Merge branch 'add-rocreate' of github.com:mashehu/tools into add-rocr…

…eate

# Conflicts:
#	CHANGELOG.md
#	nf_core/commands_pipelines.py
#	nf_core/pipelines/lint_utils.py
#	nf_core/pipelines/rocrate.py
#	nf_core/utils.py

.github/workflows/create-test-lint-wf-template.yml

@@ -150,6 +150,11 @@ jobs:
         run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
         working-directory: create-test-lint-wf
 
+      # Add empty ro-crate file
+      - name: add empty ro-crate file
+        run: touch my-prefix-testpipeline/ro-crate-metadata.json
+        working-directory: create-test-lint-wf
+
       # Run nf-core linting
       - name: nf-core pipelines lint
         run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned

nf_core/__main__.py

@@ -1732,7 +1732,7 @@ def command_schema_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 command_schema_build(directory, no_prompts, web_only, url):

nf_core/components/info.py

@@ -211,9 +211,9 @@ def get_local_yaml(self) -> Optional[Dict]:
                         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) -> Optional[dict]:
+    def get_remote_yaml(self) -> Optional[Dict]:
         """Attempt to get the meta.yml file from a remote repo.
 
         Returns:

nf_core/modules/modules_json.py

@@ -1119,8 +1119,10 @@ def dump(self, run_prettier: bool = False) -> None:
         """
         Sort the modules.json, and write it to file
         """
+        # Sort the modules.json
+        if self.modules_json is None:
+            self.load()
         if self.modules_json is not None:
-            # 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)

nf_core/pipelines/lint/files_exist.py

@@ -66,6 +66,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         conf/igenomes.config
         .github/workflows/awstest.yml
         .github/workflows/awsfulltest.yml
+        ro-crate-metadata.json
 
     Files that *must not* be present, due to being renamed or removed in the template:
 
@@ -171,6 +172,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         [Path(".github", "workflows", "awstest.yml")],
         [Path(".github", "workflows", "awsfulltest.yml")],
         [Path("modules.json")],
+        [Path("ro-crate-metadata.json")],
     ]
 
     # List of strings. Fails / warns if any of the strings exist.
@@ -198,6 +200,12 @@ def files_exist(self) -> Dict[str, List[str]]:
     ]
     files_warn_ifexists = [Path(".travis.yml")]
 
+    files_hint = [
+        [
+            ["ro-crate-metadata.json"],
+            ". Run `nf-core rocrate` to generate this file. Read more about RO-Crates in the [nf-core/tools docs](https://nf-co.re/tools#create-a-ro-crate-metadata-file).",
+        ],
+    ]
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
 
@@ -225,7 +233,11 @@ def pf(file_path: Union[str, Path]) -> Path:
         if any([pf(f).is_file() for f in files]):
             passed.append(f"File found: {self._wrap_quotes(files)}")
         else:
-            warned.append(f"File not found: {self._wrap_quotes(files)}")
+            hint = ""
+            for file_hint in files_hint:
+                if file_hint[0] == files:
+                    hint = str(file_hint[1])
+            warned.append(f"File not found: {self._wrap_quotes(files)}{hint}")
 
     # Files that cause an error if they exist
     for file in files_fail_ifexists:

requirements.txt

@@ -19,6 +19,7 @@ requests_cache
 rich-click==1.8.*
 rich>=13.3.1
 rocrate
+repo2rocrate
 tabulate
 textual==0.71.0
 trogon