nf-core · mirpedrol · Jan 27, 2025 · Jan 20, 2025 · Jan 20, 2025 · Oct 28, 2024
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.3
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py
@@ -271,9 +271,7 @@ def print_diff(
         console = Console(force_terminal=nf_core.utils.rich_force_colors())
         if current_version is not None and new_version is not None:
             log.info(
-                f"Changes in component '{Path(repo_path, component)}' between"
-                f" ({current_version}) and"
-                f" ({new_version})"
+                f"Changes in component '{Path(repo_path, component)}' between ({current_version}) and ({new_version})"
             )
         else:
             log.info(f"Changes in component '{Path(repo_path, component)}'")

diff --git a/nf_core/components/info.py b/nf_core/components/info.py
@@ -265,9 +265,9 @@ def generate_component_info_help(self):
             intro_text.append(
                 Text.from_markup(
                     ":globe_with_meridians: Repository: "
-                    f"{ '[link={self.remote_location}]' if self.remote_location.startswith('http') else ''}"
+                    f"{'[link={self.remote_location}]' if self.remote_location.startswith('http') else ''}"
                     f"{self.remote_location}"
-                    f"{'[/link]' if self.remote_location.startswith('http') else '' }"
+                    f"{'[/link]' if self.remote_location.startswith('http') else ''}"
                     "\n"
                 )
             )

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
@@ -102,7 +102,7 @@ def __init__(
                     continue
                 if isinstance(components, str):
                     raise LookupError(
-                        f"Error parsing modules.json: {components}. " f"Please check the file for errors or try again."
+                        f"Error parsing modules.json: {components}. Please check the file for errors or try again."
                     )
                 for org, comp in components:
                     self.all_remote_components.append(

diff --git a/nf_core/components/remove.py b/nf_core/components/remove.py
@@ -176,6 +176,6 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals
                     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)}. Only updated the 'installed_by' entry in modules.json."""
+                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
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
@@ -62,7 +62,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
         ).get("meta.yml")
         if lines is not None:
             yaml = ruamel.yaml.YAML()
-            meta_yaml = yaml.safe_load("".join(lines))
+            meta_yaml = yaml.load("".join(lines))
     if meta_yaml is None:
         module.failed.append(("meta_yml_exists", "Module `meta.yml` does not exist", module.meta_yml))
         return
@@ -82,7 +82,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
         if len(e.path) > 0:
             hint = f"\nCheck the entry for `{e.path[0]}`."
         if e.message.startswith("None is not of type 'object'") and len(e.path) > 2:
-            hint = f"\nCheck that the child entries of {str(e.path[0])+'.'+str(e.path[2])} are indented correctly."
+            hint = f"\nCheck that the child entries of {str(e.path[0]) + '.' + str(e.path[2])} are indented correctly."
         if e.schema and isinstance(e.schema, dict) and "message" in e.schema:
             e.message = e.schema["message"]
             incorrect_value = meta_yaml

diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
@@ -202,7 +202,7 @@ def download_workflow(self):
             raise DownloadError(e) from e
 
         summary_log = [
-            f"Pipeline revision: '{', '.join(self.revision) if len(self.revision) < 5 else self.revision[0]+',['+str(len(self.revision)-2)+' more revisions],'+self.revision[-1]}'",
+            f"Pipeline revision: '{', '.join(self.revision) if len(self.revision) < 5 else self.revision[0] + ',[' + str(len(self.revision) - 2) + ' more revisions],' + self.revision[-1]}'",
             f"Use containers: '{self.container_system}'",
         ]
         if self.container_system:
@@ -1908,8 +1908,8 @@ def __init__(
 
         log.error(self.error_type.message)
         log.info(self.error_type.helpmessage)
-        log.debug(f'Failed command:\n{" ".join(singularity_command)}')
-        log.debug(f'Singularity error messages:\n{"".join(error_msg)}')
+        log.debug(f"Failed command:\n{' '.join(singularity_command)}")
+        log.debug(f"Singularity error messages:\n{''.join(error_msg)}")
 
         raise self.error_type
 

diff --git a/nf_core/pipelines/lint/multiqc_config.py b/nf_core/pipelines/lint/multiqc_config.py
@@ -122,7 +122,7 @@ def multiqc_config(self) -> Dict[str, List[str]]:
                     f"The expected comment is:  \n"
                     f"```{hint}```  \n"
                     f"The current comment is:  \n"
-                    f"```{ mqc_yml['report_comment'].strip()}```"
+                    f"```{mqc_yml['report_comment'].strip()}```"
                 )
             else:
                 passed.append("`assets/multiqc_config.yml` contains a matching 'report_comment'.")

diff --git a/nf_core/pipelines/lint/version_consistency.py b/nf_core/pipelines/lint/version_consistency.py
@@ -53,7 +53,7 @@ def version_consistency(self):
     # Check if they are consistent
     if len(set(versions.values())) != 1:
         failed.append(
-            "The versioning is not consistent between container, release tag " "and config. Found {}".format(
+            "The versioning is not consistent between container, release tag and config. Found {}".format(
                 ", ".join([f"{k} = {v}" for k, v in versions.items()])
             )
         )

diff --git a/nf_core/pipelines/params_file.py b/nf_core/pipelines/params_file.py
@@ -19,7 +19,7 @@
     "of nextflow run with the {pipeline_name} pipeline."
 )
 
-USAGE = "Uncomment lines with a single '#' if you want to pass the parameter " "to the pipeline."
+USAGE = "Uncomment lines with a single '#' if you want to pass the parameter to the pipeline."
 
 H1_SEPERATOR = "## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 H2_SEPERATOR = "## ----------------------------------------------------------------------------"
@@ -107,7 +107,7 @@ def get_pipeline(self) -> Optional[bool]:
         # Prompt for pipeline if not supplied
         if self.pipeline is None:
             launch_type = questionary.select(
-                "Generate parameter file for local pipeline " "or remote GitHub pipeline?",
+                "Generate parameter file for local pipeline or remote GitHub pipeline?",
                 choices=["Remote pipeline", "Local path"],
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()

diff --git a/nf_core/pipelines/rocrate.py b/nf_core/pipelines/rocrate.py
@@ -212,7 +212,7 @@ def set_main_entity(self, main_entity_filename: str):
         else:
             url = self.version
         self.crate.mainEntity.append_to(
-            "url", f"https://nf-co.re/{self.crate.name.replace('nf-core/','')}/{url}/", compact=True
+            "url", f"https://nf-co.re/{self.crate.name.replace('nf-core/', '')}/{url}/", compact=True
         )
         self.crate.mainEntity.append_to("version", self.version, compact=True)
 

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
@@ -770,7 +770,7 @@ def build_schema(self, pipeline_dir, no_prompts, web_only, url):
                     if self.web_schema_build_web_url:
                         log.info(
                             "To save your work, open {}\n"
-                            f"Click the blue 'Finished' button, copy the schema and paste into this file: { self.web_schema_build_web_url, self.schema_filename}"
+                            f"Click the blue 'Finished' button, copy the schema and paste into this file: {self.web_schema_build_web_url, self.schema_filename}"
                         )
                     return False
 

diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
@@ -345,7 +345,7 @@ def create_merge_base_branch(self):
                     if merge_branch_format.match(branch)
                 ]
             )
-            new_branch = f"{self.original_merge_branch}-{max_branch+1}"
+            new_branch = f"{self.original_merge_branch}-{max_branch + 1}"
             log.info(f"Branch already existed: '{self.merge_branch}', creating branch '{new_branch}' instead.")
             self.merge_branch = new_branch
 

diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py
@@ -3,7 +3,7 @@
 from pathlib import Path
 
 import jsonschema.validators
-import yaml
+import ruamel.yaml
 
 import nf_core.components.components_utils
 from nf_core.components.lint import LintExceptionError
@@ -43,7 +43,8 @@ def meta_yml(subworkflow_lint_object, subworkflow, allow_missing: bool = False):
 
     try:
         with open(subworkflow.meta_yml) as fh:
-            meta_yaml = yaml.safe_load(fh)
+            yaml = ruamel.yaml.YAML(typ="safe")
+            meta_yaml = yaml.load(fh)
         subworkflow.passed.append(("meta_yml_exists", "Subworkflow `meta.yml` exists", subworkflow.meta_yml))
     except FileNotFoundError:
         subworkflow.failed.append(("meta_yml_exists", "Subworkflow `meta.yml` does not exist", subworkflow.meta_yml))
@@ -62,7 +63,7 @@ def meta_yml(subworkflow_lint_object, subworkflow, allow_missing: bool = False):
         if len(e.path) > 0:
             hint = f"\nCheck the entry for `{e.path[0]}`."
         if e.message.startswith("None is not of type 'object'") and len(e.path) > 2:
-            hint = f"\nCheck that the child entries of {e.path[0]}.{e.path[2]} are indented correctly."
+            hint = f"\nCheck that the child entries of {str(e.path[0]) + '.' + str(e.path[2])} are indented correctly."
         subworkflow.failed.append(
             (
                 "meta_yml_valid",

diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
@@ -296,15 +296,15 @@ def test_modules_lint_check_url(self):
                 if line.strip():
                     check_container_link_line(mocked_ModuleLint, line, registry="quay.io")
 
-            assert (
-                len(mocked_ModuleLint.passed) == passed
-            ), f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}."
-            assert (
-                len(mocked_ModuleLint.warned) == warned
-            ), f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}."
-            assert (
-                len(mocked_ModuleLint.failed) == failed
-            ), f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}."
+            assert len(mocked_ModuleLint.passed) == passed, (
+                f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}."
+            )
+            assert len(mocked_ModuleLint.warned) == warned, (
+                f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}."
+            )
+            assert len(mocked_ModuleLint.failed) == failed, (
+                f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}."
+            )
 
     def test_modules_lint_update_meta_yml(self):
         """update the meta.yml of a module"""

diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
@@ -158,9 +158,9 @@ def test_template_customisation_all_files_grouping(self):
                 str_path = str((Path(root) / file).relative_to(PIPELINE_TEMPLATE))
                 if str_path not in base_required_files:
                     try:
-                        assert (
-                            str_path in all_skipped_files
-                        ), f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                        assert str_path in all_skipped_files, (
+                            f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                        )
                     except AssertionError:
                         if "/" in str_path:
                             # Check if the parent directory is in the skipped files
@@ -170,6 +170,8 @@ def test_template_customisation_all_files_grouping(self):
                                 if upper_dir in all_skipped_files:
                                     upper_dir_present = True
                                     break
-                            assert upper_dir_present, f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                            assert upper_dir_present, (
+                                f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                            )
                         else:
                             raise