allowing new line before description field

CHANGELOG.md

@@ -6,16 +6,18 @@
 
 - Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
 - Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
-- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`)
+- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170))
 
 ### Linting
 
 ### Modules
 
-- Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175))
+- Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
 
 ### Subworkflows
 
+- Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL ([#2177](https://github.com/nf-core/tools/pull/2177))
+
 ### General
 
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]

nf_core/components/install.py

@@ -169,19 +169,19 @@ def collect_and_verify_name(self, component, modules_repo):
         if component is None:
             component = questionary.autocomplete(
                 f"{'Tool' if self.component_type == 'modules' else 'Subworkflow'} name:",
-                choices=sorted(modules_repo.get_avail_components(self.component_type)),
+                choices=sorted(modules_repo.get_avail_components(self.component_type, commit=self.sha)),
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
 
         # Check that the supplied name is an available module/subworkflow
-        if component and component not in modules_repo.get_avail_components(self.component_type):
+        if component and component not in modules_repo.get_avail_components(self.component_type, commit=self.sha):
             log.error(
                 f"{self.component_type[:-1].title()} '{component}' not found in list of available {self.component_type}."
             )
             log.info(f"Use the command 'nf-core {self.component_type} list' to view available software")
             return False
 
-        if not modules_repo.component_exists(component, self.component_type):
+        if not modules_repo.component_exists(component, self.component_type, commit=self.sha):
             warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})"
             log.warning(warn_msg)
             return False

nf_core/components/update.py

@@ -386,7 +386,7 @@ def get_single_component_info(self, component):
             )
 
         # Check that the supplied name is an available module/subworkflow
-        if component and component not in self.modules_repo.get_avail_components(self.component_type):
+        if component and component not in self.modules_repo.get_avail_components(self.component_type, commit=self.sha):
             raise LookupError(
                 f"{self.component_type[:-1].title()} '{component}' not found in list of available {self.component_type}."
                 f"Use the command 'nf-core {self.component_type} list remote' to view available software"
@@ -879,25 +879,23 @@ def update_linked_components(self, modules_to_update, subworkflows_to_update, up
             if m_update in updated:
                 continue
             original_component_type, original_update_all = self._change_component_type("modules")
-            self.update(m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist)
-            self._reset_component_type(original_component_type, original_update_all)
+            try:
+                self.update(m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist)
+            except LookupError as e:
+                # If the module to be updated is not available, check if there has been a name change
+                if "not found in list of available" in str(e):
+                    # Skip update, we check for name changes with manage_changes_in_linked_components in line #261
+                    pass
+                else:
+                    raise
+            finally:
+                self._reset_component_type(original_component_type, original_update_all)
 
     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.dir, self.component_type, self.modules_repo.repo_path, component)
             included_modules, included_subworkflows = get_components_to_install(subworkflow_directory)
-            # 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}'")
-                    install_module_object = ComponentInstall(self.dir, "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}'")
-                    install_subworkflow_object = ComponentInstall(self.dir, "subworkflows", installed_by=component)
-                    install_subworkflow_object.install(subworkflow, silent=True)
             # If a module/subworkflow has been removed from the subworkflow
             for module in modules_to_update:
                 if module not in included_modules:
@@ -909,6 +907,17 @@ def manage_changes_in_linked_components(self, component, modules_to_update, subw
                     log.info(f"Removing subworkflow '{subworkflow}' which is not included in '{component}' anymore.")
                     remove_subworkflow_object = ComponentRemove("subworkflows", self.dir)
                     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}'")
+                    install_module_object = ComponentInstall(self.dir, "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}'")
+                    install_subworkflow_object = ComponentInstall(self.dir, "subworkflows", installed_by=component)
+                    install_subworkflow_object.install(subworkflow, silent=True)
 
     def _change_component_type(self, new_component_type):
         original_component_type = self.component_type

nf_core/module-template/modules/meta.yml

@@ -1,7 +1,7 @@
 name: "{{ component_name_underscore }}"
 {% if not_empty_template -%}
 ## TODO nf-core: Add a description of the module and list keywords
-{%- endif -%}
+{% endif -%}
 description: write your description here
 keywords:
   - sort

nf_core/modules/modules_repo.py

@@ -302,7 +302,7 @@ def checkout(self, commit):
         """
         self.repo.git.checkout(commit)
 
-    def component_exists(self, component_name, component_type, checkout=True):
+    def component_exists(self, component_name, component_type, checkout=True, commit=None):
         """
         Check if a module/subworkflow exists in the branch of the repo
 
@@ -312,7 +312,7 @@ def component_exists(self, component_name, component_type, checkout=True):
         Returns:
             (bool): Whether the module/subworkflow exists in this branch of the repository
         """
-        return component_name in self.get_avail_components(component_type, checkout=checkout)
+        return component_name in self.get_avail_components(component_type, checkout=checkout, commit=commit)
 
     def get_component_dir(self, component_name, component_type):
         """
@@ -449,7 +449,7 @@ def get_commit_info(self, sha):
                 return message, date
         raise LookupError(f"Commit '{sha}' not found in the '{self.remote_url}'")
 
-    def get_avail_components(self, component_type, checkout=True):
+    def get_avail_components(self, component_type, checkout=True, commit=None):
         """
         Gets the names of the modules/subworkflows in the repository. They are detected by
         checking which directories have a 'main.nf' file
@@ -459,6 +459,8 @@ def get_avail_components(self, component_type, checkout=True):
         """
         if checkout:
             self.checkout_branch()
+        if commit is not None:
+            self.checkout(commit)
         # Get directory
         if component_type == "modules":
             directory = self.modules_dir

tests/subworkflows/update.py

@@ -8,6 +8,7 @@
 import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
+from nf_core.modules.remove import ModuleRemove
 from nf_core.modules.update import ModuleUpdate
 from nf_core.subworkflows.update import SubworkflowUpdate
 
@@ -321,6 +322,10 @@ def test_update_change_of_included_modules(self):
     # Check that tabix/tabix is there
     assert "tabix/tabix" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
     assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir()
+    # Check that ensemblevep is not there but instead we have ensemblevep/vep (due to a file re-naming)
+    assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+    assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+    assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "ensemblvep/vep").is_dir()
 
 
 def cmp_component(dir1, dir2):