perf(components): regenerate container configs once per top-level install/update

nf_core/components/install.py

@@ -169,9 +169,13 @@ def install(self, component: str | dict[str, str], silent: bool = False) -> bool
             # Install included modules and subworkflows
             self.install_included_components(component_dir)
 
-        # Regenerate container configuration files for the pipeline when modules are installed
-        if self.component_type == "modules":
-            try_generate_container_configs(self.directory, component_dir, component)
+        # Regenerate container configs once per top-level invocation
+        # (recursive installs pass silent=True).
+        if not silent:
+            if self.component_type == "modules":
+                try_generate_container_configs(self.directory, component_dir, component)
+            else:
+                try_generate_container_configs(self.directory)
 
         if not silent:
             modules_json.load()

nf_core/components/update.py

@@ -309,9 +309,6 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 self.modules_json.update(self.component_type, modules_repo, component, version, installed_by=None)
                 updated.append(component)
 
-                # Regenerate container configuration files for the pipeline when modules are updated
-                if self.component_type == "modules":
-                    try_generate_container_configs(self.directory)
                 recursive_update = True
                 modules_to_update, subworkflows_to_update = self.get_components_to_update(component)
                 if not silent and len(modules_to_update + subworkflows_to_update) > 0 and not self.update_all:
@@ -356,6 +353,11 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
             self.modules_json.load()
             self.modules_json.dump(run_prettier=True)
 
+        # Regenerate container configs once per top-level invocation
+        # (recursive updates pass silent=True; skip in --save-diff dry runs).
+        if not silent and updated and not self.save_diff_fn:
+            try_generate_container_configs(self.directory)
+
         return exit_value
 
     def get_single_component_info(self, component):

tests/modules/test_install.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from unittest import mock
 
 import pytest
 
@@ -44,6 +45,12 @@ def test_modules_install_trimgalore_twice(self):
         self.mods_install.install("trimgalore")
         assert self.mods_install.install("trimgalore") is True
 
+    @mock.patch("nf_core.components.install.try_generate_container_configs")
+    def test_modules_install_regenerates_container_configs_once(self, mock_gen):
+        """Container config regen runs exactly once for a top-level module install."""
+        assert self.mods_install.install("trimgalore") is not False
+        assert mock_gen.call_count == 1
+
     def test_modules_install_from_gitlab(self):
         """Test installing a module from GitLab"""
         assert self.mods_install_gitlab.install("fastqc") is True

tests/subworkflows/test_install.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from unittest import mock
 
 import pytest
 
@@ -191,6 +192,12 @@ def test_subworkflows_install_tracking_added_super_subworkflow(self):
             ]["installed_by"]
         ) == sorted(["subworkflows", "bam_sort_stats_samtools"])
 
+    @mock.patch("nf_core.components.install.try_generate_container_configs")
+    def test_subworkflows_install_regenerates_container_configs_once(self, mock_gen):
+        """Container config regen runs once for a top-level subworkflow install with module deps."""
+        assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False
+        assert mock_gen.call_count == 1
+
     def test_subworkflows_install_alternate_remote(self):
         """Test installing a module from a different remote with the same organization path"""
         install_obj = SubworkflowInstall(

tests/subworkflows/test_update.py

@@ -32,6 +32,25 @@ def test_install_and_update(self):
         assert update_obj.update("bam_stats_samtools") is True
         assert cmp_component(tmpdir, sw_path) is True
 
+    @mock.patch("nf_core.components.update.try_generate_container_configs")
+    def test_subworkflow_update_regenerates_container_configs_once(self, mock_gen):
+        """Container config regen runs once for a top-level update, not per linked component."""
+        assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+        mock_gen.reset_mock()
+        update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True)
+        assert update_obj.update("fastq_align_bowtie2") is True
+        assert mock_gen.call_count == 1
+
+    @mock.patch("nf_core.components.update.try_generate_container_configs")
+    def test_subworkflow_update_save_diff_skips_container_configs(self, mock_gen):
+        """``--save-diff`` is a dry run; container configs must not be regenerated."""
+        assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+        mock_gen.reset_mock()
+        patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch")
+        update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True)
+        assert update_obj.update("fastq_align_bowtie2") is True
+        assert mock_gen.call_count == 0
+
     def test_install_at_hash_and_update(self):
         """Installs an old version of a subworkflow in the pipeline and updates it"""
         assert self.subworkflow_install_old.install("fastq_align_bowtie2")