Rewrite modules create repo type check.

CHANGELOG.md

@@ -7,10 +7,12 @@
 * Removed mention of `--singularity_pull_docker_container` in pipeline `README.md`
 * Replaced equals with ~ in nf-core headers, to stop false positive unresolved conflict errors when committing with VSCode.
 * Add retry strategy for AWS megatests after releasing [nf-core/tower-action v2.2](https://github.com/nf-core/tower-action/releases/tag/v2.2)
+* Added `.nf-core.yml` file with `repository_type: pipeline` for modules commands
 
 ## General
 
 * Updated `nf-core download` to work with latest DSL2 syntax for containers ([#1379](https://github.com/nf-core/tools/issues/1379))
+* Made `nf-core modules create` detect repository type with explicit `.nf-core.yml` or `--repo-type`, instead of random readme stuff ([#1391](https://github.com/nf-core/tools/pull/1391))
 
 ### Modules
 

README.md

@@ -925,7 +925,7 @@ github.com:
     git_protocol: <ssh or https are valid choices>
 ```
 
-The easiest way to create this configuration file is through *GitHub CLI*: follow
+The easiest way to create this configuration file is through _GitHub CLI_: follow
 its [installation instructions](https://cli.github.com/manual/installation)
 and then call:
 
@@ -1116,11 +1116,17 @@ This command creates a new nf-core module from the nf-core module template.
 This ensures that your module follows the nf-core guidelines.
 The template contains extensive `TODO` messages to walk you through the changes you need to make to the template.
 
-You can create a new module using `nf-core modules create`. This will create the new module in the current working directory. To specify another directory, use `--dir <directory>`.
+You can create a new module using `nf-core modules create`.
 
-If writing a module for the shared [nf-core/modules](https://github.com/nf-core/modules) repository, the `<directory>` argument should be the path to the clone of your fork of the modules repository.
+This command can be used both when writing a module for the shared [nf-core/modules](https://github.com/nf-core/modules) repository,
+and also when creating local modules for a pipeline.
 
-Alternatively, if writing a more niche module that does not make sense to share, `<directory>` should be the path to your pipeline.
+Which type of repository you are working in is detected by the `repository_type` flag in a `.nf-core.yml` file in the root directory,
+set to either `pipeline` or `modules`.
+The command will automatically look through parent directories for this file to set the root path, so that you can run the command in a subdirectory.
+It will start in the current working directory, or whatever is specified with `--dir <directory>`.
+
+If you do not have a `.nf-core.yml` file you can specify the repository type with the `--repo-type` flag.
 
 The `nf-core modules create` command will prompt you with the relevant questions in order to create all of the necessary module files.
 

nf_core/__main__.py

@@ -498,7 +498,8 @@ def remove(ctx, dir, tool):
 @click.option("-n", "--no-meta", is_flag=True, default=False, help="Don't use meta map for sample information")
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite any files if they already exist")
 @click.option("-c", "--conda-name", type=str, default=None, help="Name of the conda package to use")
-def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_name):
+@click.option("-r", "--repo-type", type=click.Choice(["pipeline", "modules"]), default=None, help="Type of repository")
+def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_name, repo_type):
     """
     Create a new DSL2 module from the nf-core template.
 
@@ -519,7 +520,7 @@ def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_nam
 
     # Run function
     try:
-        module_create = nf_core.modules.ModuleCreate(dir, tool, author, label, has_meta, force, conda_name)
+        module_create = nf_core.modules.ModuleCreate(dir, tool, author, label, has_meta, force, conda_name, repo_type)
         module_create.create()
     except UserWarning as e:
         log.critical(e)

nf_core/modules/bump_versions.py

@@ -64,7 +64,7 @@ def bump_versions(self, module=None, all_modules=False, show_uptodate=False):
         # Get list of all modules
         _, nfcore_modules = nf_core.modules.module_utils.get_installed_modules(self.dir)
 
-        # Load the .nf-core-tools.config
+        # Load the .nf-core.yml config
         self.tools_config = nf_core.utils.load_tools_config(self.dir)
 
         # Prompt for module or all

nf_core/modules/create.py

@@ -25,7 +25,15 @@
 
 class ModuleCreate(object):
     def __init__(
-        self, directory=".", tool="", author=None, process_label=None, has_meta=None, force=False, conda_name=None
+        self,
+        directory=".",
+        tool="",
+        author=None,
+        process_label=None,
+        has_meta=None,
+        force=False,
+        conda_name=None,
+        repo_type=None,
     ):
         self.directory = directory
         self.tool = tool
@@ -36,7 +44,7 @@ def __init__(
         self.subtool = None
         self.tool_conda_name = conda_name
         self.tool_licence = None
-        self.repo_type = None
+        self.repo_type = repo_type
         self.tool_licence = ""
         self.tool_description = ""
         self.tool_doc_url = ""
@@ -75,9 +83,12 @@ def create(self):
 
         # Check whether the given directory is a nf-core pipeline or a clone of nf-core/modules
         try:
-            self.repo_type = self.get_repo_type(self.directory)
+            self.get_repo_type()
         except LookupError as e:
             raise UserWarning(e)
+        log.info(f"Repository type: [blue]{self.repo_type}")
+        if self.directory != ".":
+            log.info(f"Base directory: '{self.directory}'")
 
         log.info(
             "[yellow]Press enter to use default values [cyan bold](shown in brackets)[/] [yellow]or type your own responses. "
@@ -272,27 +283,46 @@ def render_template(self):
             template_stat = os.stat(os.path.join(os.path.dirname(nf_core.__file__), "module-template", template_fn))
             os.chmod(dest_fn, template_stat.st_mode)
 
-    def get_repo_type(self, directory):
+    def get_repo_type(self):
         """
         Determine whether this is a pipeline repository or a clone of
         nf-core/modules
         """
         # Verify that the pipeline dir exists
-        if dir is None or not os.path.exists(directory):
-            raise UserWarning(f"Could not find directory: {directory}")
-
-        readme = os.path.join(directory, "README.md")
-        # Determine repository type
-        if os.path.exists(readme):
-            with open(readme) as fh:
-                if fh.readline().rstrip().startswith("# ![nf-core/modules]"):
-                    return "modules"
-                else:
-                    return "pipeline"
-        else:
+        if dir is None or not os.path.exists(self.directory):
+            raise UserWarning(f"Could not find directory: {self.directory}")
+
+        # Try to find the root directory
+        base_dir = os.path.abspath(self.directory)
+        config_path_yml = os.path.join(base_dir, ".nf-core.yml")
+        config_path_yaml = os.path.join(base_dir, ".nf-core.yaml")
+        while (
+            not os.path.exists(config_path_yml)
+            and not os.path.exists(config_path_yaml)
+            and base_dir != os.path.dirname(base_dir)
+        ):
+            base_dir = os.path.dirname(base_dir)
+            config_path_yml = os.path.join(base_dir, ".nf-core.yml")
+            config_path_yaml = os.path.join(base_dir, ".nf-core.yaml")
+            # Reset self.directory if we found the config file (will be an absolute path)
+            if os.path.exists(config_path_yml) or os.path.exists(config_path_yaml):
+                self.directory = base_dir
+
+        # Figure out the repository type from the .nf-core.yml config file if we can
+        tools_config = nf_core.utils.load_tools_config(self.directory)
+        if tools_config.get("repository_type") in ["pipeline", "modules"]:
+            if self.repo_type is not None and self.repo_type != tools_config["repository_type"]:
+                raise UserWarning(
+                    f"'--repo-type {self.repo_type}' conflicts with [i][red]repository_type[/]: [blue]pipeline[/][/] in '{os.path.relpath(config_path_yml)}'"
+                )
+            self.repo_type = tools_config["repository_type"]
+            return
+
+        # Could be set on the command line - throw an error if not
+        if not self.repo_type:
             raise UserWarning(
-                f"This directory does not look like a clone of nf-core/modules or an nf-core pipeline: '{directory}'"
-                " Please point to a valid directory."
+                f"Can't find a '.nf-core.yml' file with 'repository_type' set to 'pipeline' or 'modules': '{self.directory}'"
+                "\nPlease use the '--repo-type' flag or create '.nf-core.yml'"
             )
 
     def get_module_dirs(self):

nf_core/pipeline-template/.nf-core.yml

@@ -0,0 +1 @@
+repository_type: pipeline