Command to generate pipeline container config files

.github/snapshots/gpu.nf.test.snap

@@ -107,7 +107,7 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.0"
+            "nextflow": "25.10.4"
         },
         "timestamp": "2025-06-16T14:29:10.076573"
     }

docs/api/_src/pipeline_lint_tests/container_configs.md

@@ -0,0 +1,5 @@
+# container_configs
+
+    ```{eval-rst}
+    .. automethod:: nf_core.pipelines.lint.PipelineLint.container_configs
+    ```

docs/api/_src/pipeline_lint_tests/index.md

@@ -5,6 +5,7 @@
     - [actions_nf_test](./actions_nf_test/)
     - [actions_schema_validation](./actions_schema_validation/)
     - [base_config](./base_config/)
+    - [container_configs](./container_configs/)
     - [files_exist](./files_exist/)
     - [files_unchanged](./files_unchanged/)
     - [included_configs](./included_configs/)

nf_core/components/install.py

@@ -20,6 +20,7 @@
 )
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
+from nf_core.pipelines.containers_utils import try_generate_container_configs
 
 log = logging.getLogger(__name__)
 
@@ -158,7 +159,7 @@ def install(self, component: str | dict[str, str], silent: bool = False) -> bool
         if not self.install_component_files(component, version, self.modules_repo, install_folder):
             return False
 
-        # Update module.json with newly installed subworkflow
+        # Update module.json with newly installed component
         modules_json.load()
         modules_json.update(
             self.component_type, self.modules_repo, component, version, self.installed_by, install_track
@@ -168,6 +169,10 @@ 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)
+
         if not silent:
             modules_json.load()
             modules_json.dump(run_prettier=True)

nf_core/components/patch.py

@@ -9,6 +9,7 @@
 from nf_core.components.components_command import ComponentCommand
 from nf_core.components.components_differ import ComponentsDiffer
 from nf_core.modules.modules_json import ModulesJson
+from nf_core.pipelines.containers_utils import try_generate_container_configs
 
 log = logging.getLogger(__name__)
 
@@ -118,7 +119,8 @@ def patch(self, component=None):
             )
 
         # Write the patch to a temporary location (otherwise it is printed to the screen later)
-        patch_temp_path = tempfile.mktemp()
+        with tempfile.NamedTemporaryFile(delete=False) as tmp:
+            patch_temp_path = tmp.name
         try:
             ComponentsDiffer.write_diff_file(
                 patch_temp_path,
@@ -156,13 +158,19 @@ def patch(self, component=None):
         shutil.move(patch_temp_path, patch_path)
         log.info(f"Patch file of '{component_fullname}' written to '{patch_path}'")
 
+        # Regenerate container configuration files for the pipeline when modules are removed
+        if self.component_type == "modules":
+            try_generate_container_configs(self.directory)
+
     def remove(self, component):
         # Check modules directory structure
         self.check_modules_structure()
 
         self.modules_json.check_up_to_date()
         self._parameter_checks(component)
         components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
+        if components is None:
+            raise ValueError(f"No components found for {self.component_type} in the pipeline")
 
         if component is None:
             self.require_prompts(

nf_core/components/remove.py

@@ -9,6 +9,7 @@
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
 from nf_core.modules.modules_json import ModulesJson
+from nf_core.pipelines.containers_utils import try_generate_container_configs
 
 from .install import ComponentInstall
 
@@ -180,6 +181,10 @@ def remove(self, component, repo_url=None, repo_path=None, removed_by=None, remo
                     # remember removed dependencies
                     if dependency_removed:
                         removed_components.append(component_name.replace("/", "_"))
+            # Regenerate container configuration files for the pipeline when modules are removed
+            if self.component_type == "modules":
+                try_generate_container_configs(self.directory)
+
             # print removed dependencies
             dependencies = set(removed_components) - {component}
             if dependencies:

nf_core/components/update.py

@@ -16,6 +16,7 @@
 from nf_core.components.remove import ComponentRemove
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
+from nf_core.pipelines.containers_utils import try_generate_container_configs
 from nf_core.utils import plural_es, plural_s, plural_y
 
 log = logging.getLogger(__name__)
@@ -307,6 +308,10 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 # Update modules.json with newly installed component
                 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:

nf_core/pipeline-template/modules.json

@@ -8,12 +8,12 @@
                     {%- if fastqc %}
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
+                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}