Merge pull request #3881 from nf-core/modules_repo_nested_crossorg_subworkflows

Preserve the value of self.modules_repo across nested calls

Author: muffato

CHANGELOG.md

@@ -41,6 +41,7 @@
 ### Modules
 
 - Add `topics` to the template + update linting ([#3779](https://github.com/nf-core/tools/pull/3779))
+- Preserve the value of self.modules_repo across nested calls ([#3881](https://github.com/nf-core/tools/pull/3881))
 
 ### Subworkflows
 

nf_core/components/install.py

@@ -194,6 +194,7 @@ def install_included_components(self, subworkflow_dir):
         """
         Install included modules and subworkflows
         """
+        ini_modules_repo = self.modules_repo
         modules_to_install, subworkflows_to_install = get_components_to_install(subworkflow_dir)
         for s_install in subworkflows_to_install:
             original_installed = self.installed_by
@@ -208,6 +209,8 @@ def install_included_components(self, subworkflow_dir):
             self.install(m_install, silent=True)
             self.component_type = original_component_type
             self.installed_by = original_installed
+        # self.install will have modified self.modules_repo. Restore its original value
+        self.modules_repo = ini_modules_repo
 
     def collect_and_verify_name(
         self, component: str | None, modules_repo: "nf_core.modules.modules_repo.ModulesRepo"

tests/subworkflows/test_install.py

@@ -95,6 +95,25 @@ def test_subworkflows_install_across_organizations(self):
             "fastq_trim_fastp_fastqc"
         ]
 
+    def test_subworkflows_install_across_organizations_only_nfcore(self):
+        """Test installing a subworkflow from a different organization but only with modules from nf-core"""
+        # The wget_subwf subworkflow contains nf-core/modules/wget (and only that). It used to not be possible to install it twice
+        # because of some org/nf-core confusion (https://github.com/nf-core/tools/issues/3876)
+        # Note that we use two SubworkflowInstall to avoid cross-contamination
+        for swfi in (self.subworkflow_install_cross_org, self.subworkflow_install_cross_org_again):
+            swfi.install("wget_subwf")
+            # 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]["subworkflows"]["nf-core-test"]["wget_subwf"][
+                "installed_by"
+            ] == ["subworkflows"]
+            # This assertion used to fail on the second attempt
+            assert (
+                "wget_subwf"
+                not in mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]
+            )
+
     def test_subworkflow_install_with_same_module(self):
         """Test installing a subworkflow with a module from a different organization that is already installed from another org"""
         # The fastq_trim_fastp_fastqc subworkflow contains the cross-org fastqc module, not the nf-core one

tests/test_subworkflows.py

@@ -108,6 +108,10 @@ def setUp(self):
         self.subworkflow_install_cross_org = nf_core.subworkflows.SubworkflowInstall(
             self.pipeline_dir, remote_url=CROSS_ORGANIZATION_URL, branch=CROSS_ORGANIZATION_BRANCH
         )
+        # Another instance to avoid cross-contamination
+        self.subworkflow_install_cross_org_again = nf_core.subworkflows.SubworkflowInstall(
+            self.pipeline_dir, remote_url=CROSS_ORGANIZATION_URL, branch=CROSS_ORGANIZATION_BRANCH
+        )
 
         self.mods_install = nf_core.modules.install.ModuleInstall(self.pipeline_dir, prompt=False, force=True)