Merge branch 'fix-module-template-org' of github.com:awgymer/nf-core-…

…tools into fix-module-template-org

CHANGELOG.md

@@ -10,6 +10,7 @@
 - `nextflow run <pipeline> --version` will now print the workflow version from the manifest and exit ([#1951](https://github.com/nf-core/tools/pull/1951))
 - Add profile for running `docker` with the ARM chips (including Apple silicon) ([#1942](https://github.com/nf-core/tools/pull/1942) and [#2034](https://github.com/nf-core/tools/pull/2034))
 - Flip execution order of parameter summary printing and parameter validation to prevent 'hiding' of parameter errors.
+- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline.
 
 ### Linting
 

nf_core/components/install.py

@@ -127,14 +127,14 @@ def install(self, component, silent=False):
             log.info(f"Use the following statement to include this {self.component_type[:-1]}:")
             Console().print(
                 Syntax(
-                    f"include {{ {component_name} }} from '.{os.path.join(install_folder, component)}/main'",
+                    f"include {{ {component_name} }} from '../{Path(install_folder, component).relative_to(self.dir)}/main'",
                     "groovy",
                     theme="ansi_dark",
                     padding=1,
                 )
             )
             if self.component_type == "subworkflows":
-                subworkflow_config = os.path.join(install_folder, component, "nextflow.config")
+                subworkflow_config = Path(install_folder, component, "nextflow.config").relative_to(self.dir)
                 if os.path.isfile(subworkflow_config):
                     log.info("Add the following config statement to use this subworkflow:")
                     Console().print(

nf_core/components/remove.py

@@ -19,13 +19,16 @@ class ComponentRemove(ComponentCommand):
     def __init__(self, component_type, pipeline_dir, remote_url=None, branch=None, no_pull=False):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
 
-    def remove(self, component, removed_by=None, force=False):
+    def remove(self, component, removed_by=None, removed_components=None, force=False):
         """
         Remove an already installed module/subworkflow
         This command only works for modules/subworkflows that are installed from 'nf-core/modules'
 
         Args:
             component (str): Name of the component to remove
+            removed_by (str): Name of the component that is removing the current component
+                (a subworkflow name if the component is a dependency or "modules" or "subworkflows" if it is not a dependency)
+            removed_components (list[str]): list of components that have been removed during a recursive remove of subworkflows
             force (bool): Force removal of component, even if there is still an include statement in a workflow file
 
         Returns:
@@ -51,6 +54,9 @@ def remove(self, component, removed_by=None, force=False):
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
 
+        if removed_components is None:
+            removed_components = []
+
         # Get the module/subworkflow directory
         component_dir = Path(self.dir, self.component_type, repo_path, component)
 
@@ -85,7 +91,7 @@ def remove(self, component, removed_by=None, force=False):
             include_stmts = self.check_if_in_include_stmts(str(removed_component_dir))
             if include_stmts:
                 # print the include statements
-                log.warn(
+                log.warning(
                     f"The {self.component_type[:-1]} '{component}' is still included in the following workflow file{nf_core.utils.plural_s(include_stmts)}:"
                 )
                 console = Console()
@@ -120,14 +126,16 @@ def remove(self, component, removed_by=None, force=False):
                         if not ComponentInstall(self.dir, self.component_type, force=True).install(
                             component, silent=True
                         ):
-                            log.warn(
+                            log.warning(
                                 f"Could not install the {self.component_type[:-1]} '{component}', please install it manually with 'nf-core {component_type} install  {component}'."
                             )
+                        removed_components.append(component)
                         return removed
             # Remove the component files of all entries removed from modules.json
             removed = (
                 True if self.clear_component_dir(component, Path(self.dir, removed_component_dir)) or removed else False
             )
+            removed_components.append(component)
 
         if removed:
             if self.component_type == "subworkflows":
@@ -136,10 +144,14 @@ def remove(self, component, removed_by=None, force=False):
                     self.component_type, component, self.modules_repo.remote_url, repo_path, {}
                 )
                 for component_name, component_type in dependent_components.items():
-                    original_component_tyoe = self.component_type
+                    if component_name in removed_components:
+                        continue
+                    original_component_type = self.component_type
                     self.component_type = component_type
-                    dependency_removed = self.remove(component_name, removed_by=removed_by)
-                    self.component_type = original_component_tyoe
+                    dependency_removed = self.remove(
+                        component_name, removed_by=removed_by, removed_components=removed_components
+                    )
+                    self.component_type = original_component_type
                     # remember removed dependencies
                     if dependency_removed:
                         removed_components.append(component_name.replace("/", "_"))
@@ -154,9 +166,9 @@ def remove(self, component, removed_by=None, force=False):
             ][component]["installed_by"]
             if installed_by == self.component_type:
                 log.error(
-                    f"Did not remove '{component}', because it was also manually installed. Only updated 'installed_by' in modules.json."
+                    f"Did not remove '{component}', because it was also manually installed. Only updated 'installed_by' entry in modules.json."
                 )
             log.info(
-                f"""Did not remove {self.component_type[:-1]} '{component}', because it was also installed by {', '.join(f"'{d}'" for d in installed_by)}."""
+                f"""Did not remove {self.component_type[:-1]} '{component}', because it was also installed by {', '.join(f"'{d}'" for d in installed_by)}. Only updated the 'installed_by' entry in modules.json."""
             )
         return removed

nf_core/modules/modules_json.py

@@ -705,15 +705,6 @@ def remove_entry(self, component_type, name, repo_url, install_dir, removed_by=N
                         # write the updated modules.json file
                         self.dump()
                         return True
-                    # write the updated modules.json file
-                    if removed_by == component_type:
-                        log.info(
-                            f"""Updated the 'installed_by' list for '{name}', but it is still installed, because it is required by {", ".join(f"'{d}'" for d in repo_entry[component_type][install_dir][name]['installed_by'])}."""
-                        )
-                    else:
-                        log.info(
-                            f"Removed {removed_by} from the 'installed_by' list of {name}, but it was also installed by other modules/subworkflows."
-                        )
                     self.dump()
                     return False
             else:

nf_core/utils.py

@@ -965,13 +965,13 @@ def load_tools_config(directory="."):
 
 
 def determine_base_dir(directory="."):
-    base_dir = Path(directory).absolute()
+    base_dir = start_dir = Path(directory).absolute()
     while not get_first_available_path(base_dir, CONFIG_PATHS) and base_dir != base_dir.parent:
         base_dir = base_dir.parent
         config_fn = get_first_available_path(base_dir, CONFIG_PATHS)
         if config_fn:
             break
-    return base_dir
+    return directory if base_dir == start_dir else base_dir
 
 
 def get_first_available_path(directory, paths):