_genome_annotation"
+        ]
+
     def test_subworkflows_install_tracking(self):
         """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
         assert self.subworkflow_install.install("bam_sort_stats_samtools")

tests/utils.py

@@ -20,6 +20,8 @@
 OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386"
 OLD_TRIMGALORE_BRANCH = "mimic-old-trimgalore"
 GITLAB_URL = "https://gitlab.com/nf-core/modules-test.git"
+CROSS_ORGANIZATION_URL = "https://github.com/jvfe/test-subworkflow-remote.git"
+CROSS_ORGANIZATION_BRANCH = "main"
 GITLAB_REPO = "nf-core-test"
 GITLAB_DEFAULT_BRANCH = "main"
 GITLAB_SUBWORKFLOWS_BRANCH = "subworkflows"