Add new command nf-core rocrate to create a Research Object (RO) crate for a pipeline

CHANGELOG.md

@@ -35,6 +35,7 @@
 - Add new subcommand: `nf-core logo-create` to output an nf-core logo for a pipeline (instead of going through the website) ([#2662](https://github.com/nf-core/tools/pull/2662))
 - Update actions/cache action to v4 ([#2666](https://github.com/nf-core/tools/pull/2666))
 - Remove redundanct v in pipeline version for emails ([#2667](https://github.com/nf-core/tools/pull/2667))
+- Add new command `nf-core rocrate` to create a Research Object (RO) crate for a pipeline ([#2680](https://github.com/nf-core/tools/pull/2680))
 
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 

nf_core/__main__.py

@@ -49,9 +49,10 @@
                 "modules",
                 "subworkflows",
                 "schema",
-                "create-logo",
                 "bump-version",
                 "sync",
+                "rocrate",
+                "create-logo",
             ],
         },
     ],
@@ -1855,7 +1856,7 @@ def validate(pipeline, params):
 @click.option(
     "--url",
     type=str,
-    default="https://nf-co.re/pipeline_schema_builder",
+    default="https://oldsite.nf-co.re/pipeline_schema_builder",
     help="Customise the builder URL (for development work)",
 )
 def build(dir, no_prompts, web_only, url):
@@ -2124,6 +2125,37 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
         sys.exit(1)
 
 
+# nf-core rocrate
+@nf_core_cli.command("rocrate")
+@click.argument(
+    "pipeline_dir",
+    type=click.Path(exists=True),
+    default=Path.cwd(),
+    required=True,
+    metavar="<pipeline directory>",
+)
+@click.option(
+    "-j",
+    "--json",
+    default="ro-crate-metadata.json",
+    type=str,
+    help="Path to save RO Crate metadata json",
+)
+@click.option("-z", "--zip", type=str, help="Path to save RO Crate zip")
+def rocrate(pipeline_dir, json, zip):
+    """
+    Make an Research Object Crate
+    """
+    import nf_core.rocrate
+
+    if json is None and zip is None:
+        log.error("Either --json or --zip must be specified")
+        sys.exit(1)
+    pipeline_dir = Path(pipeline_dir)
+    rocrate_obj = nf_core.rocrate.RoCrate(pipeline_dir)
+    rocrate_obj.create_ro_crate(pipeline_dir, metadata_fn=json, zip_fn=zip)
+
+
 # Main script is being run - launch the CLI
 if __name__ == "__main__":
     run_nf_core()

nf_core/components/components_command.py

@@ -246,10 +246,13 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                 modules_json = ModulesJson(self.dir)
                 modules_json.load()
                 if modules_json.has_git_url_and_modules():
-                    modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
-                        self.modules_repo.repo_path
-                    ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve()))
-                modules_json.dump()
+                    if modules_json.modules_json is not None:
+                        modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
+                            self.modules_repo.repo_path
+                        ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve()))
+                        modules_json.dump()
+                    else:
+                        log.error("Could not update modules.json file.")
 
     def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[str, Union[int, str]]]]:
         """

nf_core/components/info.py

@@ -1,6 +1,7 @@
 import logging
 import os
 from pathlib import Path
+from typing import Union
 
 import questionary
 import yaml
@@ -65,7 +66,7 @@ def __init__(
         no_pull=False,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
-        self.meta = None
+        self.meta = {}
         self.local_path = None
         self.remote_location = None
         self.local = None
@@ -162,7 +163,7 @@ def get_component_info(self):
 
         return self.generate_component_info_help()
 
-    def get_local_yaml(self):
+    def get_local_yaml(self) -> dict:
         """Attempt to get the meta.yml file from a locally installed module/subworkflow.
 
         Returns:
@@ -201,9 +202,9 @@ def get_local_yaml(self):
                         return yaml.safe_load(fh)
             log.debug(f"{self.component_type[:-1].title()} '{self.component}' meta.yml not found locally")
 
-        return None
+        return {}
 
-    def get_remote_yaml(self):
+    def get_remote_yaml(self) -> Union[dict, bool]:
         """Attempt to get the meta.yml file from a remote repo.
 
         Returns:

nf_core/modules/modules_json.py

@@ -43,7 +43,7 @@ def __init__(self, pipeline_dir):
         self.modules_dir = Path(self.dir, "modules")
         self.subworkflows_dir = Path(self.dir, "subworkflows")
         self.modules_json_path = Path(self.dir, "modules.json")
-        self.modules_json: Union(dict, None) = None
+        self.modules_json: Union[dict, None] = None
         self.pipeline_modules = None
         self.pipeline_subworkflows = None
         self.pipeline_components = None
@@ -1056,12 +1056,15 @@ def dump(self, run_prettier: bool = False):
         Sort the modules.json, and write it to file
         """
         # Sort the modules.json
-        self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
-        if run_prettier:
-            dump_json_with_prettier(self.modules_json_path, self.modules_json)
-        else:
-            with open(self.modules_json_path, "w") as fh:
-                json.dump(self.modules_json, fh, indent=4)
+        if self.modules_json is None:
+            self.load()
+        if self.modules_json is not None:
+            self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
+            if run_prettier:
+                dump_json_with_prettier(self.modules_json_path, self.modules_json)
+            else:
+                with open(self.modules_json_path, "w") as fh:
+                    json.dump(self.modules_json, fh, indent=4)
 
     def resolve_missing_installation(self, missing_installation, component_type):
         missing_but_in_mod_json = [