diff --git a/.github/workflows/changelog.py b/.github/workflows/changelog.py
index 27e604a9b9..bf3d267870 100644
--- a/.github/workflows/changelog.py
+++ b/.github/workflows/changelog.py
@@ -135,9 +135,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
     # If the line already contains a link to the PR, don't add it again.
     line = _skip_existing_entry_for_this_pr(line, same_section=False)
 
-    if (
-        line.startswith("## ") and not line.strip() == "# nf-core/tools: Changelog"
-    ):  # Version header, e.g. "## v2.12dev"
+    if line.startswith("## ") and line.strip() != "# nf-core/tools: Changelog":  # Version header, e.g. "## v2.12dev"
         print(f"Found version header: {line.strip()}")
         updated_lines.append(line)
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e8923d7f4..447156fe87 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### General
 
 - Lock file maintenance ([#4044](https://github.com/nf-core/tools/pull/4044))
+- Add more ruff rules (B, PTH) ([#4034](https://github.com/nf-core/tools/pull/4034))
 - Lock file maintenance ([#4045](https://github.com/nf-core/tools/pull/4045))
 - Update actions/stale digest to b5d41d4 ([#4047](https://github.com/nf-core/tools/pull/4047))
 
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index d5f75f5ccf..e39d4a17fe 100644
--- a/docs/api/_src/conf.py
+++ b/docs/api/_src/conf.py
@@ -11,12 +11,12 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import os
 import sys
+from pathlib import Path
 
 import nf_core
 
-sys.path.insert(0, os.path.abspath("../../../nf_core"))
+sys.path.insert(0, str(Path("../../../nf_core").resolve()))
 
 # -- Project information -----------------------------------------------------
 
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 3481d3ef38..61aee67f1a 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -6,6 +6,7 @@
 import sys
 from pathlib import Path
 
+import requests
 import rich
 import rich.console
 import rich.logging
@@ -123,7 +124,7 @@ def run_nf_core():
                     f"[bold bright_yellow]    There is a new version of nf-core/tools available! ({remote_vers})",
                     highlight=False,
                 )
-        except Exception as e:
+        except requests.exceptions.RequestException as e:
             log.debug(f"Could not check latest version: {e}")
         stderr.print("\n")
     # Launch the click cli
@@ -131,7 +132,7 @@ def run_nf_core():
 
 
 @tui(command="interface", help="Launch the nf-core interface")
-@click.group(context_settings=dict(help_option_names=["-h", "--help"]))
+@click.group(context_settings={"help_option_names": ["-h", "--help"]})
 @click.version_option(__version__)
 @click.option(
     "-v",
@@ -249,7 +250,7 @@ def command_pipelines_create(ctx, name, description, author, version, force, out
     is_flag=True,
     default=Path(os.environ.get("GITHUB_REF", "").strip(" '\"")).parent.name in ["master", "main"]
     and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/")
-    and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools",
+    and os.environ.get("GITHUB_REPOSITORY", "") != "nf-core/tools",
     help="Execute additional checks for release-ready workflows.",
 )
 @click.option(
@@ -485,7 +486,7 @@ def command_pipelines_create_params_file(ctx, pipeline, revision, output, force,
     "-o",
     "--params-out",
     type=click.Path(),
-    default=os.path.join(os.getcwd(), "nf-params.json"),
+    default=str(Path.cwd() / "nf-params.json"),
     help="Path to save run parameters file",
 )
 @click.option(
@@ -2220,7 +2221,7 @@ def command_list(ctx, keywords, sort, json, show_archived):
     "-o",
     "--params-out",
     type=click.Path(),
-    default=os.path.join(os.getcwd(), "nf-params.json"),
+    default=str(Path.cwd() / "nf-params.json"),
     help="Path to save run parameters file",
 )
 @click.option(
@@ -2433,7 +2434,7 @@ def command_download(
     is_flag=True,
     default=Path(os.environ.get("GITHUB_REF", "").strip(" '\"")).parent.name in ["master", "main"]
     and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/")
-    and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools",
+    and os.environ.get("GITHUB_REPOSITORY", "") != "nf-core/tools",
     help="Execute additional checks for release-ready workflows.",
 )
 @click.option(
diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index f49d021fee..8d1a4fd9a2 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -1,5 +1,4 @@
 import logging
-import os
 import sys
 from pathlib import Path
 
@@ -448,7 +447,7 @@ def pipelines_schema_docs(schema_path, output, format, force, columns):
     """
     Outputs parameter documentation for a pipeline schema.
     """
-    if not os.path.exists(schema_path):
+    if not schema_path.exists():
         log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.")
         sys.exit(1)
 
diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 375a711c99..473f5e0c83 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -50,7 +50,7 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
         try:
             if self.directory:
-                if self.directory == Path(".") and not nf_dir_req:
+                if self.directory == Path() and not nf_dir_req:
                     self.no_prompts = True
                 self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts)
         except UserWarning:
@@ -69,6 +69,7 @@ def get_local_components(self) -> list[str]:
         Get the local modules/subworkflows in a pipeline
         """
         local_component_dir = Path(self.directory, self.component_type, "local")
+        # TODO: Return list of Path objects instead of strings to avoid unnecessary conversion
         return [
             str(Path(directory).relative_to(local_component_dir))
             for directory, _, files in os.walk(local_component_dir)
@@ -85,6 +86,7 @@ def get_components_clone_modules(self) -> list[str]:
             component_base_path = Path(self.directory, self.default_modules_path)
         elif self.component_type == "subworkflows":
             component_base_path = Path(self.directory, self.default_subworkflows_path)
+        # TODO: Return list of Path objects instead of strings to avoid unnecessary conversion
         return [
             str(Path(directory).relative_to(component_base_path))
             for directory, _, files in os.walk(component_base_path)
@@ -155,6 +157,7 @@ def components_from_repo(self, install_dir: str) -> list[str]:
         if not repo_dir.exists():
             raise LookupError(f"Nothing installed from {install_dir} in pipeline")
 
+        # TODO: Return list of Path objects instead of strings to avoid unnecessary conversion
         return [
             str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files
         ]
@@ -257,6 +260,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                     and self.modules_repo.repo_path is not None
                     and modules_json.modules_json is not None
                 ):
+                    # TODO: Consider if this needs to be a string or if Path object would work
                     modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
                         self.modules_repo.repo_path
                     ][module_name]["patch"] = str(patch_path.relative_to(self.directory.resolve()))
@@ -275,18 +279,15 @@ def check_if_in_include_stmts(self, component_path: str) -> dict[str, list[dict[
         if self.repo_type == "pipeline":
             workflow_files = Path(self.directory, "workflows").glob("*.nf")
             for workflow_file in workflow_files:
-                with open(workflow_file) as fh:
+                with open(workflow_file) as fh, mmap.mmap(fh.fileno(), 0, access=mmap.ACCESS_READ) as s:
                     # Check if component path is in the file using mmap
-                    with mmap.mmap(fh.fileno(), 0, access=mmap.ACCESS_READ) as s:
-                        if s.find(component_path.encode()) != -1:
-                            # If the component path is in the file, check for include statements
-                            for i, line in enumerate(fh):
-                                if line.startswith("include") and component_path in line:
-                                    if str(workflow_file) not in include_stmts:
-                                        include_stmts[str(workflow_file)] = []
-                                    include_stmts[str(workflow_file)].append(
-                                        {"line_number": i + 1, "line": line.rstrip()}
-                                    )
+                    if s.find(component_path.encode()) != -1:
+                        # If the component path is in the file, check for include statements
+                        for i, line in enumerate(fh):
+                            if line.startswith("include") and component_path in line:
+                                if str(workflow_file) not in include_stmts:
+                                    include_stmts[str(workflow_file)] = []
+                                include_stmts[str(workflow_file)].append({"line_number": i + 1, "line": line.rstrip()})
 
             return include_stmts
         else:
diff --git a/nf_core/components/components_completion.py b/nf_core/components/components_completion.py
index 191fa32e21..8abecb4649 100644
--- a/nf_core/components/components_completion.py
+++ b/nf_core/components/components_completion.py
@@ -1,5 +1,6 @@
 import sys
 
+import git
 from click.shell_completion import CompletionItem
 
 from nf_core.modules.list import ModuleList
@@ -24,7 +25,7 @@ def autocomplete_components(ctx, param, incomplete: str, component_type: str, li
         available_components = components_list.modules_repo.get_avail_components(component_type)
 
         return [CompletionItem(comp) for comp in available_components if comp.startswith(incomplete)]
-    except Exception as e:
+    except (git.exc.GitError, LookupError, OSError) as e:
         print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr)
         return []
 
diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py
index c92480a50d..b028b55626 100644
--- a/nf_core/components/components_differ.py
+++ b/nf_core/components/components_differ.py
@@ -187,7 +187,7 @@ def write_diff_file(
                 elif diff_status == ComponentsDiffer.DiffEnum.REMOVED:
                     # The file was removed between the commits
                     fh.write(f"'{Path(dsp_from_dir, file)}' was removed\n")
-                elif limit_output and not file.suffix == ".nf":
+                elif limit_output and file.suffix != ".nf":
                     # Skip printing the diff for files other than main.nf
                     fh.write(f"Changes in '{Path(component, file)}' but not shown\n")
                 else:
@@ -286,7 +286,7 @@ def print_diff(
             elif diff_status == ComponentsDiffer.DiffEnum.REMOVED:
                 # The file was removed between the commits
                 log.info(f"'{Path(dsp_from_dir, file)}' was removed")
-            elif limit_output and not file.suffix == ".nf":
+            elif limit_output and file.suffix != ".nf":
                 # Skip printing the diff for files other than main.nf
                 log.info(f"Changes in '{Path(component, file)}' but not shown")
             else:
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 081be82684..925049b911 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -247,10 +247,10 @@ def get_channel_info_from_biotools(
     inputs = {}
     outputs = {}
 
-    def _iterate_input_output(type) -> DictWithStrAndTuple:
+    def _iterate_input_output(funct_data, type) -> DictWithStrAndTuple:
         type_info = {}
-        if type in funct:
-            for element in funct[type]:
+        if type in funct_data:
+            for element in funct_data[type]:
                 if "data" in element:
                     element_name = "_".join(element["data"]["term"].lower().split(" "))
                     uris = [element["data"]["uri"]]
@@ -272,8 +272,8 @@ def _iterate_input_output(type) -> DictWithStrAndTuple:
             if "function" in tool:
                 # Parse all tool functions
                 for funct in tool["function"]:
-                    inputs.update(_iterate_input_output("input"))
-                    outputs.update(_iterate_input_output("output"))
+                    inputs.update(_iterate_input_output(funct, "input"))
+                    outputs.update(_iterate_input_output(funct, "output"))
             return inputs, outputs
 
     # If the tool name was not found in the response
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 9fc973f77d..b30f85b0c1 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -2,7 +2,6 @@
 The ComponentCreate class handles generating of module and subworkflow templates
 """
 
-import glob
 import json
 import logging
 import re
@@ -38,7 +37,7 @@ class ComponentCreate(ComponentCommand):
     def __init__(
         self,
         component_type: str,
-        directory: Path = Path("."),
+        directory: Path = Path(),
         component: str = "",
         author: str | None = None,
         process_label: str | None = None,
@@ -403,7 +402,7 @@ def _get_component_dirs(self) -> dict[str, Path]:
                 )
 
             # If no subtool, check that there isn't already a tool/subtool
-            tool_glob = glob.glob(f"{Path(self.directory, self.component_type, self.org, self.component)}/*/main.nf")
+            tool_glob = list(Path(self.directory, self.component_type, self.org, self.component).glob("*/main.nf"))
             if not self.subtool and tool_glob and not self.migrate_pytest:
                 raise UserWarning(
                     f"Module subtool '{tool_glob[0]}' exists already, cannot make tool '{self.component_name}'"
@@ -427,7 +426,7 @@ def _get_username(self):
         try:
             gh_auth_user = json.loads(subprocess.check_output(["gh", "api", "/user"], stderr=subprocess.DEVNULL))
             author_default = f"@{gh_auth_user['login']}"
-        except Exception as e:
+        except (subprocess.CalledProcessError, FileNotFoundError) as e:
             log.debug(f"Could not find GitHub username using 'gh' cli command: [red]{e}")
 
         # Regex to valid GitHub username: https://github.com/shinnn/github-username-regex
@@ -626,7 +625,7 @@ def generate_meta_yml_file(self) -> None:
 
             if hasattr(self, "outputs") and len(self.outputs) > 0:
                 outputs_dict: dict[str, list | dict] = {}
-                for i, (output_name, ontologies) in enumerate(self.outputs.items()):
+                for _i, (output_name, ontologies) in enumerate(self.outputs.items()):
                     channel_contents: list[list[dict] | dict] = []
                     if self.has_meta:
                         channel_contents.append(
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index 69a30929e0..fa47333945 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -1,5 +1,4 @@
 import logging
-import os
 from pathlib import Path
 
 import questionary
@@ -200,9 +199,9 @@ def get_local_yaml(self) -> dict | None:
             log.debug(f"{self.component_type[:-1].title()} '{self.component}' meta.yml not found locally")
         else:
             component_base_path = Path(self.directory, self.component_type, self.org)
-            if self.component in os.listdir(component_base_path):
-                comp_dir = Path(component_base_path, self.component)
-                meta_fn = Path(comp_dir, "meta.yml")
+            comp_dir = component_base_path / self.component
+            if comp_dir.is_dir():
+                meta_fn = comp_dir / "meta.yml"
                 if meta_fn.exists():
                     log.debug(f"Found local file: {meta_fn}")
                     with open(meta_fn) as fh:
@@ -375,7 +374,7 @@ def generate_component_info_help(self):
             )
             if self.component_type == "subworkflows":
                 subworkflow_config = Path(install_folder, self.component, "nextflow.config").relative_to(self.directory)
-                if os.path.isfile(subworkflow_config):
+                if subworkflow_config.exists():
                     renderables.append(
                         Text.from_markup("\n [blue]Add the following config statement to use this subworkflow:")
                     )
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index 61e088ef16..c5c37d5236 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -1,5 +1,4 @@
 import logging
-import os
 from pathlib import Path
 
 import questionary
@@ -248,10 +247,11 @@ def collect_and_verify_name(
 
             raise ValueError
 
-        if self.current_remote.remote_url == modules_repo.remote_url:
-            if not modules_repo.component_exists(component, self.component_type, commit=self.current_sha):
-                warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})"
-                log.warning(warn_msg)
+        if self.current_remote.remote_url == modules_repo.remote_url and not modules_repo.component_exists(
+            component, self.component_type, commit=self.current_sha
+        ):
+            warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})"
+            log.warning(warn_msg)
 
         return component
 
@@ -263,7 +263,7 @@ def check_component_installed(self, component, current_version, component_dir, m
             True: if the component is not installed
             False: if the component is installed
         """
-        if (current_version is not None and os.path.exists(component_dir)) and not force:
+        if (current_version is not None and component_dir.exists()) and not force:
             # make sure included components are also installed
             if self.component_type == "subworkflows":
                 self.install_included_components(component_dir)
@@ -343,9 +343,9 @@ def check_alternate_remotes(self, modules_json):
             False: if problematic components are not found
         """
         modules_json.load()
-        for repo_url, repo_content in modules_json.modules_json.get("repos", dict()).items():
+        for repo_url, repo_content in modules_json.modules_json.get("repos", {}).items():
             for component_type in repo_content:
-                for directory in repo_content.get(component_type, dict()).keys():
+                for directory in repo_content.get(component_type, {}):
                     if directory == self.modules_repo.repo_path and repo_url != self.modules_repo.remote_url:
                         return True
         return False
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index 63c651a401..efcdc11d90 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -259,7 +259,7 @@ def _print_results(self, show_passed=False, sort_by="test", plain_text=False):
             try:
                 for lint_result in tests:
                     max_name_len = max(len(lint_result.component_name), max_name_len)
-            except Exception:
+            except (AttributeError, TypeError):
                 pass
 
         # Helper function to format test links nicely
@@ -285,8 +285,9 @@ def format_result(test_results: list[LintResult], table: Table) -> Table:
                     module_name = lint_result.component_name
 
                 # Make the filename clickable to open in VSCode
-                file_path = os.path.relpath(lint_result.file_path, self.directory)
-                file_path_link = f"[link=vscode://file/{os.path.abspath(file_path)}]{file_path}[/link]"
+                file_path_obj = Path(lint_result.file_path)
+                file_path_rel = file_path_obj.relative_to(self.directory)
+                file_path_link = f"[link=vscode://file/{file_path_obj.resolve()}]{file_path_rel}[/link]"
 
                 # Add link to the test documentation
                 tools_version = __version__
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index fa468be970..37744bf291 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -295,11 +295,8 @@ def get_inputs_from_main_nf(self) -> None:
                 return
             # get all lines between "take" and "main" or "emit"
             input_data = data.split("take:")[1].split("main:")[0].split("emit:")[0]
-            for line in input_data.split("\n"):
-                try:
-                    inputs.append(line.split()[0])
-                except IndexError:
-                    pass  # Empty lines
+            # Extract first word from non-empty lines
+            inputs = [line.split()[0] for line in input_data.split("\n") if line.split()]
             log.debug(f"Found {len(inputs)} inputs in {self.main_nf}")
             self.inputs = inputs
 
@@ -341,12 +338,8 @@ def get_outputs_from_main_nf(self):
                 log.debug(f"Could not find any outputs in {self.main_nf}")
                 return outputs
             output_data = data.split("emit:")[1].split("}")[0]
-            for line in output_data.split("\n"):
-                try:
-                    outputs.append(line.split("=")[0].split()[0])
-                except IndexError:
-                    # Empty lines
-                    pass
+            # Extract first word before '=' from non-empty lines
+            outputs = [parts[0] for line in output_data.split("\n") if (parts := line.split("=")[0].split())]
             log.debug(f"Found {len(outputs)} outputs in {self.main_nf}")
             self.outputs = outputs
 
diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py
index 59ec7a381b..d9398ead17 100644
--- a/nf_core/components/patch.py
+++ b/nf_core/components/patch.py
@@ -1,5 +1,4 @@
 import logging
-import os
 import shutil
 import tempfile
 from pathlib import Path
@@ -99,7 +98,7 @@ def patch(self, component=None):
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
             if remove:
-                os.remove(patch_path)
+                patch_path.unlink()
             else:
                 return
 
@@ -126,7 +125,9 @@ def patch(self, component=None):
             )
             log.debug(f"Patch file wrote to a temporary directory {patch_temp_path}")
         except UserWarning:
-            raise UserWarning(f"{self.component_type[:-1]} '{component_fullname}' is unchanged. No patch to compute")
+            raise UserWarning(
+                f"{self.component_type[:-1]} '{component_fullname}' is unchanged. No patch to compute"
+            ) from None
 
         # Write changes to modules.json
         self.modules_json.add_patch_entry(
@@ -213,9 +214,9 @@ def remove(self, component):
         try:
             for file in Path(temp_component_dir).glob("*"):
                 file.rename(component_path.joinpath(file.name))
-            os.rmdir(temp_component_dir)
+            Path(temp_component_dir).rmdir()
         except Exception as err:
-            raise UserWarning(f"There was a problem reverting the patched file: {err}")
+            raise UserWarning(f"There was a problem reverting the patched file: {err}") from err
 
         log.info(f"Patch for {component} reverted!")
         # Remove patch file if we could revert the patch
diff --git a/nf_core/components/remove.py b/nf_core/components/remove.py
index afe12c88a9..5d42690779 100644
--- a/nf_core/components/remove.py
+++ b/nf_core/components/remove.py
@@ -129,26 +129,23 @@ def remove(self, component, repo_url=None, repo_path=None, removed_by=None, remo
                         )
                     )
                 # ask the user if they still want to remove the component, add it back otherwise
-                if not force:
-                    if not questionary.confirm(
+                if not force and (
+                    not questionary.confirm(
                         f"Do you still want to remove the {self.component_type[:-1]} '{component}'?",
                         style=nf_core.utils.nfcore_question_style,
-                    ).unsafe_ask():
-                        # add the component back to modules.json
-                        if not ComponentInstall(self.directory, self.component_type, force=True).install(
-                            component, silent=True
-                        ):
-                            log.warning(
-                                f"Could not install the {self.component_type[:-1]} '{component}', please install it manually with 'nf-core {self.component_type} install  {component}'."
-                            )
-                        removed_components.append(component)
-                        return removed
+                    ).unsafe_ask()
+                ):
+                    # add the component back to modules.json
+                    if not ComponentInstall(self.directory, self.component_type, force=True).install(
+                        component, silent=True
+                    ):
+                        log.warning(
+                            f"Could not install the {self.component_type[:-1]} '{component}', please install it manually with 'nf-core {self.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.directory, removed_component_dir)) or removed
-                else False
-            )
+            removed = bool(self.clear_component_dir(component, Path(self.directory, removed_component_dir)) or removed)
             removed_components.append(component)
 
         if removed:
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index fcdb005e9f..bf85f21cfa 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -1,5 +1,4 @@
 import logging
-import os
 import shutil
 import tempfile
 from pathlib import Path
@@ -190,13 +189,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
             else:
                 version = modules_repo.get_latest_component_version(component, self.component_type)
 
-            if current_version is not None and not self.force:
-                if current_version == version:
-                    if self.sha or self.prompt:
-                        log.info(f"'{component_fullname}' is already installed at {version}")
-                    else:
-                        log.info(f"'{component_fullname}' is already up to date")
-                    continue
+            if current_version is not None and not self.force and current_version == version:
+                if self.sha or self.prompt:
+                    log.info(f"'{component_fullname}' is already installed at {version}")
+                else:
+                    log.info(f"'{component_fullname}' is already up to date")
+                continue
 
             # Download component files
             if not self.install_component_files(component, version, modules_repo, str(install_tmp_dir)):
@@ -300,21 +298,20 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 updated.append(component)
                 recursive_update = True
                 modules_to_update, subworkflows_to_update = self.get_components_to_update(component)
-                if not silent and len(modules_to_update + subworkflows_to_update) > 0:
-                    if not self.update_all:
-                        log.warning(
-                            f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
-                            "It is advised to keep all your modules and subworkflows up to date.\n"
-                            "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
-                        )
-                        if self.update_deps:
-                            recursive_update = True
-                        else:
-                            recursive_update = questionary.confirm(
-                                "Would you like to continue updating all modules and subworkflows?",
-                                default=True,
-                                style=nf_core.utils.nfcore_question_style,
-                            ).unsafe_ask()
+                if not silent and not self.update_all and len(modules_to_update + subworkflows_to_update) > 0:
+                    log.warning(
+                        f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
+                        "It is advised to keep all your modules and subworkflows up to date.\n"
+                        "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
+                    )
+                    if self.update_deps:
+                        recursive_update = True
+                    else:
+                        recursive_update = questionary.confirm(
+                            "Would you like to continue updating all modules and subworkflows?",
+                            default=True,
+                            style=nf_core.utils.nfcore_question_style,
+                        ).unsafe_ask()
                 if recursive_update and len(modules_to_update + subworkflows_to_update) > 0:
                     # Update linked components
                     self.update_linked_components(modules_to_update, subworkflows_to_update, updated)
@@ -383,8 +380,8 @@ def get_single_component_info(self, component):
         # Get component installation directory
         try:
             install_dir = [dir for dir, m in components if component == m][0]
-        except IndexError:
-            raise UserWarning(f"{self.component_type[:-1].title()} '{component}' not found in 'modules.json'.")
+        except IndexError as e:
+            raise UserWarning(f"{self.component_type[:-1].title()} '{component}' not found in 'modules.json'.") from e
 
         # Check if component is installed before trying to update
         if component not in choices:
@@ -403,12 +400,10 @@ def get_single_component_info(self, component):
         config_entry = None
         if self.update_config is not None:
             if any(
-                [
-                    entry.count("/") == 1
-                    and (entry.endswith("modules") or entry.endswith("subworkflows"))
-                    and not (entry.endswith(".git") or entry.endswith(".git/"))
-                    for entry in self.update_config.keys()
-                ]
+                entry.count("/") == 1
+                and (entry.endswith("modules") or entry.endswith("subworkflows"))
+                and not (entry.endswith(".git") or entry.endswith(".git/"))
+                for entry in self.update_config
             ):
                 raise UserWarning(
                     "Your '.nf-core.yml' file format is outdated. "
@@ -423,7 +418,7 @@ def get_single_component_info(self, component):
                 config_entry = self.update_config[self.modules_repo.remote_url][install_dir].get(component)
         if config_entry is not None and config_entry is not True:
             if config_entry is False:
-                log.warn(
+                log.warning(
                     f"{self.component_type[:-1].title()}'s update entry in '.nf-core.yml' for '{component}' is set to False"
                 )
                 return (self.modules_repo, None, None, None)
@@ -517,7 +512,7 @@ def get_all_components_info(self, branch=None):
                         ]
             elif isinstance(self.update_config, dict) and isinstance(self.update_config[repo_name], dict):
                 # If it is a dict, then there are entries for individual components or component directories
-                for component_dir in set([dir for dir, _ in components]):
+                for component_dir in {dir for dir, _ in components}:
                     if isinstance(self.update_config[repo_name][component_dir], str):
                         # If a string is given it is the commit SHA to which we should update to
                         custom_sha = self.update_config[repo_name][component_dir]
@@ -547,7 +542,7 @@ def get_all_components_info(self, branch=None):
                         if self.sha is not None:
                             overridden_repos.append(repo_name)
                     elif self.update_config[repo_name][component_dir] is False:
-                        for directory, component in components:
+                        for directory, _component in components:
                             if directory == component_dir:
                                 skipped_components.append(f"{component_dir}/{components}")
                     elif isinstance(self.update_config[repo_name][component_dir], dict):
@@ -664,7 +659,7 @@ def get_all_components_info(self, branch=None):
         # Loop through components_info and create on ModulesRepo object per remote and branch
         repos_and_branches = {}
         for repo_name, repo_content in components_info.items():
-            for component_dir, comps in repo_content.items():
+            for _component_dir, comps in repo_content.items():
                 for comp, sha, comp_branch in comps:
                     if branch is not None:
                         comp_branch = branch
@@ -741,7 +736,7 @@ def setup_diff_file(self, check_diff_exist=True):
         # Check if filename already exists (questionary or cli)
         while self.save_diff_fn.exists():
             if questionary.confirm(f"'{self.save_diff_fn}' exists. Remove file?").unsafe_ask():
-                os.remove(self.save_diff_fn)
+                self.save_diff_fn.unlink()
                 break
             self.save_diff_fn = questionary.path(
                 "Enter a new filename: ",
@@ -768,6 +763,7 @@ def move_files_from_tmp_dir(self, component: str, install_folder: str, repo_path
         if pipeline_path.exists():
             pipeline_files = [f.name for f in pipeline_path.iterdir() if f.is_file()]
             # check if any *.config file exists in the pipeline
+            # TODO: Use f.suffix == ".config" instead of str(f).endswith(".config")
             config_files = [f for f in pipeline_files if str(f).endswith(".config")]
             for config_file in config_files:
                 log.debug(f"Moving '{component}/{config_file}' to updated component")
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index d4f325376b..b5787c5941 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -3,6 +3,7 @@
 or for a single module
 """
 
+import contextlib
 import logging
 import os
 import re
@@ -313,10 +314,8 @@ def _print_results(self) -> None:
         # Find maximum module name length
         max_mod_name_len = 40
         for m in [self.up_to_date, self.updated, self.failed]:
-            try:
+            with contextlib.suppress(Exception):
                 max_mod_name_len = max(len(m[2]), max_mod_name_len)
-            except Exception:
-                pass
 
         def format_result(module_updates: list[tuple[str, str]], table: Table) -> Table:
             """
@@ -328,10 +327,7 @@ def format_result(module_updates: list[tuple[str, str]], table: Table) -> Table:
             row_style = None
             for module_update in module_updates:
                 if last_modname and module_update[1] != last_modname:
-                    if row_style:
-                        row_style = None
-                    else:
-                        row_style = "magenta"
+                    row_style = None if row_style else "magenta"
                 last_modname = module_update[1]
                 table.add_row(
                     Markdown(f"{module_update[1]}"),
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index d4bc1ef974..3fe02551ed 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -375,7 +375,7 @@ def _sort_meta_yml(meta_yml: dict) -> dict:
                 schema = self.load_meta_schema()
                 schema_keys = list(schema["properties"].keys())
             except (LintExceptionError, KeyError) as e:
-                raise UserWarning("Failed to load meta schema", e)
+                raise UserWarning("Failed to load meta schema", e) from e
 
             result: dict = {}
 
@@ -385,7 +385,7 @@ def _sort_meta_yml(meta_yml: dict) -> dict:
                     result[key] = meta_yml[key]
 
             # Then add any keys that aren't in the schema (to preserve custom keys)
-            for key in meta_yml.keys():
+            for key in meta_yml:
                 if key not in result:
                     result[key] = meta_yml[key]
 
@@ -413,7 +413,7 @@ def _sort_meta_yml(meta_yml: dict) -> dict:
                 versions_entry = template_meta.get("topics", {}).get("versions", [[]])[0]
                 if len(versions_entry) == 3:
                     topic_metadata = [next(iter(item.values())) for item in versions_entry]
-        except Exception as e:
+        except (OSError, yaml.YAMLError, IndexError, StopIteration) as e:
             log.debug(f"Could not load topic template metadata: {e}")
 
         def _populate_channel_elements(io_type, correct_value, meta_value, mod_io_data, meta_yml_io, check_exists=True):
@@ -488,7 +488,7 @@ def _process_element(element, index, is_output=False):
                 # Only update structure when it differs from main.nf
                 corrected_data = meta_yml_io.copy() if meta_yml_io else mod_io_data.copy()
 
-                for ch_name in mod_io_data.keys():
+                for ch_name in mod_io_data:
                     # Ensure channel exists in corrected_data
                     if ch_name not in corrected_data:
                         corrected_data[ch_name] = []
@@ -603,7 +603,7 @@ def _add_edam_ontologies(section, edam_formats, desc):
                         if extension in edam_formats:
                             expected_ontologies.append((edam_formats[extension][0], extension))
                 # remove duplicated entries
-                expected_ontologies = list({k: v for k, v in expected_ontologies}.items())
+                expected_ontologies = list(dict(expected_ontologies).items())
             if "ontologies" in section:
                 for ontology in section["ontologies"]:
                     try:
@@ -639,7 +639,7 @@ def _add_edam_ontologies(section, edam_formats, desc):
                     )
 
         if "output" in meta_yml:
-            for ch_name in corrected_meta_yml["output"].keys():
+            for ch_name in corrected_meta_yml["output"]:
                 ch_content = corrected_meta_yml["output"][ch_name][0]
                 if isinstance(ch_content, list):
                     for i, element in enumerate(ch_content):
@@ -667,7 +667,7 @@ def _add_edam_ontologies(section, edam_formats, desc):
         # Create YAML anchors for versions_* keys in output that match "versions" in topics
         # Since we now populate metadata for both output and topics, set up anchors to reference output from topics
         if "output" in corrected_meta_yml and "topics" in corrected_meta_yml:
-            versions_keys = [key for key in corrected_meta_yml["output"].keys() if key.startswith("versions_")]
+            versions_keys = [key for key in corrected_meta_yml["output"] if key.startswith("versions_")]
 
             if versions_keys and "versions" in corrected_meta_yml["topics"]:
                 # Set topics["versions"] to reference output versions (now with populated metadata)
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index fcd08b3b46..3f7251b634 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -65,15 +65,12 @@ def main_nf(
             with open(module.main_nf) as fh:
                 lines = fh.readlines()
             module.passed.append(("main_nf", "main_nf_exists", "Module file exists", module.main_nf))
-        except FileNotFoundError:
+        except FileNotFoundError as e:
             module.failed.append(("main_nf", "main_nf_exists", "Module file does not exist", module.main_nf))
-            raise FileNotFoundError(f"Module file does not exist: {module.main_nf}")
+            raise FileNotFoundError(f"Module file does not exist: {module.main_nf}") from e
 
     deprecated_i = ["initOptions", "saveFiles", "getSoftwareName", "getProcessName", "publishDir"]
-    if len(lines) > 0:
-        lines_j = "\n".join(lines)
-    else:
-        lines_j = ""
+    lines_j = "\n".join(lines) if len(lines) > 0 else ""
 
     for i in deprecated_i:
         if i in lines_j:
@@ -191,28 +188,27 @@ def main_nf(
             )
 
     # Check whether 'meta' is emitted when given as input
-    if inputs:
-        if "meta" in inputs:
-            module.has_meta = True
-            if emits:
-                if "meta" in emits:
-                    module.passed.append(
-                        (
-                            "main_nf",
-                            "main_nf_meta_output",
-                            "'meta' map emitted in output channel(s)",
-                            module.main_nf,
-                        )
+    if inputs and "meta" in inputs:
+        module.has_meta = True
+        if emits:
+            if "meta" in emits:
+                module.passed.append(
+                    (
+                        "main_nf",
+                        "main_nf_meta_output",
+                        "'meta' map emitted in output channel(s)",
+                        module.main_nf,
                     )
-                else:
-                    module.failed.append(
-                        (
-                            "main_nf",
-                            "main_nf_meta_output",
-                            "'meta' map not emitted in output channel(s)",
-                            module.main_nf,
-                        )
+                )
+            else:
+                module.failed.append(
+                    (
+                        "main_nf",
+                        "main_nf_meta_output",
+                        "'meta' map not emitted in output channel(s)",
+                        module.main_nf,
                     )
+                )
 
     # Check that a software version is emitted
     if topics:
@@ -327,7 +323,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     check_process_labels(self, lines)
 
     # Deprecated enable_conda
-    for i, raw_line in enumerate(lines):
+    for _i, raw_line in enumerate(lines):
         url = None
         line = raw_line.strip(" \n'\"}:?")
 
@@ -408,7 +404,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
         if url is None:
             continue
         try:
-            container_url = "https://" + urlunparse(url) if not url.scheme == "https" else urlunparse(url)
+            container_url = "https://" + urlunparse(url) if url.scheme != "https" else urlunparse(url)
             log.debug(f"Trying to connect to URL: {container_url}")
             response = requests.head(
                 container_url,
@@ -416,7 +412,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
                 allow_redirects=True,
             )
             log.debug(
-                f"Connected to URL: {'https://' + urlunparse(url) if not url.scheme == 'https' else urlunparse(url)}, "
+                f"Connected to URL: {'https://' + urlunparse(url) if url.scheme != 'https' else urlunparse(url)}, "
                 f"status_code: {response.status_code}"
             )
         except (requests.exceptions.RequestException, sqlite3.InterfaceError) as e:
@@ -615,7 +611,7 @@ def check_container_link_line(self, raw_line, registry):
             (
                 "main_nf",
                 "container_links",
-                f"Too many double quotes found when specifying container: {line.lstrip('container ')}",
+                f"Too many double quotes found when specifying container: {line.removeprefix('container ')}",
                 self.main_nf,
             )
         )
@@ -624,7 +620,7 @@ def check_container_link_line(self, raw_line, registry):
             (
                 "main_nf",
                 "container_links",
-                f"Correct number of double quotes found when specifying container: {line.lstrip('container ')}",
+                f"Correct number of double quotes found when specifying container: {line.removeprefix('container ')}",
                 self.main_nf,
             )
         )
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index c663b2defa..6f2d249a0b 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -336,7 +336,7 @@ def obtain_outputs(_, outputs: dict | list) -> dict | list:
     if old_structure:
         outputs = {k: v for d in outputs for k, v in d.items()}
     assert isinstance(outputs, dict)  # mypy
-    for channel_name in outputs.keys():
+    for channel_name in outputs:
         output_channel = outputs[channel_name]
         channel_elements: list = []
         for element in output_channel:
@@ -367,7 +367,7 @@ def obtain_topics(_, topics: dict) -> dict:
         formatted_topics (dict): A dictionary containing the topics and their elements obtained from main.nf or meta.yml files.
     """
     formatted_topics: dict = {}
-    for name in topics.keys():
+    for name in topics:
         content = topics[name]
         t_elements: list = []
         for element in content:
diff --git a/nf_core/modules/lint/module_deprecations.py b/nf_core/modules/lint/module_deprecations.py
index dc232a81c3..cdf2c636f3 100644
--- a/nf_core/modules/lint/module_deprecations.py
+++ b/nf_core/modules/lint/module_deprecations.py
@@ -1,5 +1,4 @@
 import logging
-import os
 
 log = logging.getLogger(__name__)
 
@@ -9,7 +8,7 @@ def module_deprecations(_, module):
     Check that the modules are up to the latest nf-core standard
     """
     module.wf_path = module.component_dir
-    if "functions.nf" in os.listdir(module.component_dir):
+    if (module.component_dir / "functions.nf").exists():
         module.failed.append(
             (
                 "module_deprecations",
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 16939a767d..114b87f892 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -120,7 +120,7 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False):
                     with open(snap_file) as snap_fh:
                         try:
                             snap_content = json.load(snap_fh)
-                            for test_name in snap_content.keys():
+                            for test_name in snap_content:
                                 if "d41d8cd98f00b204e9800998ecf8427e" in str(snap_content[test_name]):
                                     if "stub" not in test_name:
                                         module.failed.append(
diff --git a/nf_core/modules/lint/module_todos.py b/nf_core/modules/lint/module_todos.py
index ce8ec34976..15c4939f9d 100644
--- a/nf_core/modules/lint/module_todos.py
+++ b/nf_core/modules/lint/module_todos.py
@@ -36,5 +36,5 @@ def module_todos(_, module):
     mod_results = pipeline_todos(None, root_dir=module.component_dir)
     for i, warning in enumerate(mod_results["warned"]):
         module.warned.append(("module_todos", "module_todo", warning, mod_results["file_paths"][i]))
-    for i, passed in enumerate(mod_results["passed"]):
+    for _i, passed in enumerate(mod_results["passed"]):
         module.passed.append(("module_todos", "module_todo", passed, module.component_dir))
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 4c757f7b8a..348b852119 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -165,7 +165,7 @@ def get_pipeline_module_repositories(
         if repos is None:
             repos = {}
         # Check if there are any nf-core modules installed
-        if (directory / NF_CORE_MODULES_NAME).exists() and NF_CORE_MODULES_REMOTE not in repos.keys():
+        if (directory / NF_CORE_MODULES_NAME).exists() and NF_CORE_MODULES_REMOTE not in repos:
             repos[NF_CORE_MODULES_REMOTE] = {}
         # The function might rename some directories, keep track of them
         renamed_dirs = {}
@@ -253,7 +253,7 @@ def dir_tree_uncovered(self, components_directory, repos):
             repos_at_level = {Path(*repo.parts[:depth]): len(repo.parts) for repo in repos}
             for directory in fifo:
                 rel_dir = directory.relative_to(components_directory)
-                if rel_dir in repos_at_level.keys():
+                if rel_dir in repos_at_level:
                     # Go the next depth if this directory is not one of the repos
                     if depth < repos_at_level[rel_dir]:
                         temp_queue.extend(directory.iterdir())
@@ -449,6 +449,7 @@ def unsynced_components(self) -> tuple[list[str], list[str], dict]:
         # Add all modules from modules.json to missing_installation
         missing_installation = copy.deepcopy(self.modules_json["repos"])
         # Obtain the path of all installed modules
+        # TODO: Use Path.parts instead of str().startswith() to avoid unnecessary string conversion
         module_dirs = [
             Path(dir_name).relative_to(self.modules_dir)
             for dir_name, _, file_names in os.walk(self.modules_dir)
@@ -457,6 +458,7 @@ def unsynced_components(self) -> tuple[list[str], list[str], dict]:
         untracked_dirs_modules, missing_installation = self.parse_dirs(module_dirs, missing_installation, "modules")
 
         # Obtain the path of all installed subworkflows
+        # TODO: Use Path.parts instead of str().startswith() to avoid unnecessary string conversion
         subworkflow_dirs = [
             Path(dir_name).relative_to(self.subworkflows_dir)
             for dir_name, _, file_names in os.walk(self.subworkflows_dir)
@@ -492,12 +494,14 @@ def parse_dirs(self, dirs: list[Path], missing_installation: dict, component_typ
             git_url = ""
 
             for repo in missing_installation:
-                if component_type in missing_installation[repo]:
-                    if install_dir in missing_installation[repo][component_type]:
-                        if component in missing_installation[repo][component_type][install_dir]:
-                            component_in_file = True
-                            git_url = repo
-                            break
+                if (
+                    component_type in missing_installation[repo]
+                    and install_dir in missing_installation[repo][component_type]
+                    and component in missing_installation[repo][component_type][install_dir]
+                ):
+                    component_in_file = True
+                    git_url = repo
+                    break
             if not component_in_file:
                 # If it is not, add it to the list of missing components
                 untracked_dirs.append(component)
@@ -618,7 +622,7 @@ def check_up_to_date(self):
             for _, repo_entry in self.modules_json.get("repos", {}).items():
                 for component_type in ["modules", "subworkflows"]:
                     if component_type in repo_entry:
-                        for install_dir, install_dir_entry in repo_entry[component_type].items():
+                        for _install_dir, install_dir_entry in repo_entry[component_type].items():
                             for _, component in install_dir_entry.items():
                                 if "installed_by" in component and isinstance(component["installed_by"], str):
                                     log.debug(f"Updating {component} in modules.json")
@@ -640,12 +644,10 @@ def check_up_to_date(self):
         # we try to reinstall them
         if len(missing_installation) > 0:
             if "subworkflows" in [
-                c_type for _, repo_content in missing_installation.items() for c_type in repo_content.keys()
+                c_type for _, repo_content in missing_installation.items() for c_type in repo_content
             ]:
                 self.resolve_missing_installation(missing_installation, "subworkflows")
-            if "modules" in [
-                c_type for _, repo_content in missing_installation.items() for c_type in repo_content.keys()
-            ]:
+            if "modules" in [c_type for _, repo_content in missing_installation.items() for c_type in repo_content]:
                 self.resolve_missing_installation(missing_installation, "modules")
 
         # If some modules/subworkflows didn't have an entry in the 'modules.json' file
@@ -697,10 +699,10 @@ def load(self) -> None:
                 try:
                     self.modules_json = json.load(fh)
                 except json.JSONDecodeError as e:
-                    raise UserWarning(f"Unable to load JSON file '{self.modules_json_path}' due to error {e}")
+                    raise UserWarning(f"Unable to load JSON file '{self.modules_json_path}' due to error {e}") from e
 
-        except FileNotFoundError:
-            raise UserWarning("File 'modules.json' is missing")
+        except FileNotFoundError as e:
+            raise UserWarning("File 'modules.json' is missing") from e
 
     def update(
         self,
@@ -889,7 +891,7 @@ def try_apply_patch_reverse(self, component_type, component, repo_name, patch_re
         except LookupError as e:
             raise LookupError(
                 f"Failed to apply patch in reverse for {component_type[:-1]} '{component_fullname}' due to: {e}"
-            )
+            ) from e
 
         # Write the patched files to a temporary directory
         log.debug("Writing patched files to tmpdir")
@@ -1061,7 +1063,7 @@ def get_dependent_components(
         component_types = ["modules"] if component_type == "modules" else ["modules", "subworkflows"]
         # Find all components that have an entry of install by of  a given component, recursively call this function for subworkflows
         for type in component_types:
-            for repo_url in self.modules_json["repos"].keys():
+            for repo_url in self.modules_json["repos"]:
                 modules_repo = ModulesRepo(repo_url)
                 install_dir = modules_repo.repo_path
                 try:
@@ -1189,7 +1191,7 @@ def resolve_missing_from_modules_json(self, missing_from_modules_json, component
             )
         assert self.modules_json is not None  # mypy
         # Get the remotes we are missing
-        tracked_repos = {repo_url: (repo_entry) for repo_url, repo_entry in self.modules_json["repos"].items()}
+        tracked_repos = dict(self.modules_json["repos"].items())
         repos, _ = self.get_pipeline_module_repositories(component_type, self.modules_dir, tracked_repos)
 
         # Get tuples of components that miss installation and their install directory
@@ -1204,10 +1206,11 @@ def components_with_repos():
                         modules_repo.repo_path,
                     )
                     for dir_name, _, _ in os.walk(repo_url_path):
-                        if component_type == "modules":
-                            if len(Path(directory).parts) > 1:  # The module name is TOOL/SUBTOOL
-                                paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
-                                pass
+                        if (
+                            component_type == "modules" and len(Path(directory).parts) > 1
+                        ):  # The module name is TOOL/SUBTOOL
+                            paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
+                            pass
                         paths_in_directory.append(Path(dir_name).parts[-1])
                     if directory in paths_in_directory:
                         yield (modules_repo.repo_path, directory)
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index ec310c0001..3465414a13 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -61,8 +61,8 @@ def __init__(
             raise UserWarning(f"Could not find a configuration file in {self.local_repo_dir}")
         try:
             self.repo_path = repo_config.org_path
-        except KeyError:
-            raise UserWarning(f"'org_path' key not present in {config_fn.name}")
+        except KeyError as e:
+            raise UserWarning(f"'org_path' key not present in {config_fn.name}") from e
 
         # Verify that the repo seems to be correctly configured
         if self.repo_path != NF_CORE_MODULES_NAME or self.branch:
@@ -94,7 +94,7 @@ def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
         """
         self.local_repo_dir = Path(NFCORE_DIR if not in_cache else NFCORE_CACHE_DIR, self.fullname)
         try:
-            if not os.path.exists(self.local_repo_dir):
+            if not self.local_repo_dir.exists():
                 try:
                     pbar = rich.progress.Progress(
                         "[bold blue]{task.description}",
@@ -110,8 +110,8 @@ def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
                             progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"),
                         )
                     ModulesRepo.update_local_repo_status(self.fullname, True)
-                except GitCommandError:
-                    raise LookupError(f"Failed to clone from the remote: `{remote}`")
+                except GitCommandError as e:
+                    raise LookupError(f"Failed to clone from the remote: `{remote}`") from e
                 # Verify that the requested branch exists by checking it out
                 self.setup_branch(branch)
             else:
@@ -150,4 +150,4 @@ def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
                 shutil.rmtree(self.local_repo_dir)
                 self.setup_local_repo(remote, branch, hide_progress)
             else:
-                raise LookupError("Exiting due to error with local modules git repo")
+                raise LookupError("Exiting due to error with local modules git repo") from e
diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py
index 105b5af681..683bcda1cf 100644
--- a/nf_core/modules/modules_utils.py
+++ b/nf_core/modules/modules_utils.py
@@ -1,5 +1,4 @@
 import logging
-import os
 from pathlib import Path
 from urllib.parse import urlparse
 
@@ -32,7 +31,7 @@ def repo_full_name_from_remote(remote_url: str) -> str:
         path = urlparse(remote_url).path
 
     # Remove the file extension from the path
-    path, _ = os.path.splitext(path)
+    path = str(Path(path).with_suffix(""))
 
     return path
 
@@ -62,12 +61,11 @@ def get_installed_modules(directory: Path, repo_type="modules") -> tuple[list[st
 
         # Filter local modules
         if local_modules_dir.exists():
-            local_modules = os.listdir(local_modules_dir)
-            local_modules = sorted([x for x in local_modules if x.endswith(".nf")])
+            local_modules = sorted([x.name for x in local_modules_dir.iterdir() if x.suffix == ".nf"])
 
     # Get nf-core modules
     if nfcore_modules_dir.exists():
-        for m in sorted([m for m in nfcore_modules_dir.iterdir() if not m == "lib"]):
+        for m in sorted([m for m in nfcore_modules_dir.iterdir() if m != "lib"]):
             if not m.is_dir():
                 raise ModuleExceptionError(
                     f"File found in '{nfcore_modules_dir}': '{m}'! This directory should only contain module directories."
@@ -83,7 +81,7 @@ def get_installed_modules(directory: Path, repo_type="modules") -> tuple[list[st
 
     # Make full (relative) file paths and create NFCoreComponent objects
     if local_modules_dir:
-        local_modules = [os.path.join(local_modules_dir, m) for m in local_modules]
+        local_modules = [str(local_modules_dir / m) for m in local_modules]
 
     nfcore_modules = [
         NFCoreComponent(
@@ -110,13 +108,11 @@ def load_edam():
         return edam_formats
     for line in response.content.splitlines():
         fields = line.decode("utf-8").split("\t")
-        if fields[0].split("/")[-1].startswith("format"):
-            # We choose an already provided extension
-            if fields[14]:
-                extensions = fields[14].split("|")
-                for extension in extensions:
-                    if extension not in edam_formats:
-                        edam_formats[extension] = (fields[0], fields[1])  # URL, name
+        if fields[0].split("/")[-1].startswith("format") and fields[14]:  # We choose an already provided extension
+            extensions = fields[14].split("|")
+            for extension in extensions:
+                if extension not in edam_formats:
+                    edam_formats[extension] = (fields[0], fields[1])  # URL, name
     return edam_formats
 
 
diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py
index b826e7fa51..604a85801d 100644
--- a/nf_core/pipelines/bump_version.py
+++ b/nf_core/pipelines/bump_version.py
@@ -336,7 +336,7 @@ def log_change(old_content: str, new_content: str):
     old_lines = old_content.splitlines()
     new_lines = new_content.splitlines()
 
-    for old_line, new_line in zip(old_lines, new_lines):
+    for old_line, new_line in zip(old_lines, new_lines, strict=False):
         if old_line != new_line:
             stderr.print(f"          [red] - {old_line.strip()}", highlight=False)
             stderr.print(f"          [green] + {new_line.strip()}", highlight=False)
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index bfc8a97efb..c5ea0c6894 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -74,9 +74,7 @@ def __init__(
                 self.config.outdir = outdir if outdir else Path().cwd()
             except (FileNotFoundError, UserWarning):
                 log.debug("The '.nf-core.yml' configuration file was not found.")
-        elif (name and description and author) or (
-            template_config and (isinstance(template_config, str) or isinstance(template_config, Path))
-        ):
+        elif (name and description and author) or (template_config and (isinstance(template_config, (str, Path)))):
             # Obtain a CreateConfig object from the template yaml file
             self.config = self.check_template_yaml_info(template_config, name, description, author)
             self.update_config(organisation, version, force, outdir)
@@ -153,8 +151,8 @@ def check_template_yaml_info(self, template_yaml, name, description, author):
                 with open(template_yaml) as f:
                     template_yaml = yaml.safe_load(f)
                     config = CreateConfig(**template_yaml)
-            except FileNotFoundError:
-                raise UserWarning(f"Template YAML file '{template_yaml}' not found.")
+            except FileNotFoundError as e:
+                raise UserWarning(f"Template YAML file '{template_yaml}' not found.") from e
 
         # Check required fields
         missing_fields = []
@@ -221,7 +219,7 @@ def obtain_jinja_params_dict(self, features_to_skip: list[str], pipeline_dir: st
         skip_areas = [
             t_area
             for section in self.template_features_yml.values()
-            for t_area in section["features"].keys()
+            for t_area in section["features"]
             if t_area in features_to_skip and section["features"][t_area]["skippable_paths"]
             # for t_area in section["features"][t_area]["skippable_paths"]
         ]
@@ -249,13 +247,12 @@ def obtain_jinja_params_dict(self, features_to_skip: list[str], pipeline_dir: st
         jinja_params["logo_light"] = f"{jinja_params['name_noslash']}_logo_light.png"
         jinja_params["logo_dark"] = f"{jinja_params['name_noslash']}_logo_dark.png"
         jinja_params["default_branch"] = self.default_branch
-        if config_yml is not None:
-            if (
-                hasattr(config_yml, "lint")
-                and hasattr(config_yml["lint"], "nextflow_config")
-                and hasattr(config_yml["lint"]["nextflow_config"], "manifest.name")
-            ):
-                return jinja_params, skip_areas
+        if config_yml is not None and (
+            hasattr(config_yml, "lint")
+            and hasattr(config_yml["lint"], "nextflow_config")
+            and hasattr(config_yml["lint"]["nextflow_config"], "manifest.name")
+        ):
+            return jinja_params, skip_areas
 
         # Check that the pipeline name matches the requirements
         if not re.match(r"^[a-z]+$", jinja_params["short_name"]):
@@ -331,12 +328,13 @@ def render_template(self) -> None:
         for template_fn_path in template_files:
             # Skip files that are in the self.skip_paths list
             for skip_path in self.skip_paths:
+                # TODO: Use Path.parts instead of str().startswith() to avoid unnecessary string conversion
                 if str(template_fn_path.relative_to(template_dir)).startswith(skip_path):
                     break
             else:
                 if template_fn_path.is_dir():
                     continue
-                if any([s in str(template_fn_path) for s in ignore_strs]):
+                if any(s in str(template_fn_path) for s in ignore_strs):
                     log.debug(f"Ignoring '{template_fn_path}' in jinja2 template creation")
                     continue
 
@@ -368,14 +366,13 @@ def render_template(self) -> None:
                     log.debug(f"Copying file without Jinja: '{output_path}' - {e}")
                     shutil.copy(template_fn_path, output_path)
 
-                # Something else went wrong
-                except Exception as e:
+                # Jinja rendering error or other template issues
+                except (jinja2.TemplateError, OSError) as e:
                     log.error(f"Copying raw file as error rendering with Jinja: '{output_path}' - {e}")
                     shutil.copy(template_fn_path, output_path)
 
                 # Mirror file permissions
-                template_stat = os.stat(template_fn_path)
-                os.chmod(output_path, template_stat.st_mode)
+                output_path.chmod(template_fn_path.stat().st_mode)
 
         if self.config.is_nfcore:
             # Make a logo and save it, if it is a nf-core pipeline
@@ -410,7 +407,7 @@ def fix_linting(self):
         lint_config = {}
         for area in set((self.config.skip_features or []) + self.skip_areas):
             try:
-                for section_name in self.template_features_yml.keys():
+                for section_name in self.template_features_yml:
                     if area in self.template_features_yml[section_name]["features"]:
                         for lint_test in self.template_features_yml[section_name]["features"][area]["linting"]:
                             try:
@@ -502,7 +499,7 @@ def git_init_pipeline(self) -> None:
                 else:
                     raise UserWarning(
                         "Branches 'TEMPLATE' and 'dev' already exist. Use --force to overwrite existing branches."
-                    )
+                    ) from e
         if self.is_interactive:
             try:
                 log.info(f"Pipeline created: ./{self.outdir.relative_to(Path.cwd())}")
diff --git a/nf_core/pipelines/create/finaldetails.py b/nf_core/pipelines/create/finaldetails.py
index dad81689a9..4d114dd7c7 100644
--- a/nf_core/pipelines/create/finaldetails.py
+++ b/nf_core/pipelines/create/finaldetails.py
@@ -1,5 +1,6 @@
 """A Textual app to create a pipeline."""
 
+import contextlib
 from pathlib import Path
 from textwrap import dedent
 
@@ -71,10 +72,8 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
                 text_input.query_one(".validation_msg").update("\n".join(validation_result.failure_descriptions))
             else:
                 text_input.query_one(".validation_msg").update("")
-        try:
+        with contextlib.suppress(ValueError):
             self.parent.TEMPLATE_CONFIG.__dict__.update(new_config)
-        except ValueError:
-            pass
 
         # Create the new pipeline
         self._create_pipeline()
diff --git a/nf_core/pipelines/create/githubrepo.py b/nf_core/pipelines/create/githubrepo.py
index 4ddf0092e1..a9bfd56fac 100644
--- a/nf_core/pipelines/create/githubrepo.py
+++ b/nf_core/pipelines/create/githubrepo.py
@@ -1,3 +1,4 @@
+import contextlib
 import logging
 import os
 from pathlib import Path
@@ -134,13 +135,13 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
             org = None
             # Make sure that the authentication was successful
             try:
-                user.login
-                log.debug("GitHub authentication successful")
-            except GithubException:
+                user_name = user.login
+                log.debug(f"GitHub authentication successful for user '{user_name}'")
+            except GithubException as e:
                 raise UserWarning(
                     f"Could not authenticate to GitHub with user name '{github_variables['gh_username']}'."
                     "Please make sure that the provided user name and token are correct."
-                )
+                ) from e
 
             # Check if organisation exists
             # If the organisation is nf-core or it doesn't exist, the repo will be created in the user account
@@ -151,7 +152,7 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
                         f"Repo will be created in the GitHub organisation account '{github_variables['repo_org']}'"
                     )
                 except UnknownObjectException:
-                    log.warn(f"Provided organisation '{github_variables['repo_org']}' not found. ")
+                    log.warning(f"Provided organisation '{github_variables['repo_org']}' not found. ")
 
             # Create the repo
             try:
@@ -199,8 +200,8 @@ def _create_repo_and_push(self, org, repo_name, pipeline_repo, private):
             repo = org.get_repo(repo_name)
             # Check if it has a commit history
             try:
-                repo.get_commits().totalCount
-                raise UserWarning(f"GitHub repository '{repo_name}' already exists")
+                n = repo.get_commits().totalCount
+                raise UserWarning(f"GitHub repository '{repo_name}' already exists, with {n} commits")
             except GithubException:
                 # Repo is empty
                 repo_exists = True
@@ -219,12 +220,9 @@ def _create_repo_and_push(self, org, repo_name, pipeline_repo, private):
             log.info(f"GitHub repository '{repo_name}' created successfully")
             remove_hide_class(self.parent, "close_app")
 
-        # Add the remote
-        try:
+        # Add the remote (if it doesn't already exist)
+        with contextlib.suppress(git.exc.GitCommandError):
             pipeline_repo.create_remote("origin", repo.clone_url)
-        except git.exc.GitCommandError:
-            # Remote already exists
-            pass
         # Push all branches
         pipeline_repo.remotes.origin.push(all=True).raise_if_error()
 
@@ -239,8 +237,8 @@ def _get_github_credentials(self):
         gh_user = None
         gh_token = None
         # Use gh CLI config if installed
-        gh_cli_config_fn = os.path.expanduser("~/.config/gh/hosts.yml")
-        if os.path.exists(gh_cli_config_fn):
+        gh_cli_config_fn = Path.home() / ".config" / "gh" / "hosts.yml"
+        if gh_cli_config_fn.exists():
             try:
                 with open(gh_cli_config_fn) as fh:
                     gh_cli_config = yaml.safe_load(fh)
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index a0c280185d..5751ddbd77 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -19,7 +19,7 @@
 from nf_core.utils import NFCoreTemplateConfig
 
 # Use ContextVar to define a context on the model initialization
-_init_context_var: ContextVar = ContextVar("_init_context_var", default={})
+_init_context_var: ContextVar = ContextVar("_init_context_var", default=None)
 
 
 @contextmanager
@@ -45,10 +45,11 @@ class CreateConfig(NFCoreTemplateConfig):
 
     def __init__(self, /, **data: Any) -> None:
         """Custom init method to allow using a context on the model initialization."""
+        context = _init_context_var.get()
         self.__pydantic_validator__.validate_python(
             data,
             self_instance=self,
-            context=_init_context_var.get(),
+            context=context if context is not None else {},
         )
 
     @field_validator("name")
diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py
index 85ae2cdf02..9218001005 100644
--- a/nf_core/pipelines/create_logo.py
+++ b/nf_core/pipelines/create_logo.py
@@ -40,14 +40,14 @@ def create_logo(
             svg = svg.replace("#050505", "#fafafa")
 
         # save the svg
-        logo_filename = f"nf-core-{text}_logo_{theme}.svg" if not filename else filename
+        logo_filename = filename if filename else f"nf-core-{text}_logo_{theme}.svg"
         logo_filename = f"{logo_filename}.svg" if not logo_filename.lower().endswith(".svg") else logo_filename
         logo_path = Path(directory, logo_filename)
         with open(logo_path, "w") as fh:
             fh.write(svg)
 
     else:
-        logo_filename = f"nf-core-{text}_logo_{theme}.png" if not filename else filename
+        logo_filename = filename if filename else f"nf-core-{text}_logo_{theme}.png"
         logo_filename = f"{logo_filename}.png" if not logo_filename.lower().endswith(".png") else logo_filename
         cache_name = f"nf-core-{text}_logo_{theme}_{width}.png"
         logo_path = Path(directory, logo_filename)
diff --git a/nf_core/pipelines/download/container_fetcher.py b/nf_core/pipelines/download/container_fetcher.py
index faa0ddf763..bfcda9ed54 100644
--- a/nf_core/pipelines/download/container_fetcher.py
+++ b/nf_core/pipelines/download/container_fetcher.py
@@ -274,7 +274,7 @@ def gather_registries(self, workflow_directory: Path) -> set[str]:
         """
         pass
 
-    def gather_config_registries(self, workflow_directory: Path, registry_keys: list[str] = []) -> set[str]:
+    def gather_config_registries(self, workflow_directory: Path, registry_keys: list[str] | None = None) -> set[str]:
         """
         Gather the registries from the pipeline config and store them in a set.
 
@@ -286,6 +286,8 @@ def gather_config_registries(self, workflow_directory: Path, registry_keys: list
             set[str]: The set of registries defined in the pipeline config
         """
         # Fetch the pipeline config
+        if registry_keys is None:
+            registry_keys = []
         nf_config = nf_core.utils.fetch_wf_config(workflow_directory)
 
         config_registries = set()
@@ -492,5 +494,6 @@ def copy_image(self, container: str, src_path: Path, dest_path: Path) -> None:
     def cleanup(self) -> None:
         """
         Cleanup any temporary files or resources.
+        Default implementation logs completion; subclasses can override to add specific cleanup.
         """
-        pass
+        log.debug(f"Container fetching complete. Images saved to {self.get_container_output_dir()}")
diff --git a/nf_core/pipelines/download/docker.py b/nf_core/pipelines/download/docker.py
index 6d7cae8a19..23062ace0c 100644
--- a/nf_core/pipelines/download/docker.py
+++ b/nf_core/pipelines/download/docker.py
@@ -82,10 +82,10 @@ def check_and_set_implementation(self) -> None:
 
         try:
             nf_core.utils.run_cmd(docker_binary, "info")
-        except RuntimeError:
+        except RuntimeError as e:
             raise OSError(
                 "Docker daemon is required to pull images, but it is not running or unavailable to the docker client"
-            )
+            ) from e
 
         self.implementation = "docker"
 
@@ -154,7 +154,7 @@ def fetch_remote_containers(self, containers: list[tuple[str, Path]], parallel:
                         future.result()  # This will raise an exception if the pull or save failed
                     except DockerError as e:
                         log.error(f"Error while processing container {e.container}: {e.message}")
-                    except Exception as e:
+                    except OSError as e:
                         log.error(f"Unexpected error: {e}")
 
             except KeyboardInterrupt:
diff --git a/nf_core/pipelines/download/download.py b/nf_core/pipelines/download/download.py
index 05c3ccea8d..66f8b11f49 100644
--- a/nf_core/pipelines/download/download.py
+++ b/nf_core/pipelines/download/download.py
@@ -107,7 +107,7 @@ def __init__(
         self.platform = platform
         self.fullname: str | None = None
         # downloading configs is not supported for Seqera Platform downloads.
-        self.include_configs = True if download_configuration == "yes" and not bool(platform) else False
+        self.include_configs = bool(download_configuration == "yes" and not bool(platform))
         # Additional tags to add to the downloaded pipeline. This enables to mark particular commits or revisions with
         # additional tags, e.g. "stable", "testing", "validated", "production" etc. Since this requires a git-repo, it is only
         # available for the bare / Seqera Platform download.
@@ -317,7 +317,9 @@ def download_workflow_static(self) -> None:
         # Download the pipeline files for each selected revision
         log.info("Downloading workflow files from GitHub")
 
-        for revision, wf_sha, download_url in zip(self.revision, self.wf_sha.values(), self.wf_download_url.values()):
+        for revision, wf_sha, download_url in zip(
+            self.revision, self.wf_sha.values(), self.wf_download_url.values(), strict=False
+        ):
             revision_dirname = self.download_wf_files(revision=revision, wf_sha=wf_sha, download_url=download_url)
 
             if self.include_configs:
@@ -428,7 +430,7 @@ def get_revision_hash(self) -> None:
 
         for revision in self.revision:  # revision is a list of strings, but may be of length 1
             # Branch
-            if revision in self.wf_branches.keys():
+            if revision in self.wf_branches:
                 self.wf_sha = {**self.wf_sha, revision: self.wf_branches[revision]}
 
             else:
@@ -530,7 +532,7 @@ def setup_container_fetcher(self) -> None:
             else:
                 self.container_fetcher = None
         except OSError as e:
-            raise DownloadError(e)
+            raise DownloadError(e) from e
 
     def prompt_use_singularity(self, fail_message: str) -> None:
         use_singularity = questionary.confirm(
@@ -686,11 +688,11 @@ def find_container_images(
 
         except RuntimeError as e:
             log.error("Running 'nextflow inspect' failed with the following error")
-            raise DownloadError(e)
+            raise DownloadError(e) from e
 
         except KeyError as e:
             log.error("Failed to parse output of 'nextflow inspect' to extract containers")
-            raise DownloadError(e)
+            raise DownloadError(e) from e
 
     def get_container_output_dir(self) -> Path:
         assert self.outdir is not None  # mypy
diff --git a/nf_core/pipelines/download/singularity.py b/nf_core/pipelines/download/singularity.py
index 286a90bbe6..1399c7ad4a 100644
--- a/nf_core/pipelines/download/singularity.py
+++ b/nf_core/pipelines/download/singularity.py
@@ -113,10 +113,7 @@ def __init__(
                             f"Proceeding without consideration of the remote ${SINGULARITY_CACHE_DIR_ENV_VAR} index."
                         )
                         self.container_cache_index = None
-                        if os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR):
-                            container_cache_utilisation = "copy"  # default to copy if possible, otherwise skip.
-                        else:
-                            container_cache_utilisation = None
+                        container_cache_utilisation = "copy" if os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR) else None
             else:
                 log.warning("[red]No remote cache index specified, skipping remote container download.[/]")
 
@@ -372,7 +369,7 @@ def read_remote_singularity_containers(container_cache_index: Path) -> list[str]
                     containers_remote.append(match.group(0))
             if n_total_images == 0:
                 raise LookupError("Could not find valid container names in the index file.")
-            containers_remote = sorted(list(set(containers_remote)))
+            containers_remote = sorted(set(containers_remote))
             log.debug(containers_remote)
             return containers_remote
 
@@ -487,7 +484,8 @@ def update_file_progress(input_params: tuple[str, Path], status: FileDownloader.
             container, output_path = input_params
             try:
                 self.progress.advance_remote_fetch_task()
-            except Exception as e:
+            except RuntimeError as e:
+                # Rich progress may raise RuntimeError if called from wrong thread
                 log.error(f"Error updating progress bar: {e}")
 
             if status == FileDownloader.Status.DONE:
@@ -636,6 +634,12 @@ def _ensure_output_dir_exists(self) -> None:
             log.debug(f"Container output directory not found, creating: {self.get_container_output_dir()}")
             self.get_container_output_dir().mkdir(parents=True, exist_ok=True)
 
+    def cleanup(self) -> None:
+        """
+        Cleanup any temporary files or resources.
+        """
+        super().cleanup()
+
 
 # Distinct errors for the Singularity container download, required for acting on the exceptions
 class SingularityError(Exception):
@@ -889,31 +893,34 @@ def download_file(self, remote_path: str, output_path: Path) -> None:
         # Set up download progress bar as a new task
         nice_name = self.nice_name(remote_path)
 
-        with self.progress.sub_task(nice_name, start=False, total=False, progress_type="download") as task:
+        with (
+            self.progress.sub_task(nice_name, start=False, total=False, progress_type="download") as task,
+            intermediate_file(output_path) as fh,
+        ):
             # Open file handle and download
             # This temporary will be automatically renamed to the target if there are no errors
-            with intermediate_file(output_path) as fh:
-                # Disable caching as this breaks streamed downloads
-                with requests_cache.disabled():
-                    r = requests.get(remote_path, allow_redirects=True, stream=True, timeout=60 * 5)
-                    filesize = r.headers.get("Content-length")
-                    if filesize:
-                        self.progress.update(task, total=int(filesize))
-                        self.progress.start_task(task)
-
-                    # Stream download
-                    has_content = False
-                    for data in r.iter_content(chunk_size=io.DEFAULT_BUFFER_SIZE):
-                        # Check that the user didn't hit ctrl-c
-                        if self.kill_with_fire:
-                            raise KeyboardInterrupt
-                        self.progress.update(task, advance=len(data))
-                        fh.write(data)
-                        has_content = True
-
-                    # Check that we actually downloaded something
-                    if not has_content:
-                        raise DownloadError(f"Downloaded file '{remote_path}' is empty")
-
-                # Set image file permissions to user=read,write,execute group/all=read,execute
-                os.chmod(fh.name, 0o755)
+
+            # Disable caching as this breaks streamed downloads
+            with requests_cache.disabled():
+                r = requests.get(remote_path, allow_redirects=True, stream=True, timeout=60 * 5)
+                filesize = r.headers.get("Content-length")
+                if filesize:
+                    self.progress.update(task, total=int(filesize))
+                    self.progress.start_task(task)
+
+                # Stream download
+                has_content = False
+                for data in r.iter_content(chunk_size=io.DEFAULT_BUFFER_SIZE):
+                    # Check that the user didn't hit ctrl-c
+                    if self.kill_with_fire:
+                        raise KeyboardInterrupt
+                    self.progress.update(task, advance=len(data))
+                    fh.write(data)
+                    has_content = True
+
+                # Check that we actually downloaded something
+                if not has_content:
+                    raise DownloadError(f"Downloaded file '{remote_path}' is empty")
+
+            # Set image file permissions to user=read,write,execute group/all=read,execute
+            Path(fh.name).chmod(0o755)
diff --git a/nf_core/pipelines/download/utils.py b/nf_core/pipelines/download/utils.py
index 17c3426d64..bde3845c09 100644
--- a/nf_core/pipelines/download/utils.py
+++ b/nf_core/pipelines/download/utils.py
@@ -21,9 +21,11 @@ def copy_container_load_scripts(container_system: str, dest_dir: Path, make_exec
     container_load_scripts_subpackage = "nf_core.pipelines.download.load_scripts"
     script_name = f"{container_system}-load.sh"
     dest_path = dest_dir / script_name
-    with importlib.resources.open_text(container_load_scripts_subpackage, script_name) as src:
-        with open(dest_path, "w") as dest:
-            shutil.copyfileobj(src, dest)
+    with (
+        importlib.resources.open_text(container_load_scripts_subpackage, script_name) as src,
+        open(dest_path, "w") as dest,
+    ):
+        shutil.copyfileobj(src, dest)
     if make_exec:
         dest_path.chmod(0o775)
     return script_name, dest_path
@@ -47,16 +49,16 @@ def intermediate_file(output_path: Path) -> Generator[tempfile._TemporaryFileWra
     if output_path.is_symlink():
         raise DownloadError(f"Output path '{output_path}' is a symbolic link")
 
-    tmp = tempfile.NamedTemporaryFile(dir=output_path.parent, delete=False)
-    try:
-        yield tmp
-        tmp.close()
-        Path(tmp.name).rename(output_path)
-    except:
-        tmp_path = Path(tmp.name)
-        if tmp_path.exists():
-            tmp_path.unlink()
-        raise
+    with tempfile.NamedTemporaryFile(dir=output_path.parent, delete=False) as tmp:
+        tmp_name = tmp.name
+        try:
+            yield tmp
+        except BaseException:
+            # File is closed automatically when exiting with block
+            Path(tmp_name).unlink(missing_ok=True)
+            raise
+    # File is now closed, safe to rename
+    Path(tmp_name).rename(output_path)
 
 
 @contextlib.contextmanager
@@ -85,7 +87,7 @@ def intermediate_file_no_creation(output_path: Path) -> Generator[Path, None, No
 
 
 @contextlib.contextmanager
-def intermediate_dir_with_cd(original_dir: Path, base_dir: Path = Path(".")):
+def intermediate_dir_with_cd(original_dir: Path, base_dir: Path = Path()):
     """
     Context manager to provide and change into a tempdir and ensure its removal and return to the
     original_dir upon exceptions.
diff --git a/nf_core/pipelines/download/workflow_repo.py b/nf_core/pipelines/download/workflow_repo.py
index 184555ac19..2c324a7cf7 100644
--- a/nf_core/pipelines/download/workflow_repo.py
+++ b/nf_core/pipelines/download/workflow_repo.py
@@ -150,8 +150,8 @@ def setup_local_repo(self, remote, location=None, in_cache=True):
                             progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"),
                         )
                     super().update_local_repo_status(self.fullname, True)
-                except GitCommandError:
-                    raise DownloadError(f"Failed to clone from the remote: `{remote}`")
+                except GitCommandError as e:
+                    raise DownloadError(f"Failed to clone from the remote: `{remote}`") from e
             else:
                 self.repo = git.Repo(self.local_repo_dir)
 
diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index 364da1c113..8fce38e83a 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -45,7 +45,7 @@ def __init__(
         self.pipeline = pipeline
         self.pipeline_revision = revision
         self.schema_obj = None
-        self.use_params_file = False if command_only else True
+        self.use_params_file = not command_only
         self.params_in = params_in
         self.params_out = params_out if params_out else Path.cwd() / "nf-params.json"
         self.save_all = save_all
@@ -117,17 +117,18 @@ def launch_pipeline(self):
                 ).unsafe_ask()
 
         # Check if the output file exists already
-        if os.path.exists(self.params_out):
+        if self.params_out.exists():
             # if params_in has the same name as params_out, don't ask to overwrite
-            if self.params_in and os.path.abspath(self.params_in) == os.path.abspath(self.params_out):
+            params_in_path = Path(self.params_in) if self.params_in else None
+            if params_in_path and params_in_path.exists() and params_in_path.samefile(self.params_out):
                 log.warning(
                     f"The parameter input file has the same name as the output file! {os.path.relpath(self.params_out)} will be overwritten."
                 )
             else:
                 log.warning(f"Parameter output file already exists! {os.path.relpath(self.params_out)}")
             if Confirm.ask("[yellow]Do you want to overwrite this file?"):
-                if not (self.params_in and os.path.abspath(self.params_in) == os.path.abspath(self.params_out)):
-                    os.remove(self.params_out)
+                if not (params_in_path and params_in_path.exists() and params_in_path.samefile(self.params_out)):
+                    self.params_out.unlink()
                     log.info(f"Deleted {self.params_out}\n")
             else:
                 log.info("Exiting. Use --params-out to specify a custom output filename.")
@@ -195,10 +196,10 @@ def get_pipeline_schema(self):
         self.schema_obj = nf_core.pipelines.schema.PipelineSchema()
 
         # Check if this is a local directory
-        localpath = os.path.abspath(os.path.expanduser(self.pipeline))
-        if os.path.exists(localpath):
+        localpath = Path(self.pipeline).expanduser().resolve()
+        if localpath.exists():
             # Set the nextflow launch command to use full paths
-            self.pipeline = localpath
+            self.pipeline = str(localpath)
             self.nextflow_cmd = f"nextflow run {localpath}"
         else:
             # Assume nf-core if no org given
@@ -225,12 +226,11 @@ def get_pipeline_schema(self):
         except AssertionError:
             # No schema found
             # Check that this was actually a pipeline
-            if self.schema_obj.pipeline_dir is None or not os.path.exists(self.schema_obj.pipeline_dir):
+            pipeline_dir_path = Path(self.schema_obj.pipeline_dir) if self.schema_obj.pipeline_dir else None
+            if pipeline_dir_path is None or not pipeline_dir_path.exists():
                 log.error(f"Could not find pipeline: {self.pipeline} ({self.schema_obj.pipeline_dir})")
                 return False
-            if not os.path.exists(os.path.join(self.schema_obj.pipeline_dir, "nextflow.config")) and not os.path.exists(
-                os.path.join(self.schema_obj.pipeline_dir, "main.nf")
-            ):
+            if not (pipeline_dir_path / "nextflow.config").exists() and not (pipeline_dir_path / "main.nf").exists():
                 log.error("Could not find a 'main.nf' or 'nextflow.config' file, are you sure this is a pipeline?")
                 return False
 
@@ -321,12 +321,12 @@ def launch_web_gui(self):
                 raise AssertionError(
                     f'web_response["status"] should be "recieved", but it is "{web_response["status"]}"'
                 )
-        except AssertionError:
+        except AssertionError as e:
             log.debug(f"Response content:\n{json.dumps(web_response, indent=4)}")
             raise AssertionError(
                 f"Web launch response not recognised: {self.web_schema_launch_url}\n "
                 "See verbose log for full response (nf-core -v launch)"
-            )
+            ) from e
         else:
             self.web_schema_launch_web_url = web_response["web_url"]
             self.web_schema_launch_api_url = web_response["api_url"]
@@ -363,10 +363,12 @@ def get_web_launch_response(self):
                 # Sanitise form inputs, set proper variable types etc
                 self.sanitise_web_response()
             except KeyError as e:
-                raise AssertionError(f"Missing return key from web API: {e}")
+                raise AssertionError(f"Missing return key from web API: {e}") from e
             except Exception as e:
                 log.debug(web_response)
-                raise AssertionError(f"Unknown exception ({type(e).__name__}) - see verbose log for details. {e}")
+                raise AssertionError(
+                    f"Unknown exception ({type(e).__name__}) - see verbose log for details. {e}"
+                ) from e
             return True
         else:
             log.debug(f"Response content:\n{json.dumps(web_response, indent=4)}")
@@ -571,7 +573,7 @@ def single_param_to_questionary(self, param_id, param_obj, answers=None, print_h
         # Overwrite default with parsed schema, includes --params-in etc
         if self.schema_obj is not None and param_id in self.schema_obj.input_params:
             if param_obj["type"] == "boolean" and isinstance(self.schema_obj.input_params[param_id], str):
-                question["default"] = "true" == self.schema_obj.input_params[param_id].lower()
+                question["default"] = self.schema_obj.input_params[param_id].lower() == "true"
             else:
                 question["default"] = self.schema_obj.input_params[param_id]
 
@@ -725,7 +727,7 @@ def build_command(self):
                     if isinstance(val, bool) and val:
                         self.nextflow_cmd += f" --{param}"
                     # No quotes for numbers
-                    elif (isinstance(val, int) or isinstance(val, float)) and val:
+                    elif (isinstance(val, (int, float))) and val:
                         self.nextflow_cmd += " --{} {}".format(param, str(val).replace('"', '\\"'))
                     # everything else
                     else:
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index 13e3b7afe7..dc17996be2 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -209,7 +209,7 @@ def _lint_pipeline(self) -> None:
             log.info("Including --release mode tests")
 
         # Check that we recognise all --fix arguments
-        unrecognised_fixes = list(test for test in self.fix if test not in self.lint_tests)
+        unrecognised_fixes = [test for test in self.fix if test not in self.lint_tests]
         if len(unrecognised_fixes):
             raise AssertionError(
                 "Unrecognised lint test{} for '--fix': '{}'".format(
@@ -239,11 +239,11 @@ def _lint_pipeline(self) -> None:
             log.info("Attempting to automatically fix failing tests")
             try:
                 repo = git.Repo(self.wf_path)
-            except InvalidGitRepositoryError:
+            except InvalidGitRepositoryError as e:
                 raise AssertionError(
                     f"'{self.wf_path}' does not appear to be a git repository, "
                     "this is required when running with '--fix'"
-                )
+                ) from e
             # Check that we have no uncommitted changes
             if repo.is_dirty(untracked_files=True):
                 raise AssertionError(
@@ -606,12 +606,8 @@ def run_linting(
             )
         log.info("Only running tests: '{}'".format("', '".join(key)))
 
-    # Check if we were given any keys, and if they match any pipeline tests
-    if key:
-        pipeline_keys = list(set(key).intersection(set(PipelineLint._get_all_lint_tests(release_mode))))
-    else:
-        # If no key is supplied, run all tests
-        pipeline_keys = None
+    # Check if we were given any keys, and if they match any pipeline tests. If no key is supplied, run all tests
+    pipeline_keys = list(set(key).intersection(set(PipelineLint._get_all_lint_tests(release_mode)))) if key else None
 
     # Create the lint object
     lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned, hide_progress)
@@ -649,8 +645,8 @@ def run_linting(
             )
         else:
             # If no key is supplied, run the default modules tests
-            module_lint_tests = list(("module_changes", "module_version"))
-            subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
+            module_lint_tests = ["module_changes", "module_version"]
+            subworkflow_lint_tests = ["subworkflow_changes", "subworkflow_version"]
         module_lint_obj.filter_tests_by_key(module_lint_tests)
         if subworkflow_lint_obj is not None:
             subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
@@ -704,7 +700,6 @@ def run_linting(
         lint_obj._save_json_results(json_fn)
 
     # Reminder about --release mode flag if we had failures
-    if len(lint_obj.failed) > 0:
-        if release_mode:
-            log.info("Reminder: Lint tests were run in --release mode.")
+    if len(lint_obj.failed) > 0 and release_mode:
+        log.info("Reminder: Lint tests were run in --release mode.")
     return lint_obj, module_lint_obj, subworkflow_lint_obj
diff --git a/nf_core/pipelines/lint/actions_awsfulltest.py b/nf_core/pipelines/lint/actions_awsfulltest.py
index 5c6fdb2717..b740f49803 100644
--- a/nf_core/pipelines/lint/actions_awsfulltest.py
+++ b/nf_core/pipelines/lint/actions_awsfulltest.py
@@ -34,7 +34,7 @@ def actions_awsfulltest(self) -> dict[str, list[str]]:
         try:
             with open(fn) as fh:
                 wf = yaml.safe_load(fh)
-        except Exception as e:
+        except (OSError, yaml.YAMLError) as e:
             return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
 
         aws_profile = "-profile test "
@@ -42,11 +42,11 @@ def actions_awsfulltest(self) -> dict[str, list[str]]:
         # Check that the action is only turned on for published releases
         try:
             if wf[True]["pull_request_review"]["types"] != ["submitted"]:
-                raise AssertionError()
+                raise AssertionError
             if "workflow_dispatch" not in wf[True]:
-                raise AssertionError()
+                raise AssertionError
             if wf[True]["release"]["types"] != ["published"]:
-                raise AssertionError()
+                raise AssertionError
         except (AssertionError, KeyError, TypeError):
             failed.append("`.github/workflows/awsfulltest.yml` is not triggered correctly")
         else:
@@ -55,8 +55,8 @@ def actions_awsfulltest(self) -> dict[str, list[str]]:
         # Warn if `-profile test` is still unchanged
         try:
             steps = wf["jobs"]["run-platform"]["steps"]
-            if not any(aws_profile in step["run"] for step in steps if "run" in step.keys()):
-                raise AssertionError()
+            if not any(aws_profile in step["run"] for step in steps if "run" in step):
+                raise AssertionError
         except (AssertionError, KeyError, TypeError):
             passed.append("`.github/workflows/awsfulltest.yml` does not use `-profile test`")
         else:
diff --git a/nf_core/pipelines/lint/actions_awstest.py b/nf_core/pipelines/lint/actions_awstest.py
index 7e4c0fc497..d61d39f966 100644
--- a/nf_core/pipelines/lint/actions_awstest.py
+++ b/nf_core/pipelines/lint/actions_awstest.py
@@ -29,15 +29,15 @@ def actions_awstest(self):
     try:
         with open(fn) as fh:
             wf = yaml.safe_load(fh)
-    except Exception as e:
+    except (OSError, yaml.YAMLError) as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
 
     # Check that the action is only turned on for workflow_dispatch
     try:
         if "workflow_dispatch" not in wf[True]:
-            raise AssertionError()
+            raise AssertionError
         if "push" in wf[True] or "pull_request" in wf[True]:
-            raise AssertionError()
+            raise AssertionError
     except (AssertionError, KeyError, TypeError):
         return {"failed": ["'.github/workflows/awstest.yml' is not triggered correctly"]}
     else:
diff --git a/nf_core/pipelines/lint/actions_nf_test.py b/nf_core/pipelines/lint/actions_nf_test.py
index 42761c3323..312b806ebe 100644
--- a/nf_core/pipelines/lint/actions_nf_test.py
+++ b/nf_core/pipelines/lint/actions_nf_test.py
@@ -45,7 +45,7 @@ def actions_nf_test(self):
     try:
         with open(fn) as fh:
             ciwf = yaml.safe_load(fh)
-    except Exception as e:
+    except (OSError, yaml.YAMLError) as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
 
     # Check that the action is turned on for the correct events
@@ -53,9 +53,9 @@ def actions_nf_test(self):
         # NB: YAML dict key 'on' is evaluated to a Python dict key True
         pr_subtree = ciwf[True]["pull_request"]
         if pr_subtree is None:
-            raise AssertionError()
+            raise AssertionError
         if "published" not in ciwf[True]["release"]["types"]:
-            raise AssertionError()
+            raise AssertionError
     except (AssertionError, KeyError, TypeError):
         failed.append("'.github/workflows/nf-test.yml' is not triggered on expected events")
     else:
@@ -65,7 +65,7 @@ def actions_nf_test(self):
     try:
         nxf_ver = ciwf["jobs"]["nf-test"]["strategy"]["matrix"]["NXF_VER"]
         if not any(i == self.minNextflowVersion for i in nxf_ver):
-            raise AssertionError()
+            raise AssertionError
     except (KeyError, TypeError):
         failed.append("'.github/workflows/nf-test.yml' does not check minimum NF version")
     except AssertionError:
diff --git a/nf_core/pipelines/lint/actions_schema_validation.py b/nf_core/pipelines/lint/actions_schema_validation.py
index cefbb009fa..e3d18e6efa 100644
--- a/nf_core/pipelines/lint/actions_schema_validation.py
+++ b/nf_core/pipelines/lint/actions_schema_validation.py
@@ -45,21 +45,21 @@ def actions_schema_validation(self) -> dict[str, list[str]]:
         try:
             with open(wf_path) as fh:
                 wf_json = yaml.safe_load(fh)
-        except Exception as e:
+        except (OSError, yaml.YAMLError) as e:
             failed.append(f"Could not parse yaml file: {wf}, {e}")
             continue
 
         # yaml parses 'on' as True --> try to fix it before schema validation
         try:
             wf_json["on"] = wf_json.pop(True)
-        except Exception:
+        except KeyError:
             failed.append(f"Missing 'on' keyword in {wf}")
 
         # Validate the workflow
         try:
             jsonschema.validate(wf_json, schema)
             passed.append(f"Workflow validation passed: {wf}")
-        except Exception as e:
+        except jsonschema.ValidationError as e:
             failed.append(f"Workflow validation failed for {wf}: {e}")
 
     return {"passed": passed, "failed": failed, "warned": warned}
diff --git a/nf_core/pipelines/lint/configs.py b/nf_core/pipelines/lint/configs.py
index c90b5faec1..05b4bde59e 100644
--- a/nf_core/pipelines/lint/configs.py
+++ b/nf_core/pipelines/lint/configs.py
@@ -30,7 +30,7 @@ def lint_file(self, lint_name: str, file_path: Path) -> dict[str, list[str]]:
             try:
                 with open(fn) as fh:
                     config = fh.read()
-            except Exception as e:
+            except OSError as e:
                 return {"failed": [f"Could not parse file: {fn}, {e}"]}
 
             # find sections with a withName: prefix
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index e99b97c246..202906c184 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -224,18 +224,18 @@ def pf(file_path: str | Path) -> Path:
 
     # Files that cause an error if they don't exist
     for files in files_fail:
-        if any([str(f) in ignore_files for f in files]):
+        if any(str(f) in ignore_files for f in files):
             continue
-        if any([pf(f).is_file() for f in files]):
+        if any(pf(f).is_file() for f in files):
             passed.append(f"File found: {self._wrap_quotes(files)}")
         else:
             failed.append(f"File not found: {self._wrap_quotes(files)}")
 
     # Files that cause a warning if they don't exist
     for files in files_warn:
-        if any([str(f) in ignore_files for f in files]):
+        if any(str(f) in ignore_files for f in files):
             continue
-        if any([pf(f).is_file() for f in files]):
+        if any(pf(f).is_file() for f in files):
             passed.append(f"File found: {self._wrap_quotes(files)}")
         else:
             hint = ""
diff --git a/nf_core/pipelines/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py
index 8ff61171d3..4f9fe3fcd2 100644
--- a/nf_core/pipelines/lint/files_unchanged.py
+++ b/nf_core/pipelines/lint/files_unchanged.py
@@ -1,6 +1,5 @@
 import filecmp
 import logging
-import os
 import re
 import shutil
 import tempfile
@@ -156,11 +155,11 @@ def _tf(file_path: str | Path) -> Path:
     # Files that must be completely unchanged from template
     for files in files_exact:
         # Ignore if file specified in linting config
-        if any([str(f) in ignore_files for f in files]):
+        if any(str(f) in ignore_files for f in files):
             ignored.append(f"File ignored due to lint config: {self._wrap_quotes(files)}")
 
         # Ignore if we can't find the file
-        elif not any([_pf(f).is_file() for f in files]):
+        elif not any(_pf(f).is_file() for f in files):
             ignored.append(f"File does not exist: {self._wrap_quotes(files)}")
 
         # Check that the file has an identical match
@@ -170,8 +169,8 @@ def _tf(file_path: str | Path) -> Path:
                     if filecmp.cmp(_pf(f), _tf(f), shallow=True):
                         passed.append(f"`{f}` matches the template")
                     else:
-                        if f.name.endswith(".png") and int(os.stat(_pf(f)).st_size / 500) == int(
-                            os.stat(_tf(f)).st_size / 500
+                        if f.name.endswith(".png") and int(_pf(f).stat().st_size / 500) == int(
+                            _tf(f).stat().st_size / 500
                         ):
                             # almost the same file, good enough for the logo
                             log.debug(f"Files are almost the same. Will pass: {f}")
@@ -196,11 +195,11 @@ def _tf(file_path: str | Path) -> Path:
     # Files that can be added to, but that must contain the template contents
     for files in files_partial:
         # Ignore if file specified in linting config
-        if any([str(f) in ignore_files for f in files]):
+        if any(str(f) in ignore_files for f in files):
             ignored.append(f"File ignored due to lint config: {self._wrap_quotes(files)}")
 
         # Ignore if we can't find the file
-        elif not any([_pf(f).is_file() for f in files]):
+        elif not any(_pf(f).is_file() for f in files):
             ignored.append(f"File does not exist: {self._wrap_quotes(files)}")
 
         # Check that the file contains the template file contents
diff --git a/nf_core/pipelines/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py
index dc9faadf5d..17ad46b663 100644
--- a/nf_core/pipelines/lint/modules_json.py
+++ b/nf_core/pipelines/lint/modules_json.py
@@ -24,7 +24,7 @@ def modules_json(self) -> dict[str, list[str]]:
     if _modules_json and modules_json_dict is not None:
         all_modules_passed = True
 
-        for repo in modules_json_dict["repos"].keys():
+        for repo in modules_json_dict["repos"]:
             # Check if the modules.json has been updated to keep the
             if "modules" not in modules_json_dict["repos"][repo] or not repo.startswith("http"):
                 failed.append(
@@ -33,7 +33,7 @@ def modules_json(self) -> dict[str, list[str]]:
                 )
                 continue
 
-            for dir in modules_json_dict["repos"][repo]["modules"].keys():
+            for dir in modules_json_dict["repos"][repo]["modules"]:
                 for module, module_entry in modules_json_dict["repos"][repo]["modules"][dir].items():
                     if not Path(modules_dir, dir, module).exists():
                         failed.append(
diff --git a/nf_core/pipelines/lint/multiqc_config.py b/nf_core/pipelines/lint/multiqc_config.py
index 01b6b06dec..254caa925a 100644
--- a/nf_core/pipelines/lint/multiqc_config.py
+++ b/nf_core/pipelines/lint/multiqc_config.py
@@ -57,7 +57,7 @@ def multiqc_config(self) -> dict[str, list[str]]:
         try:
             with open(fn) as fh:
                 mqc_yml = yaml.safe_load(fh)
-        except Exception as e:
+        except (OSError, yaml.YAMLError) as e:
             return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
 
         # check if required sections are present
@@ -137,7 +137,7 @@ def multiqc_config(self) -> dict[str, list[str]]:
         # Check that export_plots is activated
         try:
             if not mqc_yml["export_plots"]:
-                raise AssertionError()
+                raise AssertionError
         except (AssertionError, KeyError, TypeError):
             failed.append("`assets/multiqc_config.yml` does not contain 'export_plots: true'.")
         else:
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 0020c97749..f5913f5521 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -208,7 +208,7 @@ def nextflow_config(self) -> dict[str, list[str]]:
             if cf in ignore_configs:
                 ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
                 break
-            if cf in self.nf_config.keys():
+            if cf in self.nf_config:
                 passed.append(f"Config variable found: {self._wrap_quotes(cf)}")
                 break
         else:
@@ -218,7 +218,7 @@ def nextflow_config(self) -> dict[str, list[str]]:
             if cf in ignore_configs:
                 ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
                 break
-            if cf in self.nf_config.keys():
+            if cf in self.nf_config:
                 passed.append(f"Config variable found: {self._wrap_quotes(cf)}")
                 break
         else:
@@ -227,7 +227,7 @@ def nextflow_config(self) -> dict[str, list[str]]:
         if cf in ignore_configs:
             ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
             break
-        if cf not in self.nf_config.keys():
+        if cf not in self.nf_config:
             passed.append(f"Config variable (correctly) not found: {self._wrap_quotes(cf)}")
         else:
             failed.append(f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}")
@@ -235,13 +235,7 @@ def nextflow_config(self) -> dict[str, list[str]]:
     # Check and warn if the process configuration is done with deprecated syntax
 
     process_with_deprecated_syntax = list(
-        set(
-            [
-                match.group(1)
-                for ck in self.nf_config.keys()
-                if (match := re.match(r"^(process\.\$.*?)\.+.*$", ck)) is not None
-            ]
-        )
+        {match.group(1) for ck in self.nf_config if (match := re.match(r"^(process\.\$.*?)\.+.*$", ck)) is not None}
     )
     for pd in process_with_deprecated_syntax:
         warned.append(f"Process configuration is done with deprecated_syntax: {pd}")
@@ -265,7 +259,7 @@ def nextflow_config(self) -> dict[str, list[str]]:
         try:
             manifest_name = self.nf_config.get("manifest.name", "").strip("'\"")
             if not manifest_name.startswith(f"{org_name}/"):
-                raise AssertionError()
+                raise AssertionError
         except (AssertionError, IndexError):
             failed.append(f"Config ``manifest.name`` did not begin with ``{org_name}/``:\n    {manifest_name}")
         else:
@@ -276,7 +270,7 @@ def nextflow_config(self) -> dict[str, list[str]]:
         try:
             manifest_homepage = self.nf_config.get("manifest.homePage", "").strip("'\"")
             if not manifest_homepage.startswith(f"https://github.com/{org_name}/"):
-                raise AssertionError()
+                raise AssertionError
         except (AssertionError, IndexError):
             failed.append(
                 f"Config variable ``manifest.homePage`` did not begin with https://github.com/{org_name}/:\n    {manifest_homepage}"
@@ -415,11 +409,11 @@ def nextflow_config(self) -> dict[str, list[str]]:
     schema.load_schema()
     schema.get_schema_defaults()  # Get default values from schema
     schema.get_schema_types()  # Get types from schema
-    for param_name in schema.schema_defaults.keys():
+    for param_name in schema.schema_defaults:
         param = "params." + param_name
         if param in ignore_defaults:
             ignored.append(f"Config default ignored: {param}")
-        elif param in self.nf_config.keys():
+        elif param in self.nf_config:
             config_default: str | float | int | None = None
             schema_default: str | float | int | None = None
             if schema.schema_types[param_name] == "boolean":
diff --git a/nf_core/pipelines/lint/nf_test_content.py b/nf_core/pipelines/lint/nf_test_content.py
index 045c27f540..c0cd92159a 100644
--- a/nf_core/pipelines/lint/nf_test_content.py
+++ b/nf_core/pipelines/lint/nf_test_content.py
@@ -106,7 +106,7 @@ def nf_test_content(self) -> dict[str, list[str]]:
             ignored.append(f"'{test_fn.relative_to(self.wf_path)}' checking ignored")
             continue
 
-        checks_passed = {check: False for check in test_checks}
+        checks_passed = dict.fromkeys(test_checks, False)
         with open(test_fn) as fh:
             for line in fh:
                 for check_name, check_info in test_checks.items():
@@ -145,7 +145,7 @@ def nf_test_content(self) -> dict[str, list[str]]:
         failed.append(f"'{conf_fn.relative_to(self.wf_path)}' does not exist")
     else:
         if nf_test_content_conf is None or str(conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf:
-            checks_passed = {check: False for check in config_checks}
+            checks_passed = dict.fromkeys(config_checks, False)
             with open(conf_fn) as fh:
                 for line in fh:
                     line = line.strip()
@@ -187,7 +187,7 @@ def nf_test_content(self) -> dict[str, list[str]]:
         failed.append(f"'{nf_test_conf_fn.relative_to(self.wf_path)}' does not exist")
     else:
         if nf_test_content_conf is None or str(nf_test_conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf:
-            checks_passed = {check: False for check in nf_test_checks}
+            checks_passed = dict.fromkeys(nf_test_checks, False)
             with open(nf_test_conf_fn) as fh:
                 for line in fh:
                     line = line.strip()
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index a774192769..b787405169 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -1,7 +1,7 @@
 import ast
-import glob
 import logging
 import re
+from pathlib import Path
 
 log = logging.getLogger(__name__)
 
@@ -22,20 +22,19 @@ def plugin_includes(self) -> dict[str, list[str]]:
 
     plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
     workflow_files = [
-        file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")
+        file for file in Path(self.wf_path).rglob("*.nf") if file.relative_to(self.wf_path).parts[0] != "modules"
     ]
     test_passed = True
     for file in workflow_files:
-        with open(file) as of:
-            plugin_includes = re.findall(plugin_include_pattern, of.read())
-            for include in plugin_includes:
-                if include not in ["nf-validation", "nf-schema"]:
-                    continue
-                if include != validation_plugin:
-                    test_passed = False
-                    failed.append(
-                        f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`"
-                    )
+        plugin_includes = re.findall(plugin_include_pattern, file.read_text())
+        for include in plugin_includes:
+            if include not in ["nf-validation", "nf-schema"]:
+                continue
+            if include != validation_plugin:
+                test_passed = False
+                failed.append(
+                    f"Found a `{include}` plugin import in `{file.relative_to(self.wf_path)}`, but `{validation_plugin}` was used in `nextflow.config`"
+                )
 
     if test_passed:
         passed.append("No wrong validation plugin imports have been found")
diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
index d16125021c..ad7179ed22 100644
--- a/nf_core/pipelines/lint/readme.py
+++ b/nf_core/pipelines/lint/readme.py
@@ -61,7 +61,7 @@ def readme(self):
             nf_badge_version = match.group(1).strip("'\"")
             try:
                 if nf_badge_version != self.minNextflowVersion:
-                    raise AssertionError()
+                    raise AssertionError
             except (AssertionError, KeyError):
                 failed.append(
                     f"README Nextflow minimum version badge does not match config. Badge: `{nf_badge_version}`, "
diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py
index b586cc5242..8571f7832d 100644
--- a/nf_core/pipelines/lint/schema_description.py
+++ b/nf_core/pipelines/lint/schema_description.py
@@ -27,7 +27,7 @@ def schema_description(self):
     ignore_params = self.lint_config.get("schema_description", []) if self.lint_config is not None else []
 
     # Get ungrouped params
-    if "properties" in self.schema_obj.schema.keys():
+    if "properties" in self.schema_obj.schema:
         ungrouped_params = self.schema_obj.schema["properties"].keys()
         for up in ungrouped_params:
             if up in ignore_params:
@@ -37,13 +37,13 @@ def schema_description(self):
 
     # Iterate over groups and add warning for parameters without a description
     defs_notation = self.schema_obj.defs_notation
-    for group_key in self.schema_obj.schema[defs_notation].keys():
+    for group_key in self.schema_obj.schema[defs_notation]:
         group = self.schema_obj.schema[defs_notation][group_key]
         for param_key, param in group["properties"].items():
             if param_key in ignore_params:
                 ignored.append(f"Ignoring description check for param in schema: `{param_key}`")
                 continue
-            if "description" not in param.keys():
+            if "description" not in param:
                 warned.append(f"No description provided in schema for parameter: `{param_key}`")
 
     for ip in ignore_params:
diff --git a/nf_core/pipelines/lint/system_exit.py b/nf_core/pipelines/lint/system_exit.py
index 435a2452d0..b891fea7a0 100644
--- a/nf_core/pipelines/lint/system_exit.py
+++ b/nf_core/pipelines/lint/system_exit.py
@@ -18,8 +18,8 @@ def system_exit(self):
     root_dir = Path(self.wf_path)
 
     # Get all groovy and nf files
-    groovy_files = [f for f in root_dir.rglob("*.groovy")]
-    nf_files = [f for f in root_dir.rglob("*.nf")]
+    groovy_files = list(root_dir.rglob("*.groovy"))
+    nf_files = list(root_dir.rglob("*.nf"))
     to_check = nf_files + groovy_files
 
     for file in to_check:
diff --git a/nf_core/pipelines/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py
index 0cb669e553..01f4ea5f2b 100644
--- a/nf_core/pipelines/lint/template_strings.py
+++ b/nf_core/pipelines/lint/template_strings.py
@@ -50,17 +50,16 @@ def template_strings(self):
         # Skip binary files
         binary_ftypes = ["image", "application/java-archive"]
         (ftype, encoding) = mimetypes.guess_type(fn)
-        if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
+        if encoding is not None or (ftype is not None and any(ftype.startswith(ft) for ft in binary_ftypes)):
             continue
 
         with open(fn, encoding="latin1") as fh:
-            lnum = 0
-            for line in fh:
-                lnum += 1
+            for i, line in enumerate(fh):
+                i += 1
                 cc_matches = re.findall(r"[^$]{{[^:}]*}}", line)
                 if len(cc_matches) > 0:
                     for cc_match in cc_matches:
-                        failed.append(f"Found a Jinja template string in `{fn}` L{lnum}: {cc_match}")
+                        failed.append(f"Found a Jinja template string in `{fn}` L{i}: {cc_match}")
                         num_matches += 1
     if num_matches == 0:
         passed.append(f"Did not find any Jinja template strings ({len(self.files)} files)")
diff --git a/nf_core/pipelines/lint/version_consistency.py b/nf_core/pipelines/lint/version_consistency.py
index e344d25e5d..c939938a46 100644
--- a/nf_core/pipelines/lint/version_consistency.py
+++ b/nf_core/pipelines/lint/version_consistency.py
@@ -47,7 +47,7 @@ def version_consistency(self):
         os.environ.get("GITHUB_REF", "").startswith("refs/tags/")
         and os.environ.get("GITHUB_REPOSITORY", "") != "nf-core/tools"
     ):
-        versions["GITHUB_REF"] = os.path.basename(os.environ["GITHUB_REF"].strip(" '\""))
+        versions["GITHUB_REF"] = Path(os.environ["GITHUB_REF"].strip(" '\"")).name
 
     # Get version from the .nf-core.yml template
     yaml = YAML()
diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py
index b9ff9533d3..24b3b4dfb9 100644
--- a/nf_core/pipelines/lint_utils.py
+++ b/nf_core/pipelines/lint_utils.py
@@ -165,7 +165,7 @@ def run_prettier_on_file(file: Path | str | list[str]) -> None:
             if ": SyntaxError: " in e.stdout.decode():
                 log.critical(f"Can't format {file} because it has a syntax error.\n{e.stdout.decode()}")
             elif "files were modified by this hook" in e.stdout.decode():
-                all_lines = [line for line in e.stdout.decode().split("\n")]
+                all_lines = list(e.stdout.decode().split("\n"))
                 files = "\n".join(all_lines[3:])
                 log.debug(f"The following files were modified by prettier:\n {files}")
             else:
diff --git a/nf_core/pipelines/list.py b/nf_core/pipelines/list.py
index 5822557d64..96ca9da59e 100644
--- a/nf_core/pipelines/list.py
+++ b/nf_core/pipelines/list.py
@@ -22,6 +22,26 @@
 nf_core.utils.setup_requests_cachedir()
 
 
+def get_nextflow_assets_dir(workflow_name: str | None = None) -> Path:
+    """
+    Get the Nextflow assets directory path.
+
+    Args:
+        workflow_name: Optional workflow name to append to the path (e.g., "nf-core/rnaseq")
+
+    Returns:
+        Path to the Nextflow assets directory, optionally with workflow_name appended
+    """
+    if nxf_assets := os.getenv("NXF_ASSETS"):
+        base_dir = Path(nxf_assets)
+    elif nxf_home := os.getenv("NXF_HOME"):
+        base_dir = Path(nxf_home) / "assets"
+    else:
+        base_dir = Path(os.getenv("HOME") or "", ".nextflow", "assets")
+
+    return base_dir / workflow_name if workflow_name else base_dir
+
+
 def list_workflows(filter_by=None, sort_by="release", as_json=False, show_archived=False):
     """Prints out a list of all nf-core workflows.
 
@@ -53,12 +73,12 @@ def autocomplete_pipelines(ctx, param, incomplete: str):
         matches = [CompletionItem(wor) for wor in available_workflows if wor.startswith(incomplete)]
 
         return matches
-    except Exception as e:
+    except (OSError, AttributeError) as e:
         print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr)
         return []
 
 
-def get_local_wf(workflow: str | Path, revision=None) -> str | None:
+def get_local_wf(workflow: str | Path, revision=None) -> Path | None:
     """
     Check if this workflow has a local copy and use nextflow to pull it if not
     """
@@ -69,16 +89,17 @@ def get_local_wf(workflow: str | Path, revision=None) -> str | None:
     wfs = Workflows()
     wfs.get_local_nf_workflows()
     for wf in wfs.local_workflows:
-        if workflow == wf.full_name:
-            if revision is None or revision == wf.commit_sha or revision == wf.branch or revision == wf.active_tag:
-                if wf.active_tag:
-                    print_revision = f"v{wf.active_tag}"
-                elif wf.branch:
-                    print_revision = f"{wf.branch} - {wf.commit_sha[:7]}"
-                else:
-                    print_revision = wf.commit_sha
-                log.info(f"Using local workflow: {workflow} ({print_revision})")
-                return wf.local_path
+        if workflow == wf.full_name and (
+            revision is None or revision == wf.commit_sha or revision == wf.branch or revision == wf.active_tag
+        ):
+            if wf.active_tag:
+                print_revision = f"v{wf.active_tag}"
+            elif wf.branch:
+                print_revision = f"{wf.branch} - {wf.commit_sha[:7]}"
+            else:
+                print_revision = wf.commit_sha
+            log.info(f"Using local workflow: {workflow} ({print_revision})")
+            return wf.local_path
 
     # Wasn't local, fetch it
     log.info(f"Downloading workflow: {workflow} ({revision})")
@@ -131,17 +152,16 @@ def get_local_nf_workflows(self):
         Local workflows are stored in :attr:`self.local_workflows` list.
         """
         # Try to guess the local cache directory (much faster than calling nextflow)
-        if len(os.environ.get("NXF_ASSETS", "")) > 0:
-            nextflow_wfdir = os.environ.get("NXF_ASSETS")
-        elif len(os.environ.get("NXF_HOME", "")) > 0:
-            nextflow_wfdir = os.path.join(os.environ.get("NXF_HOME"), "assets")
-        else:
-            nextflow_wfdir = os.path.join(os.getenv("HOME"), ".nextflow", "assets")
-        if os.path.isdir(nextflow_wfdir):
+        nextflow_wfdir = get_nextflow_assets_dir()
+        if nextflow_wfdir.is_dir():
             log.debug("Guessed nextflow assets directory - pulling pipeline dirnames")
-            for org_name in os.listdir(nextflow_wfdir):
-                for wf_name in os.listdir(os.path.join(nextflow_wfdir, org_name)):
-                    self.local_workflows.append(LocalWorkflow(f"{org_name}/{wf_name}"))
+            self.local_workflows.extend(
+                LocalWorkflow(f"{org_dir.name}/{wf_dir.name}")
+                for org_dir in nextflow_wfdir.iterdir()
+                if org_dir.is_dir()
+                for wf_dir in org_dir.iterdir()
+                if wf_dir.is_dir()
+            )
 
         # Fetch details about local cached pipelines with `nextflow list`
         else:
@@ -223,7 +243,8 @@ def print_summary(self):
             def sort_pulled_date(wf):
                 try:
                     return wf.local_wf.last_pull * -1
-                except Exception:
+                except AttributeError:
+                    # local_wf is None or doesn't have last_pull attribute
                     return 0
 
             filtered_workflows.sort(key=sort_pulled_date)
@@ -258,10 +279,7 @@ def sort_pulled_date(wf):
                     revision = f"{wf.local_wf.branch} - {wf.local_wf.commit_sha[:7]}"
                 else:
                     revision = wf.local_wf.commit_sha
-                if wf.local_is_latest:
-                    is_latest = f"[green]Yes ({revision})"
-                else:
-                    is_latest = f"[red]No ({revision})"
+                is_latest = f"[green]Yes ({revision})" if wf.local_is_latest else f"[red]No ({revision})"
             else:
                 is_latest = "[dim]-"
 
@@ -350,13 +368,8 @@ def get_local_nf_workflow_details(self):
 
         if self.local_path is None:
             # Try to guess the local cache directory
-            if len(os.environ.get("NXF_ASSETS", "")) > 0:
-                nf_wfdir = os.path.join(os.environ.get("NXF_ASSETS"), self.full_name)
-            elif len(os.environ.get("NXF_HOME", "")) > 0:
-                nf_wfdir = os.path.join(os.environ.get("NXF_HOME"), "assets", self.full_name)
-            else:
-                nf_wfdir = os.path.join(os.getenv("HOME"), ".nextflow", "assets", self.full_name)
-            if os.path.isdir(nf_wfdir):
+            nf_wfdir = get_nextflow_assets_dir(self.full_name)
+            if nf_wfdir.is_dir():
                 log.debug(f"Guessed nextflow assets workflow directory: {nf_wfdir}")
                 self.local_path = nf_wfdir
 
@@ -378,7 +391,7 @@ def get_local_nf_workflow_details(self):
                 repo = git.Repo(self.local_path)
                 self.commit_sha = str(repo.head.commit.hexsha)
                 self.remote_url = str(repo.remotes.origin.url)
-                self.last_pull = os.stat(os.path.join(self.local_path, ".git", "FETCH_HEAD")).st_mtime
+                self.last_pull = (Path(self.local_path) / ".git" / "FETCH_HEAD").stat().st_mtime
                 self.last_pull_date = datetime.fromtimestamp(self.last_pull).strftime("%Y-%m-%d %H:%M:%S")
                 self.last_pull_pretty = pretty_date(self.last_pull)
 
@@ -415,10 +428,7 @@ def pretty_date(time):
     """
 
     now = datetime.now()
-    if isinstance(time, datetime):
-        diff = now - time
-    else:
-        diff = now - datetime.fromtimestamp(time)
+    diff = now - time if isinstance(time, datetime) else now - datetime.fromtimestamp(time)
     second_diff = diff.seconds
     day_diff = diff.days
 
diff --git a/nf_core/pipelines/params_file.py b/nf_core/pipelines/params_file.py
index a4f7bff321..50b4cb8a32 100644
--- a/nf_core/pipelines/params_file.py
+++ b/nf_core/pipelines/params_file.py
@@ -171,7 +171,7 @@ def format_group(self, definition, show_hidden=False) -> str:
         return out
 
     def format_param(
-        self, name: str, properties: dict, required_properties: list[str] = [], show_hidden: bool = False
+        self, name: str, properties: dict, required_properties: list[str] | None = None, show_hidden: bool = False
     ) -> str | None:
         """
         Format a single parameter of the schema as commented YAML
@@ -186,6 +186,8 @@ def format_param(
             str: Section of a params-file.yml for given parameter
             None: If the parameter is skipped because it is hidden and show_hidden is not set
         """
+        if required_properties is None:
+            required_properties = []
         out = ""
         hidden = properties.get("hidden", False)
 
diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py
index 46197e9cc8..882f432587 100644
--- a/nf_core/pipelines/refgenie.py
+++ b/nf_core/pipelines/refgenie.py
@@ -52,12 +52,12 @@ def _print_nf_config(rgc):
         for asset in asset_list:
             try:
                 pth = rgc.seek(genome, asset)
-            # Catch general exception instead of refgencof exception --> no refgenconf import needed
-            except Exception:
+            # Catch refgenconf exceptions without importing refgenconf
+            except (OSError, RuntimeError):
                 log.warning(f"{genome}/{asset} is incomplete, ignoring...")
             else:
                 # Translate an alias name to the alias used in the pipeline
-                if asset in alias_translations.keys():
+                if asset in alias_translations:
                     log.info(f"Translating refgenie asset alias {asset} to {alias_translations[asset]}.")
                     asset = alias_translations[asset]
                 genomes_str += f'      {asset.ljust(20, " ")} = "{pth}"\n'
@@ -72,23 +72,24 @@ def _update_nextflow_home_config(refgenie_genomes_config_file, nxf_home):
     for the 'refgenie_genomes_config_file' if not already defined
     """
     # Check if NXF_HOME/config exists and has a
+    refgenie_config_path = Path(refgenie_genomes_config_file).resolve()
     include_config_string = dedent(
         f"""
         ///// >>> nf-core + RefGenie >>> /////
         // !! Contents within this block are managed by 'nf-core/tools' !!
         // Includes auto-generated config file with RefGenie genome assets
-        includeConfig '{os.path.abspath(refgenie_genomes_config_file)}'
+        includeConfig '{refgenie_config_path}'
         ///// <<< nf-core + RefGenie <<< /////
         """
     )
     nxf_home_config = Path(nxf_home) / "config"
-    if os.path.exists(nxf_home_config):
+    if nxf_home_config.exists():
         # look for include statement in config
         has_include_statement = False
         with open(nxf_home_config) as fh:
             lines = fh.readlines()
             for line in lines:
-                if re.match(rf"\s*includeConfig\s*'{os.path.abspath(refgenie_genomes_config_file)}'", line):
+                if re.match(rf"\s*includeConfig\s*'{re.escape(str(refgenie_config_path))}'", line):
                     has_include_statement = True
                     break
 
@@ -164,9 +165,9 @@ def update_config(rgc):
     if not nxf_home:
         try:
             nxf_home = Path.home() / ".nextflow"
-            if not os.path.exists(nxf_home):
+            if not nxf_home.exists():
                 log.info(f"Creating NXF_HOME directory at {nxf_home}")
-                os.makedirs(nxf_home, exist_ok=True)
+                nxf_home.mkdir(parents=True, exist_ok=True)
         except RuntimeError:
             nxf_home = False
 
diff --git a/nf_core/pipelines/rocrate.py b/nf_core/pipelines/rocrate.py
index 199110e7a3..c7ca451ad9 100644
--- a/nf_core/pipelines/rocrate.py
+++ b/nf_core/pipelines/rocrate.py
@@ -94,23 +94,22 @@ def create_rocrate(self, json_path: None | Path = None, zip_path: None | Path =
         """
 
         # Check that the checkout pipeline version is the same as the requested version
-        if self.version != "":
-            if self.version != self.pipeline_obj.nf_config.get("manifest.version"):
-                # using git checkout to get the requested version
-                log.info(f"Checking out pipeline version {self.version}")
-                if self.pipeline_obj.repo is None:
-                    log.error(f"Pipeline repository not found in {self.pipeline_dir}")
-                    sys.exit(1)
-                try:
-                    self.pipeline_obj.repo.git.checkout(self.version)
-                    self.pipeline_obj = Pipeline(self.pipeline_dir)
-                    self.pipeline_obj._load()
-                except InvalidGitRepositoryError:
-                    log.error(f"Could not find a git repository in {self.pipeline_dir}")
-                    sys.exit(1)
-                except GitCommandError:
-                    log.error(f"Could not checkout version {self.version}")
-                    sys.exit(1)
+        if self.version != "" and self.version != self.pipeline_obj.nf_config.get("manifest.version"):
+            # using git checkout to get the requested version
+            log.info(f"Checking out pipeline version {self.version}")
+            if self.pipeline_obj.repo is None:
+                log.error(f"Pipeline repository not found in {self.pipeline_dir}")
+                sys.exit(1)
+            try:
+                self.pipeline_obj.repo.git.checkout(self.version)
+                self.pipeline_obj = Pipeline(self.pipeline_dir)
+                self.pipeline_obj._load()
+            except InvalidGitRepositoryError:
+                log.error(f"Could not find a git repository in {self.pipeline_dir}")
+                sys.exit(1)
+            except GitCommandError:
+                log.error(f"Could not checkout version {self.version}")
+                sys.exit(1)
         self.version = self.pipeline_obj.nf_config.get("manifest.version", "")
         self.make_workflow_rocrate()
 
@@ -206,10 +205,7 @@ def set_main_entity(self, main_entity_filename: str):
             "dateModified", str(datetime.now().strftime("%Y-%m-%dT%H:%M:%SZ")), compact=True
         )
         self.crate.mainEntity.append_to("sdPublisher", {"@id": "https://nf-co.re/"}, compact=True)
-        if self.version.endswith("dev"):
-            url = "dev"
-        else:
-            url = self.version
+        url = "dev" if self.version.endswith("dev") else self.version
         self.crate.mainEntity.append_to(
             "url", f"https://nf-co.re/{self.crate.name.replace('nf-core/', '')}/{url}/", compact=True
         )
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index e9c1689e73..9086a96ecc 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -169,11 +169,11 @@ def load_lint_schema(self):
         except json.decoder.JSONDecodeError as e:
             error_msg = f"[bold red]Could not parse schema JSON:[/] {e}"
             log.error(error_msg)
-            raise AssertionError(error_msg)
+            raise AssertionError(error_msg) from e
         except AssertionError as e:
             error_msg = f"[red][✗] Pipeline schema does not follow nf-core specs:\n {e}"
             log.error(error_msg)
-            raise AssertionError(error_msg)
+            raise AssertionError(error_msg) from e
 
     def load_schema(self):
         """Load a pipeline schema from a file"""
@@ -279,10 +279,10 @@ def load_input_params(self, params_path):
                 try:
                     params = json.load(fh)
                 except json.JSONDecodeError as e:
-                    raise UserWarning(f"Unable to load JSON file '{params_path}' due to error {e}")
+                    raise UserWarning(f"Unable to load JSON file '{params_path}' due to error {e}") from e
                 self.input_params.update(params)
             log.debug(f"Loaded JSON input params: {params_path}")
-        except Exception as json_e:
+        except (OSError, UserWarning) as json_e:
             log.debug(f"Could not load input params as JSON: {json_e}")
             # This failed, try to load as YAML
             try:
@@ -293,7 +293,7 @@ def load_input_params(self, params_path):
             except Exception as yaml_e:
                 error_msg = f"Could not load params file as either JSON or YAML:\n JSON: {json_e}\n YAML: {yaml_e}"
                 log.error(error_msg)
-                raise AssertionError(error_msg)
+                raise AssertionError(error_msg) from yaml_e
 
     def validate_params(self):
         """Check given parameters against a schema and validate"""
@@ -322,7 +322,7 @@ def validate_default_params(self):
             jsonschema.validate(self.schema_defaults, strip_required(self.schema))
         except jsonschema.exceptions.ValidationError as e:
             log.debug(f"Complete error message:\n{e}")
-            raise AssertionError(f"Default parameters are invalid: {e.message}")
+            raise AssertionError(f"Default parameters are invalid: {e.message}") from e
         for param, default in self.schema_defaults.items():
             if default in ("null", "", None, "None") or default is False:
                 log.warning(
@@ -335,7 +335,7 @@ def validate_default_params(self):
             self.get_wf_params()
 
         # Go over group keys
-        for group_key, group in self.schema.get(self.defs_notation, {}).items():
+        for _group_key, group in self.schema.get(self.defs_notation, {}).items():
             group_properties = group.get("properties")
             for param in group_properties:
                 if param in self.ignored_params:
@@ -369,7 +369,7 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
         """
 
         # If we have a default in the schema, check it matches the config
-        if "default" in schema_param and (
+        if "default" in schema_param and (  # noqa SIM102
             (schema_param["type"] == "boolean" and str(config_default).lower() != str(schema_param["default"]).lower())
             and (str(schema_param["default"]) != str(config_default).strip("'\""))
         ):
@@ -385,16 +385,12 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
             return
 
         # Check variable types in nextflow.config
-        if schema_param["type"] == "string":
-            if str(config_default) in ["false", "true", "''"]:
-                self.invalid_nextflow_config_default_parameters[param] = (
-                    f"String should not be set to `{config_default}`"
-                )
-        if schema_param["type"] == "boolean":
-            if str(config_default) not in ["false", "true"]:
-                self.invalid_nextflow_config_default_parameters[param] = (
-                    f"Booleans should only be true or false, not `{config_default}`"
-                )
+        if schema_param["type"] == "string" and str(config_default) in ["false", "true", "''"]:
+            self.invalid_nextflow_config_default_parameters[param] = f"String should not be set to `{config_default}`"
+        if schema_param["type"] == "boolean" and str(config_default) not in ["false", "true"]:
+            self.invalid_nextflow_config_default_parameters[param] = (
+                f"Booleans should only be true or false, not `{config_default}`"
+            )
         if schema_param["type"] == "integer":
             try:
                 int(config_default)
@@ -429,13 +425,13 @@ def validate_schema(self, schema=None):
                 jsonschema.Draft7Validator.check_schema(schema)
                 log.debug("JSON Schema Draft7 validated")
             except jsonschema.exceptions.SchemaError as e:
-                raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
+                raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}") from e
         elif self.schema_draft == "https://json-schema.org/draft/2020-12/schema":
             try:
                 jsonschema.Draft202012Validator.check_schema(schema)
                 log.debug("JSON Schema Draft2020-12 validated")
             except jsonschema.exceptions.SchemaError as e:
-                raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
+                raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}") from e
         else:
             raise AssertionError(
                 f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`"
@@ -727,24 +723,23 @@ def build_schema(self, pipeline_dir, no_prompts, web_only, url):
             self.save_schema()
 
         # If running interactively, send to the web for customisation
-        if not self.no_prompts:
-            if Confirm.ask(":rocket:  Launch web builder for customisation and editing?"):
-                try:
-                    self.launch_web_builder()
-                except AssertionError as e:
-                    log.error(e.args[0])
-                    # Extra help for people running offline
-                    if "Could not connect" in e.args[0]:
-                        log.info(
-                            f"If you're working offline, now copy your schema ({self.schema_filename}) and paste at https://nf-co.re/pipeline_schema_builder"
-                        )
-                        log.info("When you're finished, you can paste the edited schema back into the same file")
-                    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}"
-                        )
-                    return False
+        if not self.no_prompts and Confirm.ask(":rocket:  Launch web builder for customisation and editing?"):
+            try:
+                self.launch_web_builder()
+            except AssertionError as e:
+                log.error(e.args[0])
+                # Extra help for people running offline
+                if "Could not connect" in e.args[0]:
+                    log.info(
+                        f"If you're working offline, now copy your schema ({self.schema_filename}) and paste at https://nf-co.re/pipeline_schema_builder"
+                    )
+                    log.info("When you're finished, you can paste the edited schema back into the same file")
+                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}"
+                    )
+                return False
 
     def get_wf_params(self):
         """
@@ -833,7 +828,7 @@ def remove_schema_notfound_configs_single_schema(self, schema):
         schema = copy.deepcopy(schema)
         params_removed = []
         # Use iterator so that we can delete the key whilst iterating
-        for p_key in [k for k in schema.get("properties", {}).keys()]:
+        for p_key in list(schema.get("properties", {})):
             if self.prompt_remove_schema_notfound_config(p_key):
                 del schema["properties"][p_key]
                 # Remove required flag if set
@@ -908,14 +903,16 @@ def add_schema_found_configs(self):
                 and (p_key not in self.schema_defaults)
                 and (p_key not in self.ignored_params)
                 and (p_def := self.build_schema_param(p_val).get("default"))
-            ):
-                if self.no_prompts or Confirm.ask(
+            ) and (
+                self.no_prompts
+                or Confirm.ask(
                     f":sparkles: Default for [bold]'params.{p_key}'[/] is not in schema (def='{p_def}'). "
                     "[blue]Update pipeline schema?"
-                ):
-                    s_key_def = s_key + ("default",)
-                    nf_core.utils.nested_setitem(self.schema, s_key_def, p_def)
-                    log.debug(f"Updating '{p_key}' default to '{p_def}' in pipeline schema")
+                )
+            ):
+                s_key_def = s_key + ("default",)
+                nf_core.utils.nested_setitem(self.schema, s_key_def, p_def)
+                log.debug(f"Updating '{p_key}' default to '{p_def}' in pipeline schema")
         return params_added
 
     def build_schema_param(self, p_val):
@@ -973,12 +970,12 @@ def launch_web_builder(self):
                 raise AssertionError(
                     f'web_response["status"] should be "recieved", but it is "{web_response["status"]}"'
                 )
-        except AssertionError:
+        except AssertionError as e:
             log.debug(f"Response content:\n{json.dumps(web_response, indent=4)}")
             raise AssertionError(
                 f"Pipeline schema builder response not recognised: {self.web_schema_build_url}\n"
                 " See verbose log for full response (nf-core -v schema)"
-            )
+            ) from e
         else:
             self.web_schema_build_web_url = web_response["web_url"]
             self.web_schema_build_api_url = web_response["api_url"]
@@ -1004,7 +1001,7 @@ def get_web_builder_response(self):
                 self.remove_schema_empty_definitions()
                 self.validate_schema()
             except AssertionError as e:
-                raise AssertionError(f"Response from schema builder did not pass validation:\n {e}")
+                raise AssertionError(f"Response from schema builder did not pass validation:\n {e}") from e
             else:
                 self.save_schema()
                 return True
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index 7ce358cd07..248c01ddbb 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -166,7 +166,7 @@ def sync(self) -> None:
                 self.make_pull_request()
             except PullRequestExceptionError as e:
                 self.reset_target_dir()
-                raise PullRequestExceptionError(e)
+                raise PullRequestExceptionError(e) from e
 
         self.reset_target_dir()
 
@@ -184,8 +184,8 @@ def inspect_sync_dir(self):
         # Check that the pipeline_dir is a git repo
         try:
             self.repo = git.Repo(self.pipeline_dir)
-        except InvalidGitRepositoryError:
-            raise SyncExceptionError(f"'{self.pipeline_dir}' does not appear to be a git repository")
+        except InvalidGitRepositoryError as e:
+            raise SyncExceptionError(f"'{self.pipeline_dir}' does not appear to be a git repository") from e
 
         # get current branch so we can switch back later
         self.original_branch = self.repo.active_branch.name
@@ -211,8 +211,8 @@ def get_wf_config(self):
             if self.from_branch and self.repo.active_branch.name != self.from_branch:
                 log.info(f"Checking out workflow branch '{self.from_branch}'")
                 self.repo.git.checkout(self.from_branch)
-        except GitCommandError:
-            raise SyncExceptionError(f"Branch `{self.from_branch}` not found!")
+        except GitCommandError as e:
+            raise SyncExceptionError(f"Branch `{self.from_branch}` not found!") from e
 
         # If not specified, get the name of the active branch
         if not self.from_branch:
@@ -242,8 +242,8 @@ def checkout_template_branch(self):
             # Try to check out an existing local branch called TEMPLATE
             try:
                 self.repo.git.checkout("TEMPLATE")
-            except GitCommandError:
-                raise SyncExceptionError("Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'")
+            except GitCommandError as e:
+                raise SyncExceptionError("Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'") from e
 
     def delete_tracked_template_branch_files(self):
         """
@@ -264,7 +264,7 @@ def _delete_tracked_files(self):
             try:
                 file_path.unlink()
             except Exception as e:
-                raise SyncExceptionError(e)
+                raise SyncExceptionError(e) from e
 
     def _clean_up_empty_dirs(self):
         """
@@ -280,14 +280,14 @@ def _clean_up_empty_dirs(self):
             if curr_dir == str(self.pipeline_dir):
                 continue
 
-            subdir_set = set(Path(curr_dir) / d for d in sub_dirs)
+            subdir_set = {Path(curr_dir) / d for d in sub_dirs}
             currdir_is_empty = (len(subdir_set - deleted) == 0) and (len(files) == 0)
             if currdir_is_empty:
                 log.debug(f"Deleting empty directory {curr_dir}")
                 try:
                     Path(curr_dir).rmdir()
                 except Exception as e:
-                    raise SyncExceptionError(e)
+                    raise SyncExceptionError(e) from e
                 deleted.add(Path(curr_dir))
 
     def make_template_pipeline(self):
@@ -332,7 +332,7 @@ def make_template_pipeline(self):
         except Exception as err:
             # Reset to where you were to prevent git getting messed up.
             self.repo.git.reset("--hard")
-            raise SyncExceptionError(f"Failed to rebuild pipeline from template with error:\n{err}")
+            raise SyncExceptionError(f"Failed to rebuild pipeline from template with error:\n{err}") from err
 
     def commit_template_changes(self):
         """If we have any changes with the new template files, make a git commit"""
@@ -350,7 +350,7 @@ def commit_template_changes(self):
             self.made_changes = True
             log.info("Committed changes to 'TEMPLATE' branch")
         except Exception as e:
-            raise SyncExceptionError(f"Could not commit changes to TEMPLATE:\n{e}")
+            raise SyncExceptionError(f"Could not commit changes to TEMPLATE:\n{e}") from e
         return True
 
     def push_template_branch(self):
@@ -358,11 +358,11 @@ def push_template_branch(self):
         and try to make a PR. If we don't have the auth token, try to figure out a URL
         for the PR and print this to the console.
         """
-        log.info(f"Pushing TEMPLATE branch to remote: '{os.path.basename(self.pipeline_dir)}'")
+        log.info(f"Pushing TEMPLATE branch to remote: '{self.pipeline_dir.name}'")
         try:
             self.repo.git.push()
         except GitCommandError as e:
-            raise PullRequestExceptionError(f"Could not push TEMPLATE branch:\n  {e}")
+            raise PullRequestExceptionError(f"Could not push TEMPLATE branch:\n  {e}") from e
 
     def create_merge_base_branch(self):
         """Create a new branch from the updated TEMPLATE branch
@@ -389,7 +389,7 @@ def create_merge_base_branch(self):
         try:
             self.repo.create_head(self.merge_branch)
         except GitCommandError as e:
-            raise SyncExceptionError(f"Could not create new branch '{self.merge_branch}'\n{e}")
+            raise SyncExceptionError(f"Could not create new branch '{self.merge_branch}'\n{e}") from e
 
     def push_merge_branch(self):
         """Push the newly created merge branch to the remote repository"""
@@ -398,7 +398,7 @@ def push_merge_branch(self):
             origin = self.repo.remote()
             origin.push(self.merge_branch)
         except GitCommandError as e:
-            raise PullRequestExceptionError(f"Could not push branch '{self.merge_branch}':\n  {e}")
+            raise PullRequestExceptionError(f"Could not push branch '{self.merge_branch}':\n  {e}") from e
 
     def make_pull_request(self):
         """Create a pull request to a base branch (default: dev),
@@ -443,7 +443,7 @@ def make_pull_request(self):
                 )
             except Exception as e:
                 stderr.print_exception()
-                raise PullRequestExceptionError(f"Something went badly wrong - {e}")
+                raise PullRequestExceptionError(f"Something went badly wrong - {e}") from e
             else:
                 self.gh_pr_returned_data = r.json()
                 self.pr_url = self.gh_pr_returned_data["html_url"]
@@ -463,7 +463,8 @@ def _parse_json_response(response) -> tuple[Any, str]:
         try:
             json_data = json.loads(response.content)
             return json_data, json.dumps(json_data, indent=4)
-        except Exception:
+        except json.JSONDecodeError:
+            # Response content is not valid JSON
             return response.content, str(response.content)
 
     def reset_target_dir(self):
@@ -474,7 +475,7 @@ def reset_target_dir(self):
         try:
             self.repo.git.checkout(self.original_branch)
         except GitCommandError as e:
-            raise SyncExceptionError(f"Could not reset to original branch `{self.original_branch}`:\n{e}")
+            raise SyncExceptionError(f"Could not reset to original branch `{self.original_branch}`:\n{e}") from e
 
     def _get_ignored_files(self) -> list[str]:
         """
diff --git a/nf_core/subworkflows/lint/subworkflow_if_empty_null.py b/nf_core/subworkflows/lint/subworkflow_if_empty_null.py
index 481e31e3ed..bce4c168e2 100644
--- a/nf_core/subworkflows/lint/subworkflow_if_empty_null.py
+++ b/nf_core/subworkflows/lint/subworkflow_if_empty_null.py
@@ -22,7 +22,7 @@ def subworkflow_if_empty_null(_, subworkflow):
         subworkflow.warned.append(
             ("subworkflow_if_empty_null", "subworkflow_if_empty_null", warning, swf_results["file_paths"][i])
         )
-    for i, passed in enumerate(swf_results["passed"]):
+    for _i, passed in enumerate(swf_results["passed"]):
         subworkflow.passed.append(
             ("subworkflow_if_empty_null", "subworkflow_if_empty_null", passed, subworkflow.component_dir)
         )
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index 168fac9fc2..804903626d 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -139,7 +139,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent, allow_missing: bool = Fal
                     with open(snap_file) as snap_fh:
                         try:
                             snap_content = json.load(snap_fh)
-                            for test_name in snap_content.keys():
+                            for test_name in snap_content:
                                 if "d41d8cd98f00b204e9800998ecf8427e" in str(snap_content[test_name]):
                                     if "stub" not in test_name:
                                         subworkflow.failed.append(
diff --git a/nf_core/subworkflows/lint/subworkflow_todos.py b/nf_core/subworkflows/lint/subworkflow_todos.py
index 05286bf11c..cec6bb2c45 100644
--- a/nf_core/subworkflows/lint/subworkflow_todos.py
+++ b/nf_core/subworkflows/lint/subworkflow_todos.py
@@ -36,5 +36,5 @@ def subworkflow_todos(_, subworkflow):
     swf_results = pipeline_todos(None, root_dir=subworkflow.component_dir)
     for i, warning in enumerate(swf_results["warned"]):
         subworkflow.warned.append(("subworkflow_todos", "subworkflow_todo", warning, swf_results["file_paths"][i]))
-    for i, passed in enumerate(swf_results["passed"]):
+    for _i, passed in enumerate(swf_results["passed"]):
         subworkflow.passed.append(("subworkflow_todos", "subworkflow_todo", passed, subworkflow.component_dir))
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index eb5e406bfa..18356cfdfb 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -92,8 +92,8 @@ def get_remote_branches(remote_url):
         """
         try:
             unparsed_branches = git.Git().ls_remote(remote_url)
-        except git.GitCommandError:
-            raise LookupError(f"Was unable to fetch branches from '{remote_url}'")
+        except git.GitCommandError as e:
+            raise LookupError(f"Was unable to fetch branches from '{remote_url}'") from e
         else:
             branches = {}
             for branch_info in unparsed_branches.split("\n"):
@@ -133,8 +133,8 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
             if config_fn is not None and repo_config is not None:
                 try:
                     self.repo_path = repo_config.org_path
-                except KeyError:
-                    raise UserWarning(f"'org_path' key not present in {config_fn.name}")
+                except KeyError as e:
+                    raise UserWarning(f"'org_path' key not present in {config_fn.name}") from e
 
             # Verify that the repo seems to be correctly configured
             if self.repo_path != NF_CORE_MODULES_NAME or self.branch:
@@ -165,10 +165,9 @@ def verify_sha(self, prompt, sha):
             log.error("Cannot use '--sha' and '--prompt' at the same time!")
             return False
 
-        if sha:
-            if not self.sha_exists_on_branch(sha):
-                log.error(f"Commit SHA '{sha}' doesn't exist in '{self.remote_url}'")
-                return False
+        if sha and not self.sha_exists_on_branch(sha):
+            log.error(f"Commit SHA '{sha}' doesn't exist in '{self.remote_url}'")
+            return False
 
         return True
 
@@ -206,17 +205,19 @@ def branch_exists(self):
         """
         try:
             self.checkout_branch()
-        except GitCommandError:
-            raise LookupError(f"Branch '{self.branch}' not found in '{self.remote_url}'")
+        except GitCommandError as e:
+            raise LookupError(f"Branch '{self.branch}' not found in '{self.remote_url}'") from e
 
     def verify_branch(self):
         """
         Verifies the active branch conforms to the correct directory structure
         """
-        dir_names = os.listdir(self.local_repo_dir)
-        if "modules" not in dir_names:
+        assert self.local_repo_dir is not None, "Repository must be initialized before verifying branch"
+        local_repo_path = Path(self.local_repo_dir)
+
+        if not Path(local_repo_path, "modules").exists():
             err_str = f"Repository '{self.remote_url}' ({self.branch}) does not contain the 'modules/' directory"
-            if "software" in dir_names:
+            if Path(local_repo_path, "software").exists():
                 err_str += (
                     ".\nAs of nf-core/tools version 2.0, the 'software/' directory should be renamed to 'modules/'"
                 )
@@ -336,7 +337,7 @@ def component_files_identical(self, component_name, base_path, commit, component
         else:
             self.checkout(commit)
         component_files = ["main.nf", "meta.yml"]
-        files_identical = {file: True for file in component_files}
+        files_identical = dict.fromkeys(component_files, True)
         component_dir = self.get_component_dir(component_name, component_type)
         for file in component_files:
             try:
@@ -399,7 +400,7 @@ def get_component_git_log(
                 "To solve this, you can try to remove the cloned rempository and run the command again.\n"
                 f"This repository is typically found at `{self.local_repo_dir}`"
             )
-            raise UserWarning
+            raise UserWarning from None
         commits = iter(commits_new + commits_old)
 
         return commits
@@ -413,7 +414,7 @@ def get_latest_component_version(self, component_name, component_type):
             if not git_logs:
                 return None
             return git_logs[0]["git_sha"]
-        except Exception as e:
+        except (git.exc.GitError, KeyError) as e:
             log.debug(f"Could not get latest version of {component_name}: {e}")
             return None
 
diff --git a/nf_core/test_datasets/list.py b/nf_core/test_datasets/list.py
index 3531eef1ce..f773598431 100644
--- a/nf_core/test_datasets/list.py
+++ b/nf_core/test_datasets/list.py
@@ -56,7 +56,7 @@ def list_datasets(
     tree = list_files_by_branch(branch, all_branches, ignored_file_prefixes)
 
     out = []
-    for b in tree.keys():
+    for b in tree:
         files = sorted(tree[b])
         for f in files:
             if generate_nf_path:
diff --git a/nf_core/test_datasets/test_datasets_utils.py b/nf_core/test_datasets/test_datasets_utils.py
index 14719c6d8c..86491bfce3 100644
--- a/nf_core/test_datasets/test_datasets_utils.py
+++ b/nf_core/test_datasets/test_datasets_utils.py
@@ -82,11 +82,15 @@ def get_remote_branch_names() -> list[str]:
     return branches
 
 
-def get_remote_tree_for_branch(branch: str, only_files: bool = True, ignored_prefixes: list[str] = []) -> list[str]:
+def get_remote_tree_for_branch(
+    branch: str, only_files: bool = True, ignored_prefixes: list[str] | None = None
+) -> list[str]:
     """
     For a given branch name, return the file tree by querying the github API
     at the endpoint at `/repos/nf-core/test-datasets/git/trees/`
     """
+    if ignored_prefixes is None:
+        ignored_prefixes = []
     gh_filetree_file_value = "blob"  # value in nodes used to refer to "files"
     gh_response_filetree_key = "tree"  # key in response to refer to the filetree
     gh_filetree_type_key = "type"  # key in filetree nodes used to refer to their type
@@ -127,20 +131,18 @@ def get_remote_tree_for_branch(branch: str, only_files: bool = True, ignored_pre
 
 def list_files_by_branch(
     branch: str = "",
-    branches: list[str] = [],
-    ignored_file_prefixes: list[str] = [
-        ".",
-        "CITATION",
-        "LICENSE",
-        "README",
-        "docs",
-    ],
+    branches: list[str] | None = None,
+    ignored_file_prefixes: list[str] | None = None,
 ) -> dict[str, list[str]]:
     """
     Lists files for all branches in the test-datasets github repo.
     Returns dictionary with branchnames as keys and file-lists as values
     """
 
+    if ignored_file_prefixes is None:
+        ignored_file_prefixes = [".", "CITATION", "LICENSE", "README", "docs"]
+    if branches is None:
+        branches = []
     if len(branches) == 0:
         log.debug("Fetching list of remote branch names")
         branches = get_remote_branch_names()
@@ -151,7 +153,7 @@ def list_files_by_branch(
             log.error(f"No branches matching '{branch}'")
 
     log.debug("Fetching remote trees")
-    tree = dict()
+    tree = {}
     for b in branches:
         tree[b] = get_remote_tree_for_branch(b, only_files=True, ignored_prefixes=ignored_file_prefixes)
 
@@ -235,7 +237,7 @@ def get_or_prompt_file_selection(files: list[str], query: str | None) -> str:
             "File:", choices=files, style=nfcore_question_style, default=query, qmark=AUTOCOMPLETION_HINT
         ).unsafe_ask()
 
-        file_selected = any([selection == file for file in files])
+        file_selected = any(selection == file for file in files)
         if not file_selected:
             stdout.print("Please select a file.")
 
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 86de5a5fd1..2e16d78255 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -20,7 +20,7 @@
 import sys
 import time
 from collections.abc import Callable, Generator
-from contextlib import contextmanager
+from contextlib import contextmanager, suppress
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Literal
 
@@ -91,7 +91,10 @@
     os.environ.get("XDG_CACHE_HOME", Path(os.getenv("HOME") or "", ".cache")),
     "nfcore",
 )
-NFCORE_DIR = Path(os.environ.get("XDG_CONFIG_HOME", os.path.join(os.getenv("HOME") or "", ".config")), "nfcore")
+NFCORE_DIR = Path(
+    os.environ.get("XDG_CONFIG_HOME") or Path(os.getenv("HOME") or "") / ".config",
+    "nfcore",
+)
 
 
 def unquote(s: str) -> str:
@@ -152,11 +155,10 @@ def check_if_outdated(
             with concurrent.futures.ThreadPoolExecutor() as executor:
                 future = executor.submit(fetch_remote_version, source_url)
                 remote_version = future.result()
-        except Exception as e:
+        except requests.exceptions.RequestException as e:
             log.debug(f"Could not check for nf-core updates: {e}")
-    if remote_version is not None:
-        if Version(remote_version) > Version(current_version):
-            is_outdated = True
+    if remote_version is not None and Version(remote_version) > Version(current_version):
+        is_outdated = True
     return (is_outdated, current_version, remote_version)
 
 
@@ -204,7 +206,7 @@ def __init__(self, wf_path: Path) -> None:
         try:
             self.repo = git.Repo(self.wf_path)
             self.git_sha = self.repo.head.object.hexsha
-        except Exception as e:
+        except git.exc.GitError as e:
             log.debug(f"Could not find git hash for pipeline: {self.wf_path}. {e}")
 
         # Overwrite if we have the last commit from the PR - otherwise we get a merge commit hash
@@ -285,8 +287,7 @@ def is_pipeline_directory(wf_path):
         UserWarning: If one of the files are missing
     """
     for fn in ["main.nf", "nextflow.config"]:
-        path = os.path.join(wf_path, fn)
-        if not os.path.isfile(path):
+        if not Path(wf_path, fn).is_file():
             if wf_path == ".":
                 warning = f"Current directory is not a pipeline - '{fn}' is missing."
             else:
@@ -332,7 +333,7 @@ def get_nf_version() -> tuple[int, int, int, bool] | None:
             is_edge,
         )
         return parsed_version_tuple
-    except Exception as e:
+    except (subprocess.CalledProcessError, IndexError, ValueError) as e:
         log.warning(f"Error getting Nextflow version: {e}")
         return None
 
@@ -417,10 +418,7 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
                 # Log warning but don't raise - just regenerate the cache
                 log.warning(f"Unable to load cached JSON file '{cache_path}' due to error: {e}")
                 log.debug("Removing corrupted cache file and regenerating...")
-                try:
-                    cache_path.unlink()
-                except OSError:
-                    pass  # If we can't delete it, just continue
+                cache_path.unlink(missing_ok=True)
     log.debug("No config cache found")
 
     # Call `nextflow config`
@@ -481,7 +479,7 @@ def run_cmd(executable: str, cmd: str) -> tuple[bytes, bytes] | None:
         if e.errno == errno.ENOENT:
             raise RuntimeError(
                 f"It looks like {executable} is not installed. Please ensure it is available in your PATH."
-            )
+            ) from e
         else:
             return None
     except subprocess.CalledProcessError as e:
@@ -491,7 +489,7 @@ def run_cmd(executable: str, cmd: str) -> tuple[bytes, bytes] | None:
         else:
             raise RuntimeError(
                 f"Command '{full_cmd}' returned non-zero error code '{e.returncode}':\n[red]> {e.stderr.decode()}{e.stdout.decode()}"
-            )
+            ) from e
 
 
 def setup_nfcore_dir() -> bool:
@@ -534,7 +532,7 @@ def setup_nfcore_cachedir(cache_fn: str | Path) -> Path:
         if not Path(cachedir).exists():
             Path(cachedir).mkdir(parents=True)
     except PermissionError:
-        log.warn(f"Could not create cache directory: {cachedir}")
+        log.warning(f"Could not create cache directory: {cachedir}")
 
     return cachedir
 
@@ -559,8 +557,8 @@ def wait_cli_function(poll_func: Callable[[], bool], refresh_per_second: int = 2
                 if poll_func():
                     break
                 time.sleep(2)
-    except KeyboardInterrupt:
-        raise AssertionError("Cancelled!")
+    except KeyboardInterrupt as e:
+        raise AssertionError("Cancelled!") from e
 
 
 def poll_nfcore_web_api(api_url: str, post_data: dict | None = None) -> dict:
@@ -579,10 +577,10 @@ def poll_nfcore_web_api(api_url: str, post_data: dict | None = None) -> dict:
             else:
                 log.debug(f"requesting {api_url} with {post_data}")
                 response = requests.post(url=api_url, data=post_data)
-        except requests.exceptions.Timeout:
-            raise AssertionError(f"URL timed out: {api_url}")
-        except requests.exceptions.ConnectionError:
-            raise AssertionError(f"Could not connect to URL: {api_url}")
+        except requests.exceptions.Timeout as e:
+            raise AssertionError(f"URL timed out: {api_url}") from e
+        except requests.exceptions.ConnectionError as e:
+            raise AssertionError(f"Could not connect to URL: {api_url}") from e
         else:
             if response.status_code != 200 and response.status_code != 301:
                 response_content = response.content
@@ -598,8 +596,8 @@ def poll_nfcore_web_api(api_url: str, post_data: dict | None = None) -> dict:
             try:
                 web_response = json.loads(response.content)
                 if "status" not in web_response:
-                    raise AssertionError()
-            except (json.decoder.JSONDecodeError, AssertionError, TypeError):
+                    raise AssertionError
+            except (json.decoder.JSONDecodeError, AssertionError, TypeError) as e:
                 response_content = response.content
                 if isinstance(response_content, bytes):
                     response_content = response_content.decode()
@@ -607,7 +605,7 @@ def poll_nfcore_web_api(api_url: str, post_data: dict | None = None) -> dict:
                 raise AssertionError(
                     f"nf-core website API results response not recognised: {api_url}\n "
                     "See verbose log for full response"
-                )
+                ) from e
             else:
                 return web_response
 
@@ -657,8 +655,8 @@ def __call__(self, r):
                 return r
 
         # Default auth if we're running and the gh CLI tool is installed
-        gh_cli_config_fn = os.path.expanduser("~/.config/gh/hosts.yml")
-        if self.auth is None and os.path.exists(gh_cli_config_fn):
+        gh_cli_config_fn = Path.home() / ".config" / "gh" / "hosts.yml"
+        if self.auth is None and gh_cli_config_fn.exists():
             try:
                 with open(gh_cli_config_fn) as fh:
                     gh_cli_config = yaml.safe_load(fh)
@@ -667,7 +665,7 @@ def __call__(self, r):
                         gh_cli_config["github.com"]["oauth_token"],
                     )
                     self.auth_mode = f"gh CLI config: {gh_cli_config['github.com']['user']}"
-            except Exception:
+            except (OSError, KeyError, yaml.YAMLError):
                 ex_type, ex_value, _ = sys.exc_info()
                 if ex_type is not None:
                     output = rich.markup.escape(f"{ex_type.__name__}: {ex_value}")
@@ -696,7 +694,7 @@ def log_content_headers(self, request, post_data=None):
             log.debug(json.dumps(dict(request.headers), indent=4))
             log.debug(json.dumps(request.json(), indent=4))
             log.debug(json.dumps(post_data, indent=4))
-        except Exception as e:
+        except (json.JSONDecodeError, TypeError) as e:
             log.debug(f"Could not parse JSON response from GitHub API! {e}")
             log.debug(request.headers)
             log.debug(request.content)
@@ -812,10 +810,10 @@ def anaconda_package(dep, dep_channels=None):
         anaconda_api_url = f"https://api.anaconda.org/package/{ch}/{depname}"
         try:
             response = requests.get(anaconda_api_url, timeout=10)
-        except requests.exceptions.Timeout:
-            raise LookupError(f"Anaconda API timed out: {anaconda_api_url}")
-        except requests.exceptions.ConnectionError:
-            raise LookupError("Could not connect to Anaconda API")
+        except requests.exceptions.Timeout as e:
+            raise LookupError(f"Anaconda API timed out: {anaconda_api_url}") from e
+        except requests.exceptions.ConnectionError as e:
+            raise LookupError("Could not connect to Anaconda API") from e
         else:
             if response.status_code == 200:
                 return response.json()
@@ -840,10 +838,8 @@ def parse_anaconda_licence(anaconda_response, version=None):
     # Licence for each version
     for f in anaconda_response["files"]:
         if not version or version == f.get("version"):
-            try:
+            with suppress(KeyError):
                 licences.add(f["attrs"]["license"])
-            except KeyError:
-                pass
     # Main licence field
     if len(list(licences)) == 0 and isinstance(anaconda_response["license"], str):
         licences.add(anaconda_response["license"])
@@ -881,10 +877,10 @@ def pip_package(dep):
     pip_api_url = f"https://pypi.python.org/pypi/{pip_depname}/json"
     try:
         response = requests.get(pip_api_url, timeout=10)
-    except requests.exceptions.Timeout:
-        raise LookupError(f"PyPI API timed out: {pip_api_url}")
-    except requests.exceptions.ConnectionError:
-        raise LookupError(f"PyPI API Connection error: {pip_api_url}")
+    except requests.exceptions.Timeout as e:
+        raise LookupError(f"PyPI API timed out: {pip_api_url}") from e
+    except requests.exceptions.ConnectionError as e:
+        raise LookupError(f"PyPI API Connection error: {pip_api_url}") from e
     else:
         if response.status_code == 200:
             return response.json()
@@ -916,8 +912,8 @@ def get_tag_date(tag_date):
 
     try:
         response = requests.get(biocontainers_api_url)
-    except requests.exceptions.ConnectionError:
-        raise LookupError("Could not connect to biocontainers.pro API")
+    except requests.exceptions.ConnectionError as e:
+        raise LookupError("Could not connect to biocontainers.pro API") from e
     else:
         if response.status_code == 200:
             try:
@@ -959,8 +955,8 @@ def get_tag_date(tag_date):
                 if singularity_image is None:
                     raise LookupError(f"Could not find singularity container for {package}")
                 return docker_image_name, singularity_image["image_name"]
-            except TypeError:
-                raise LookupError(f"Could not find docker or singularity container for {package}")
+            except TypeError as e:
+                raise LookupError(f"Could not find docker or singularity container for {package}") from e
         elif response.status_code != 404:
             raise LookupError(f"Unexpected response code `{response.status_code}` for {biocontainers_api_url}")
         elif response.status_code == 404:
@@ -1005,7 +1001,7 @@ def is_file_binary(path):
     binary_extensions = [".jpeg", ".jpg", ".png", ".zip", ".gz", ".jar", ".tar"]
 
     # Check common file extensions
-    _, file_extension = os.path.splitext(path)
+    file_extension = Path(path).suffix
     if file_extension in binary_extensions:
         return True
 
@@ -1043,7 +1039,7 @@ def prompt_remote_pipeline_name(wfs):
     if pipeline.count("/") == 1:
         try:
             gh_api.safe_get(f"https://api.github.com/repos/{pipeline}")
-        except Exception:
+        except requests.exceptions.RequestException:
             # No repo found - pass and raise error at the end
             pass
         else:
@@ -1072,7 +1068,7 @@ def prompt_pipeline_release_branch(
 
     # Releases
     if len(wf_releases) > 0:
-        for tag in map(lambda release: release.get("tag_name"), wf_releases):
+        for tag in (release.get("tag_name") for release in wf_releases):
             tag_display = [
                 ("fg:ansiblue", f"{tag}  "),
                 ("class:choice-default", "[release]"),
@@ -1081,7 +1077,7 @@ def prompt_pipeline_release_branch(
             tag_set.append(str(tag))
 
     # Branches
-    for branch in wf_branches.keys():
+    for branch in wf_branches:
         branch_display = [
             ("fg:ansiyellow", f"{branch}  "),
             ("class:choice-default", "[branch]"),
@@ -1112,7 +1108,7 @@ class SingularityCacheFilePathValidator(questionary.Validator):
 
     def validate(self, value):
         if len(value.text):
-            if os.path.isfile(value.text):
+            if Path(value.text).is_file():
                 return True
             else:
                 raise questionary.ValidationError(
@@ -1147,12 +1143,10 @@ def get_repo_releases_branches(pipeline, wfs):
             pipeline = wf.full_name
 
             # Store releases and stop loop
-            wf_releases = list(
-                sorted(
-                    wf.releases,
-                    key=lambda k: k.get("published_at_timestamp", 0),
-                    reverse=True,
-                )
+            wf_releases = sorted(
+                wf.releases,
+                key=lambda k: k.get("published_at_timestamp", 0),
+                reverse=True,
             )
             break
 
@@ -1173,12 +1167,10 @@ def get_repo_releases_branches(pipeline, wfs):
                     raise AssertionError(f"Not able to find pipeline '{pipeline}'")
             except AttributeError:
                 # Success! We have a list, which doesn't work with .get() which is looking for a dict key
-                wf_releases = list(
-                    sorted(
-                        rel_r.json(),
-                        key=lambda k: k.get("published_at_timestamp", 0),
-                        reverse=True,
-                    )
+                wf_releases = sorted(
+                    rel_r.json(),
+                    key=lambda k: k.get("published_at_timestamp", 0),
+                    reverse=True,
                 )
 
                 # Get release tag commit hashes
@@ -1465,7 +1457,7 @@ def load_tools_config(directory: str | Path = ".") -> tuple[Path | None, NFCoreY
         error_message = f"Config file '{config_fn}' is invalid"
         for error in e.errors():
             error_message += f"\n{error['loc'][0]}: {error['msg']}\ninput: {error['input']}"
-        raise AssertionError(error_message)
+        raise AssertionError(error_message) from e
 
     wf_config = fetch_wf_config(Path(directory))
     if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config:
diff --git a/pyproject.toml b/pyproject.toml
index 125d35a6a6..d2c0483e4c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -124,7 +124,20 @@ target-version = "py310"
 cache-dir = "~/.cache/ruff"
 
 [tool.ruff.lint]
-select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+select = [
+    "I",                     # isort
+    "E1", "E4", "E7", "E9",  # pycodestyle errors (partial)
+    "F",                     # pyflakes
+    "UP",                    # pyupgrade
+    "N",                     # pep8-naming
+    "B",                     # flake8-bugbear - catches common bugs and design problems
+    "RSE",                   # flake8-raise - unnecessary parentheses on raised exceptions
+    "PTH",                   # flake8-use-pathlib - prefer pathlib over os.path
+    "SIM",                   # flake8-simplify - simplifies code patterns
+    "C4",                    # flake8-comprehensions - better list/dict/set comprehensions
+    "BLE",                   # flake8-blind-except - catches blind except clauses
+]
+ignore = ["PTH123"]
 
 [tool.ruff.lint.isort]
 known-first-party = ["nf_core"]
diff --git a/tests/components/test_components_utils.py b/tests/components/test_components_utils.py
index 03f69a10c0..da677143f2 100644
--- a/tests/components/test_components_utils.py
+++ b/tests/components/test_components_utils.py
@@ -71,11 +71,11 @@ def test_environment_variables_override(self):
         try:
             with mock.patch.dict(os.environ, mock_env):
                 importlib.reload(nf_core.components.constants)
-                assert nf_core.components.constants.NF_CORE_MODULES_NAME == mock_env["NF_CORE_MODULES_NAME"]
-                assert nf_core.components.constants.NF_CORE_MODULES_REMOTE == mock_env["NF_CORE_MODULES_REMOTE"]
+                assert mock_env["NF_CORE_MODULES_NAME"] == nf_core.components.constants.NF_CORE_MODULES_NAME
+                assert mock_env["NF_CORE_MODULES_REMOTE"] == nf_core.components.constants.NF_CORE_MODULES_REMOTE
                 assert (
-                    nf_core.components.constants.NF_CORE_MODULES_DEFAULT_BRANCH
-                    == mock_env["NF_CORE_MODULES_DEFAULT_BRANCH"]
+                    mock_env["NF_CORE_MODULES_DEFAULT_BRANCH"]
+                    == nf_core.components.constants.NF_CORE_MODULES_DEFAULT_BRANCH
                 )
         finally:
             importlib.reload(nf_core.components.constants)
diff --git a/tests/conftest.py b/tests/conftest.py
index fbaf10dfbd..126a2954e1 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,5 +1,6 @@
 """Global pytest configuration for nf-core tests setting up worker-specific cache directories to avoid git lock issues."""
 
+import contextlib
 import os
 import shutil
 import tempfile
@@ -42,12 +43,8 @@ def pytest_unconfigure(config):
 
     # Clean up temporary directories
     if hasattr(config, "_temp_cache_dir"):
-        try:
+        with contextlib.suppress(OSError, FileNotFoundError):
             shutil.rmtree(config._temp_cache_dir)
-        except (OSError, FileNotFoundError):
-            pass
     if hasattr(config, "_temp_config_dir"):
-        try:
+        with contextlib.suppress(OSError, FileNotFoundError):
             shutil.rmtree(config._temp_config_dir)
-        except (OSError, FileNotFoundError):
-            pass
diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py
index f6886d2ea8..21a44226b3 100644
--- a/tests/modules/lint/test_environment_yml.py
+++ b/tests/modules/lint/test_environment_yml.py
@@ -179,7 +179,7 @@ def test_environment_yml_invalid_files(tmp_path, invalid_content, filename):
     """Test that invalid YAML files raise exceptions"""
     test_file, module, lint = setup_test_environment(tmp_path, invalid_content, filename)
 
-    with pytest.raises(Exception):
+    with pytest.raises(ruamel.yaml.YAMLError):
         environment_yml(lint, module)
 
 
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index df4da94ec7..b793602e19 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -419,13 +419,13 @@ def test_get_outputs_with_hidden_attribute(tmp_path):
 
     # Check that the path pattern doesn't include "hidden: true"
     path_key = list(prof_output[0][1].keys())[0]
-    assert '"*.{prof,pidx}*"' == path_key, f"Expected '\"*.{{prof,pidx}}*\"', got '{path_key}'"
+    assert path_key == '"*.{prof,pidx}*"', f"Expected '\"*.{{prof,pidx}}*\"', got '{path_key}'"
     assert "hidden" not in path_key, f"Pattern should not contain 'hidden': {path_key}"
 
     # Check the data output also doesn't include "hidden: true"
     data_output = component.outputs["data"]
     data_path_key = list(data_output[0].keys())[0]
-    assert '"data.csv"' == data_path_key, f"Expected '\"data.csv\"', got '{data_path_key}'"
+    assert data_path_key == '"data.csv"', f"Expected '\"data.csv\"', got '{data_path_key}'"
     assert "hidden" not in data_path_key, f"Pattern should not contain 'hidden': {data_path_key}"
 
 
diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py
index f3b377be33..63e6eb9c2c 100644
--- a/tests/modules/test_bump_versions.py
+++ b/tests/modules/test_bump_versions.py
@@ -1,4 +1,3 @@
-import os
 import re
 import tempfile
 from pathlib import Path
@@ -18,7 +17,7 @@ class TestModulesBumpVersions(TestModules):
     def test_modules_bump_versions_single_module(self):
         """Test updating a single module"""
         # Change the bpipe/test version to an older version
-        env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
+        env_yml_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
         with open(env_yml_path) as fh:
             content = fh.read()
         new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content)
@@ -98,7 +97,7 @@ def test_modules_bump_versions_fail(self):
     def test_modules_bump_versions_fail_unknown_version(self):
         """Fail because of an unknown version"""
         # Change the bpipe/test version to an older version
-        env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
+        env_yml_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
         with open(env_yml_path) as fh:
             content = fh.read()
         new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content)
diff --git a/tests/modules/test_create.py b/tests/modules/test_create.py
index cf0efc6b04..6a5420db8e 100644
--- a/tests/modules/test_create.py
+++ b/tests/modules/test_create.py
@@ -1,4 +1,3 @@
-import os
 import shutil
 from pathlib import Path
 from unittest import mock
@@ -32,7 +31,7 @@ def test_modules_create_succeed(self):
             )
             with requests_cache.disabled():
                 module_create.create()
-        assert os.path.exists(os.path.join(self.pipeline_dir, "modules", "local", "trimgalore/main.nf"))
+        assert Path(self.pipeline_dir, "modules", "local", "trimgalore/main.nf").exists()
 
     def test_modules_create_fail_exists(self):
         """Fail at creating the same module twice"""
@@ -44,9 +43,8 @@ def test_modules_create_fail_exists(self):
             )
             with requests_cache.disabled():
                 module_create.create()
-            with pytest.raises(UserWarning) as excinfo:
-                with requests_cache.disabled():
-                    module_create.create()
+            with pytest.raises(UserWarning) as excinfo, requests_cache.disabled():
+                module_create.create()
         assert "module directory exists:" in str(excinfo.value)
 
     def test_modules_create_nfcore_modules(self):
@@ -59,10 +57,8 @@ def test_modules_create_nfcore_modules(self):
             )
             with requests_cache.disabled():
                 module_create.create()
-        assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "main.nf"))
-        assert os.path.exists(
-            os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "tests", "main.nf.test")
-        )
+        assert Path(self.nfcore_modules, "modules", "nf-core", "fastqc", "main.nf").exists()
+        assert Path(self.nfcore_modules, "modules", "nf-core", "fastqc", "tests", "main.nf.test").exists()
 
     def test_modules_create_nfcore_modules_subtool(self):
         """Create a tool/subtool module in a nf-core/modules clone"""
@@ -74,10 +70,8 @@ def test_modules_create_nfcore_modules_subtool(self):
             )
             with requests_cache.disabled():
                 module_create.create()
-        assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "main.nf"))
-        assert os.path.exists(
-            os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "tests", "main.nf.test")
-        )
+        assert Path(self.nfcore_modules, "modules", "nf-core", "star", "index", "main.nf").exists()
+        assert Path(self.nfcore_modules, "modules", "nf-core", "star", "index", "tests", "main.nf.test").exists()
 
     @mock.patch("rich.prompt.Confirm.ask")
     def test_modules_migrate(self, mock_rich_ask):
@@ -115,7 +109,7 @@ def test_modules_migrate(self, mock_rich_ask):
         # Check that pytest_modules.yml is updated
         with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
             modules_yml = yaml.safe_load(fh)
-        assert "samtools/sort" not in modules_yml.keys()
+        assert "samtools/sort" not in modules_yml
 
     @mock.patch("rich.prompt.Confirm.ask")
     def test_modules_migrate_no_delete(self, mock_rich_ask):
@@ -138,7 +132,7 @@ def test_modules_migrate_no_delete(self, mock_rich_ask):
         # Check that pytest_modules.yml is updated
         with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
             modules_yml = yaml.safe_load(fh)
-        assert "samtools/sort" not in modules_yml.keys()
+        assert "samtools/sort" not in modules_yml
 
     @mock.patch("rich.prompt.Confirm.ask")
     def test_modules_migrate_symlink(self, mock_rich_ask):
diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py
index 029eb32ccd..db0e522dba 100644
--- a/tests/modules/test_modules_json.py
+++ b/tests/modules/test_modules_json.py
@@ -23,7 +23,7 @@ def test_get_modules_json(self):
             try:
                 mod_json_sb = json.load(fh)
             except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
+                raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}") from e
 
         mod_json_obj = ModulesJson(self.pipeline_dir)
         mod_json = mod_json_obj.get_modules_json()
@@ -40,10 +40,10 @@ def test_mod_json_update(self):
         mod_json = mod_json_obj.get_modules_json()
         assert "MODULE_NAME" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
         assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]
-        assert "GIT_SHA" == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["git_sha"]
+        assert mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["git_sha"] == "GIT_SHA"
         assert (
-            NF_CORE_MODULES_DEFAULT_BRANCH
-            == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"]
+            mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"]
+            == NF_CORE_MODULES_DEFAULT_BRANCH
         )
         assert (
             "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed_by"]
@@ -214,7 +214,7 @@ def test_mod_json_dump(self):
             try:
                 mod_json_new = json.load(f)
             except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
+                raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}") from e
         assert mod_json == mod_json_new
 
     def test_mod_json_with_empty_modules_value(self):
diff --git a/tests/modules/test_modules_utils.py b/tests/modules/test_modules_utils.py
index 9a19f06159..8ef8d9d404 100644
--- a/tests/modules/test_modules_utils.py
+++ b/tests/modules/test_modules_utils.py
@@ -45,7 +45,7 @@ def test_filter_modules_by_name_tool_family(self):
         # Test filtering by tool family (super-tool)
         filtered = nf_core.modules.modules_utils.filter_modules_by_name(nfcore_modules, "samtools")
 
-        assert set(m.component_name for m in filtered) == {"samtools/view", "samtools/sort", "samtools/index"}
+        assert {m.component_name for m in filtered} == {"samtools/view", "samtools/sort", "samtools/index"}
 
     def test_filter_modules_by_name_exact_match_preferred(self):
         """Test that exact matches are preferred over prefix matches"""
diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py
index f608278618..ff881b41ad 100644
--- a/tests/modules/test_patch.py
+++ b/tests/modules/test_patch.py
@@ -1,4 +1,3 @@
-import os
 import tempfile
 from pathlib import Path
 from unittest import mock
@@ -324,11 +323,13 @@ def test_create_patch_update_fail(self):
         ).install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, temp_dir)
 
         temp_module_dir = temp_dir / BISMARK_ALIGN
-        for file in os.listdir(temp_module_dir):
-            assert file in os.listdir(module_path)
-            with open(module_path / file) as fh:
+        temp_files = {f.name for f in temp_module_dir.iterdir()}
+        module_files = {f.name for f in module_path.iterdir()}
+        for file_name in temp_files:
+            assert file_name in module_files
+            with open(module_path / file_name) as fh:
                 installed = fh.read()
-            with open(temp_module_dir / file) as fh:
+            with open(temp_module_dir / file_name) as fh:
                 shouldbe = fh.read()
             assert installed == shouldbe
 
diff --git a/tests/modules/test_remove.py b/tests/modules/test_remove.py
index 2caece7ce5..c63b3d4377 100644
--- a/tests/modules/test_remove.py
+++ b/tests/modules/test_remove.py
@@ -1,4 +1,3 @@
-import os
 from pathlib import Path
 
 from ..test_modules import TestModules
@@ -11,7 +10,7 @@ def test_modules_remove_trimgalore(self):
         assert self.mods_install.directory is not None
         module_path = Path(self.mods_install.directory, "modules", "nf-core", "modules", "trimgalore")
         assert self.mods_remove.remove("trimgalore")
-        assert os.path.exists(module_path) is False
+        assert not module_path.exists()
 
     def test_modules_remove_trimgalore_uninstalled(self):
         """Test removing TrimGalore! module without installing it"""
@@ -23,4 +22,4 @@ def test_modules_remove_multiqc_from_gitlab(self):
         assert self.mods_install.directory is not None
         module_path = Path(self.mods_install_gitlab.directory, "modules", "nf-core-test", "multiqc")
         assert self.mods_remove_gitlab.remove("multiqc", force=True)
-        assert os.path.exists(module_path) is False
+        assert not module_path.exists()
diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py
index 807f67cb81..be3df24256 100644
--- a/tests/modules/test_update.py
+++ b/tests/modules/test_update.py
@@ -167,7 +167,7 @@ def test_update_with_config_fixed_version(self):
         # Fix the trimgalore version in the .nf-core.yml to an old version
         update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
@@ -192,7 +192,7 @@ def test_update_with_config_dont_update(self):
         # Set the trimgalore field to no update in the .nf-core.yml
         update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
@@ -221,7 +221,7 @@ def test_update_with_config_fix_all(self):
         # Fix the version of all nf-core modules in the .nf-core.yml to an old version
         update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
@@ -245,7 +245,7 @@ def test_update_with_config_no_updates(self):
         # Fix the version of all nf-core modules in the .nf-core.yml to an old version
         update_config = {GITLAB_URL: False}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
diff --git a/tests/pipelines/download/test_container.py b/tests/pipelines/download/test_container.py
index 63fa7b9c07..a699eaa73f 100644
--- a/tests/pipelines/download/test_container.py
+++ b/tests/pipelines/download/test_container.py
@@ -60,13 +60,12 @@ def test_download_progress_sub_task(self):
             assert progress.tasks == []
 
             # Add another sub-task, this time that raises an exception
-            with pytest.raises(ValueError):
-                with progress.sub_task("Sub-task", total=28) as sub_task_id:
-                    assert sub_task_id == 1
-                    assert len(progress.tasks) == 1
-                    assert progress.task_ids[0] == sub_task_id
-                    assert progress.tasks[0].total == 28
-                    raise ValueError("This is a test error")
+            with pytest.raises(ValueError), progress.sub_task("Sub-task", total=28) as sub_task_id:
+                assert sub_task_id == 1
+                assert len(progress.tasks) == 1
+                assert progress.task_ids[0] == sub_task_id
+                assert progress.tasks[0].total == 28
+                raise ValueError("This is a test error")
 
             # The sub-task should also be gone now
             assert progress.tasks == []
diff --git a/tests/pipelines/download/test_singularity.py b/tests/pipelines/download/test_singularity.py
index c7a05dbca3..eb6bfe1bbb 100644
--- a/tests/pipelines/download/test_singularity.py
+++ b/tests/pipelines/download/test_singularity.py
@@ -658,7 +658,7 @@ def test_file_download(self, outdir):
                 output_path = outdir / Path(src_url).name
                 downloader.download_file(src_url, output_path)
                 assert (output_path).exists()
-                assert os.path.getsize(output_path) == 27
+                assert output_path.stat().st_size == 27
                 assert (
                     "nf_core.pipelines.download.singularity",
                     logging.DEBUG,
@@ -704,7 +704,7 @@ def test_file_download(self, outdir):
             # Fire in the hole ! The download will be aborted and no output file will be created
             src_url = "https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/sarscov2/genome/genome.fasta.fai"
             output_path = outdir / Path(src_url).name
-            os.unlink(output_path)
+            output_path.unlink()
             downloader.kill_with_fire = True
             with pytest.raises(KeyboardInterrupt):
                 downloader.download_file(src_url, output_path)
diff --git a/tests/pipelines/download/test_utils.py b/tests/pipelines/download/test_utils.py
index f3d35b333f..a04a65de15 100644
--- a/tests/pipelines/download/test_utils.py
+++ b/tests/pipelines/download/test_utils.py
@@ -1,4 +1,3 @@
-import os
 import subprocess
 import unittest
 from pathlib import Path
@@ -33,7 +32,7 @@ def test_intermediate_file(self, outdir):
             tmp.write(b"Hello, World!")
 
         assert output_path.exists()
-        assert os.path.getsize(output_path) == 13
+        assert output_path.stat().st_size == 13
         assert not tmp_path.exists()
 
         # Run an external command as in pull_image
@@ -43,40 +42,36 @@ def test_intermediate_file(self, outdir):
             subprocess.check_call([f"echo 'Hello, World!' > {tmp_path}"], shell=True)
 
         assert (output_path).exists()
-        assert os.path.getsize(output_path) == 14  # Extra \n !
+        assert output_path.stat().st_size == 14  # Extra \n !
         assert not (tmp_path).exists()
 
         # Code that fails. The file shall not exist
 
         # Directly write to the file and raise an exception
         output_path = outdir / "testfile3"
-        with pytest.raises(ValueError):
-            with intermediate_file(output_path) as tmp:
-                tmp_path = Path(tmp.name)
-                tmp.write(b"Hello, World!")
-                raise ValueError("This is a test error")
+        with pytest.raises(ValueError), intermediate_file(output_path) as tmp:
+            tmp_path = Path(tmp.name)
+            tmp.write(b"Hello, World!")
+            raise ValueError("This is a test error")
 
         assert not (output_path).exists()
         assert not (tmp_path).exists()
 
         # Run an external command and raise an exception
         output_path = outdir / "testfile4"
-        with pytest.raises(subprocess.CalledProcessError):
-            with intermediate_file(output_path) as tmp:
-                tmp_path = Path(tmp.name)
-                subprocess.check_call([f"echo 'Hello, World!' > {tmp_path}"], shell=True)
-                subprocess.check_call(["ls", "/dummy"])
+        with pytest.raises(subprocess.CalledProcessError), intermediate_file(output_path) as tmp:
+            tmp_path = Path(tmp.name)
+            subprocess.check_call([f"echo 'Hello, World!' > {tmp_path}"], shell=True)
+            subprocess.check_call(["ls", "/dummy"])
 
         assert not (output_path).exists()
         assert not (tmp_path).exists()
 
         # Test for invalid output paths
-        with pytest.raises(DownloadError):
-            with intermediate_file(outdir) as tmp:
-                pass
+        with pytest.raises(DownloadError), intermediate_file(outdir) as tmp:
+            pass
 
         output_path = outdir / "testfile5"
-        os.symlink("/dummy", output_path)
-        with pytest.raises(DownloadError):
-            with intermediate_file(output_path) as tmp:
-                pass
+        output_path.symlink_to("/dummy")
+        with pytest.raises(DownloadError), intermediate_file(output_path) as tmp:
+            pass
diff --git a/tests/pipelines/lint/test_configs.py b/tests/pipelines/lint/test_configs.py
index 7bb6329b5b..3b179c9f84 100644
--- a/tests/pipelines/lint/test_configs.py
+++ b/tests/pipelines/lint/test_configs.py
@@ -21,7 +21,7 @@ def test_withname_in_modules_config(self):
         result = lint_obj.modules_config()
         assert len(result["failed"]) == 0
         assert any(
-            ["`FASTQC` found in `conf/modules.config` and Nextflow scripts." in passed for passed in result["passed"]]
+            "`FASTQC` found in `conf/modules.config` and Nextflow scripts." in passed for passed in result["passed"]
         )
 
     def test_superfluous_withname_in_modules_config_fails(self):
diff --git a/tests/pipelines/lint/test_merge_markers.py b/tests/pipelines/lint/test_merge_markers.py
index 3094d8f8d1..d724eb4e43 100644
--- a/tests/pipelines/lint/test_merge_markers.py
+++ b/tests/pipelines/lint/test_merge_markers.py
@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 
 import nf_core.pipelines.lint
 
@@ -10,10 +10,10 @@ def test_merge_markers_found(self):
         """Missing 'jobs' field should result in failure"""
         new_pipeline = self._make_pipeline_copy()
 
-        with open(os.path.join(new_pipeline, "main.nf")) as fh:
+        with open(Path(new_pipeline, "main.nf")) as fh:
             main_nf_content = fh.read()
         main_nf_content = ">>>>>>>\n" + main_nf_content
-        with open(os.path.join(new_pipeline, "main.nf"), "w") as fh:
+        with open(Path(new_pipeline, "main.nf"), "w") as fh:
             fh.write(main_nf_content)
 
         lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index f8c3c1f31f..d71b25280b 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -1,4 +1,3 @@
-import os
 import re
 from pathlib import Path
 
@@ -55,7 +54,7 @@ def test_nextflow_config_dev_in_release_mode_failed(self):
     def test_nextflow_config_missing_test_profile_failed(self):
         """Test failure if config file does not contain `test` profile."""
         # Change the name of the test profile so there is no such profile
-        nf_conf_file = os.path.join(self.new_pipeline, "nextflow.config")
+        nf_conf_file = Path(self.new_pipeline, "nextflow.config")
         with open(nf_conf_file) as f:
             content = f.read()
             fail_content = re.sub(r"\btest\b", "testfail", content)
diff --git a/tests/pipelines/lint/test_rocrate_readme_sync.py b/tests/pipelines/lint/test_rocrate_readme_sync.py
index cd600481e2..6ac0068e9c 100644
--- a/tests/pipelines/lint/test_rocrate_readme_sync.py
+++ b/tests/pipelines/lint/test_rocrate_readme_sync.py
@@ -19,7 +19,7 @@ def test_rocrate_readme_sync_fixed(self):
             try:
                 rocrate = json.load(f)
             except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{json_path}' due to error {e}")
+                raise UserWarning(f"Unable to load JSON file '{json_path}' due to error {e}") from e
         rocrate["@graph"][0]["description"] = "This is a test script"
         with open(json_path, "w") as f:
             json.dump(rocrate, f, indent=4)
diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index d2ee4dd246..ccd125d17e 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -72,13 +72,13 @@ def test_pipeline_creation_initiation_with_yml(self, tmp_path):
             default_branch=self.default_branch,
         )
         pipeline.init_pipeline()
-        assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+        assert Path(pipeline.outdir, ".git").is_dir()
         assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch()
 
         # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input
-        assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
-        assert os.path.exists(os.path.join(pipeline.outdir, ".nf-core.yml"))
-        with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
+        assert not Path(pipeline.outdir, "pipeline_template.yml").exists()
+        assert Path(pipeline.outdir, ".nf-core.yml").exists()
+        with open(Path(pipeline.outdir, ".nf-core.yml")) as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
             assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
@@ -89,13 +89,13 @@ def test_pipeline_creation_initiation_customize_template(self, tmp_path):
             outdir=tmp_path, template_config=PIPELINE_TEMPLATE_YML, default_branch=self.default_branch
         )
         pipeline.init_pipeline()
-        assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+        assert Path(pipeline.outdir, ".git").is_dir()
         assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch()
 
         # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input
-        assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
-        assert os.path.exists(os.path.join(pipeline.outdir, ".nf-core.yml"))
-        with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
+        assert not Path(pipeline.outdir, "pipeline_template.yml").exists()
+        assert Path(pipeline.outdir, ".nf-core.yml").exists()
+        with open(Path(pipeline.outdir, ".nf-core.yml")) as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
             assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
@@ -151,7 +151,7 @@ def test_template_customisation_all_files_grouping(self):
         ]
         all_skipped_files = []
         for section in template_features_yml.values():
-            for feature in section["features"].keys():
+            for feature in section["features"]:
                 if section["features"][feature]["skippable_paths"]:
                     all_skipped_files.extend(section["features"][feature]["skippable_paths"])
 
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index ed23872f66..e97f2f10b6 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -325,7 +325,7 @@ def test_build_command_params(self):
             try:
                 saved_json = json.load(fh)
             except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}")
+                raise UserWarning(f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}") from e
 
         assert saved_json == {"input": "custom_input"}
 
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index f8e029beeb..2d77d34d73 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -59,14 +59,14 @@ def test_load_lint_config_ignore_all_tests(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
 
         # Make a config file listing all test names
-        config_dict = {"repository_type": "pipeline", "lint": {test_name: False for test_name in lint_obj.lint_tests}}
+        config_dict = {"repository_type": "pipeline", "lint": dict.fromkeys(lint_obj.lint_tests, False)}
         with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh:
             yaml.dump(config_dict, fh)
 
         # Load the new lint config file and check
         lint_obj._load_lint_config()
         assert lint_obj.lint_config is not None
-        assert sorted(list(lint_obj.lint_config.model_dump(exclude_none=True))) == sorted(lint_obj.lint_tests)
+        assert sorted(lint_obj.lint_config.model_dump(exclude_none=True)) == sorted(lint_obj.lint_tests)
 
         # Try running linting and make sure that all tests are ignored
         lint_obj._lint_pipeline()
@@ -113,7 +113,7 @@ def test_json_output(self, tmp_dir):
             try:
                 saved_json = json.load(fh)
             except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}")
+                raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}") from e
         assert saved_json["num_tests_pass"] > 0
         assert saved_json["num_tests_warned"] > 0
         assert saved_json["num_tests_ignored"] == 0
diff --git a/tests/pipelines/test_list.py b/tests/pipelines/test_list.py
index aacc3805e8..d1227a4727 100644
--- a/tests/pipelines/test_list.py
+++ b/tests/pipelines/test_list.py
@@ -106,14 +106,14 @@ def test_local_workflows_compare_and_fail_silently(self):
 
         rwf_ex.releases = None
 
-    @mock.patch("nf_core.pipelines.list.LocalWorkflow")
-    def test_parse_local_workflow_and_succeed(self, mock_local_wf):
+    def test_parse_local_workflow_and_succeed(self):
         test_path = self.tmp_nxf / "nf-core"
-        if not os.path.isdir(test_path):
-            os.makedirs(test_path)
+        if not test_path.is_dir():
+            test_path.mkdir(parents=True)
+        # Create a dummy workflow directory (not just a file)
+        dummy_wf_path = self.tmp_nxf / "nf-core" / "dummy-wf"
+        dummy_wf_path.mkdir(parents=True, exist_ok=True)
         assert os.environ["NXF_ASSETS"] == self.tmp_nxf_str
-        with open(self.tmp_nxf / "nf-core/dummy-wf", "w") as f:
-            f.write("dummy")
         workflows_obj = nf_core.pipelines.list.Workflows()
         workflows_obj.get_local_nf_workflows()
         assert len(workflows_obj.local_workflows) == 1
@@ -122,21 +122,24 @@ def test_parse_local_workflow_and_succeed(self, mock_local_wf):
     @mock.patch("subprocess.check_output")
     def test_parse_local_workflow_home(self, mock_local_wf, mock_subprocess):
         test_path = self.tmp_nxf / "nf-core"
-        if not os.path.isdir(test_path):
-            os.makedirs(test_path)
+        if not test_path.is_dir():
+            test_path.mkdir(parents=True)
         assert os.environ["NXF_ASSETS"] == self.tmp_nxf_str
         with open(self.tmp_nxf / "nf-core/dummy-wf", "w") as f:
             f.write("dummy")
         workflows_obj = nf_core.pipelines.list.Workflows()
         workflows_obj.get_local_nf_workflows()
 
-    @mock.patch("os.stat")
     @mock.patch("git.Repo")
-    def test_local_workflow_investigation(self, mock_repo, mock_stat):
+    def test_local_workflow_investigation(self, mock_repo):
         local_wf = nf_core.pipelines.list.LocalWorkflow("dummy")
         local_wf.local_path = self.tmp_nxf.parent
-        mock_repo.head.commit.hexsha = "h00r4y"
-        mock_stat.st_mode = 1
+        # Create the .git/FETCH_HEAD file that the code expects
+        git_dir = self.tmp_nxf.parent / ".git"
+        git_dir.mkdir(parents=True, exist_ok=True)
+        (git_dir / "FETCH_HEAD").touch()
+        mock_repo.return_value.head.commit.hexsha = "h00r4y"
+        mock_repo.return_value.remotes.origin.url = "https://github.com/nf-core/dummy"
         local_wf.get_local_nf_workflow_details()
 
     def test_worflow_filter(self):
diff --git a/tests/pipelines/test_refgenie.py b/tests/pipelines/test_refgenie.py
index 734a2368bd..2b824f599e 100644
--- a/tests/pipelines/test_refgenie.py
+++ b/tests/pipelines/test_refgenie.py
@@ -24,7 +24,7 @@ def setUp(self):
         # avoids adding includeConfig statement to config file outside the current tmpdir
         try:
             self.NXF_HOME_ORIGINAL = os.environ["NXF_HOME"]
-        except Exception:
+        except KeyError:
             self.NXF_HOME_ORIGINAL = None
         os.environ["NXF_HOME"] = str(self.NXF_HOME)
 
diff --git a/tests/pipelines/test_rocrate.py b/tests/pipelines/test_rocrate.py
index a073beae31..47b914593a 100644
--- a/tests/pipelines/test_rocrate.py
+++ b/tests/pipelines/test_rocrate.py
@@ -41,7 +41,6 @@ def test_rocrate_creation(self):
         """Run the nf-core rocrate command"""
 
         # Run the command
-        self.rocrate_obj
         assert self.rocrate_obj.create_rocrate(self.pipeline_dir, self.pipeline_dir)
 
         # Check that the crate was created
diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py
index efc2798969..364fd994e7 100644
--- a/tests/pipelines/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -1,7 +1,6 @@
 """Tests covering the pipeline schema code."""
 
 import json
-import os
 import shutil
 import tempfile
 import unittest
@@ -27,20 +26,20 @@ def setUp(self):
         self.schema_obj.schema_draft = "https://json-schema.org/draft/2020-12/schema"
         self.schema_obj.defs_notation = "$defs"
         self.schema_obj.validation_plugin = "nf-schema"
-        self.root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+        self.root_repo_dir = Path(__file__).resolve().parent.parent
 
         # Create a test pipeline in temp directory
         self.tmp_dir = tempfile.mkdtemp()
-        self.template_dir = os.path.join(self.tmp_dir, "wf")
+        self.template_dir = Path(self.tmp_dir, "wf")
         create_obj = nf_core.pipelines.create.create.PipelineCreate(
             "testpipeline", "a description", "Me", outdir=self.template_dir, no_git=True
         )
         create_obj.init_pipeline()
 
-        self.template_schema = os.path.join(self.template_dir, "nextflow_schema.json")
+        self.template_schema = self.template_dir / "nextflow_schema.json"
 
     def tearDown(self):
-        if os.path.exists(self.tmp_dir):
+        if Path(self.tmp_dir).exists():
             shutil.rmtree(self.tmp_dir)
 
     def test_load_lint_schema(self):
@@ -55,7 +54,7 @@ def test_load_lint_schema_nofile(self):
 
     def test_load_lint_schema_notjson(self):
         """Check that linting raises properly if a non-JSON file is given"""
-        self.schema_obj.get_schema_path(os.path.join(self.template_dir, "nextflow.config"))
+        self.schema_obj.get_schema_path(self.template_dir / "nextflow.config")
         with pytest.raises(AssertionError):
             self.schema_obj.load_lint_schema()
 
diff --git a/tests/pipelines/test_sync.py b/tests/pipelines/test_sync.py
index 746b2db76a..4e6f6f80db 100644
--- a/tests/pipelines/test_sync.py
+++ b/tests/pipelines/test_sync.py
@@ -118,7 +118,7 @@ def test_inspect_sync_dir_dirty(self):
                 psync.inspect_sync_dir()
             assert exc_info.value.args[0].startswith("Uncommitted changes found in pipeline directory!")
         finally:
-            os.remove(test_fn)
+            test_fn.unlink()
 
     def test_inspect_sync_ignored_files(self):
         """
@@ -180,7 +180,8 @@ def test_delete_tracked_template_branch_files(self):
         psync.checkout_template_branch()
         psync.delete_tracked_template_branch_files()
         top_level_ignored = self._get_top_level_ignored(psync)
-        assert set(os.listdir(self.pipeline_dir)) == set([".git"]).union(top_level_ignored)
+        pipeline_contents = {f.name for f in Path(self.pipeline_dir).iterdir()}
+        assert pipeline_contents == {".git"}.union(top_level_ignored)
 
     def test_delete_tracked_template_branch_files_unlink_throws_error(self):
         """Test that SyncExceptionError is raised when Path.unlink throws an exception"""
@@ -299,11 +300,13 @@ def test_create_template_pipeline(self):
         psync.checkout_template_branch()
         psync.delete_tracked_template_branch_files()
         top_level_ignored = self._get_top_level_ignored(psync)
-        assert set(os.listdir(self.pipeline_dir)) == set([".git"]).union(top_level_ignored)
+        pipeline_contents = {f.name for f in Path(self.pipeline_dir).iterdir()}
+        assert pipeline_contents == {".git"}.union(top_level_ignored)
         # Now create the new template
         psync.make_template_pipeline()
-        assert "main.nf" in os.listdir(self.pipeline_dir)
-        assert "nextflow.config" in os.listdir(self.pipeline_dir)
+        pipeline_path = Path(self.pipeline_dir)
+        assert (pipeline_path / "main.nf").exists()
+        assert (pipeline_path / "nextflow.config").exists()
 
     def test_commit_template_changes_nochanges(self):
         """Try to commit the TEMPLATE branch, but no changes were made"""
diff --git a/tests/subworkflows/test_create.py b/tests/subworkflows/test_create.py
index 704a23772e..ec93d8311d 100644
--- a/tests/subworkflows/test_create.py
+++ b/tests/subworkflows/test_create.py
@@ -81,7 +81,7 @@ def test_subworkflows_migrate(self, mock_rich_ask):
         # Check that pytest_modules.yml is updated
         with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
             modules_yml = yaml.safe_load(fh)
-        assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
+        assert "subworkflows/bam_stats_samtools" not in modules_yml
 
     @mock.patch("rich.prompt.Confirm.ask")
     def test_subworkflows_migrate_no_delete(self, mock_rich_ask):
@@ -106,4 +106,4 @@ def test_subworkflows_migrate_no_delete(self, mock_rich_ask):
         # Check that pytest_modules.yml is updated
         with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
             modules_yml = yaml.safe_load(fh)
-        assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
+        assert "subworkflows/bam_stats_samtools" not in modules_yml
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index 80aeb1d113..f64a616bbf 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -230,16 +230,13 @@ def test_subworkflows_lint_include_multiple_alias(self):
         assert len(subworkflow_lint.passed) > 0
         assert len(subworkflow_lint.warned) == 6
         assert any(
-            [x.message == "Included component 'SAMTOOLS_STATS_1' used in main.nf" for x in subworkflow_lint.passed]
+            x.message == "Included component 'SAMTOOLS_STATS_1' used in main.nf" for x in subworkflow_lint.passed
         )
         assert any(
-            [x.message == "Included component 'SAMTOOLS_STATS_2' not used in main.nf" for x in subworkflow_lint.warned]
+            x.message == "Included component 'SAMTOOLS_STATS_2' not used in main.nf" for x in subworkflow_lint.warned
         )
         assert any(
-            [
-                x.message.endswith("Can be ignored if the module is using topic channels")
-                for x in subworkflow_lint.warned
-            ]
+            x.message.endswith("Can be ignored if the module is using topic channels") for x in subworkflow_lint.warned
         )
 
         # cleanup
@@ -276,7 +273,7 @@ def test_subworkflows_lint_capitalization_fail(self):
         assert len(subworkflow_lint.failed) >= 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
         assert len(subworkflow_lint.warned) >= 0
-        assert any([x.lint_test == "workflow_capitals" for x in subworkflow_lint.failed])
+        assert any(x.lint_test == "workflow_capitals" for x in subworkflow_lint.failed)
 
         # cleanup
         self.subworkflow_remove.remove("bam_stats_samtools", force=True)
@@ -302,7 +299,7 @@ def test_subworkflows_absent_version(self):
         assert len(subworkflow_lint.failed) == 0
         assert len(subworkflow_lint.passed) > 0
         assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
-        assert any([x.lint_test == "test_snap_versions" for x in subworkflow_lint.warned])
+        assert any(x.lint_test == "test_snap_versions" for x in subworkflow_lint.warned)
 
         # cleanup
         with open(snap_file, "w") as fh:
@@ -319,7 +316,7 @@ def test_subworkflows_missing_test_dir(self):
         assert len(subworkflow_lint.failed) == 1
         assert len(subworkflow_lint.passed) > 0
         assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
-        assert any([x.lint_test == "test_dir_exists" for x in subworkflow_lint.failed])
+        assert any(x.lint_test == "test_dir_exists" for x in subworkflow_lint.failed)
 
         # cleanup
         shutil.copytree(test_dir_copy, test_dir)
@@ -507,10 +504,7 @@ def test_lint_clean_patch(self):
         # TODO: Add count test back, once we have finished topic conversion
         # assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
         assert any(
-            [
-                x.message.endswith("Can be ignored if the module is using topic channels")
-                for x in subworkflow_lint.warned
-            ]
+            x.message.endswith("Can be ignored if the module is using topic channels") for x in subworkflow_lint.warned
         )
 
     def test_lint_broken_patch(self):
@@ -532,8 +526,5 @@ def test_lint_broken_patch(self):
         # TODO: Add count test back, once we have finished topic conversion
         # assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
         assert any(
-            [
-                x.message.endswith("Can be ignored if the module is using topic channels")
-                for x in subworkflow_lint.warned
-            ]
+            x.message.endswith("Can be ignored if the module is using topic channels") for x in subworkflow_lint.warned
         )
diff --git a/tests/subworkflows/test_patch.py b/tests/subworkflows/test_patch.py
index 659ae2b1c4..b186bc1807 100644
--- a/tests/subworkflows/test_patch.py
+++ b/tests/subworkflows/test_patch.py
@@ -1,4 +1,3 @@
-import os
 import tempfile
 from pathlib import Path
 from unittest import mock
@@ -274,11 +273,13 @@ def test_create_patch_update_fail(self):
         ).install_component_files("bam_sort_stats_samtools", FAIL_SHA, update_obj.modules_repo, temp_dir)
 
         temp_module_dir = temp_dir / "bam_sort_stats_samtools"
-        for file in os.listdir(temp_module_dir):
-            assert file in os.listdir(swf_path)
-            with open(swf_path / file) as fh:
+        temp_files = {f.name for f in temp_module_dir.iterdir()}
+        swf_files = {f.name for f in swf_path.iterdir()}
+        for file_name in temp_files:
+            assert file_name in swf_files
+            with open(swf_path / file_name) as fh:
                 installed = fh.read()
-            with open(temp_module_dir / file) as fh:
+            with open(temp_module_dir / file_name) as fh:
                 shouldbe = fh.read()
             assert installed == shouldbe
 
diff --git a/tests/subworkflows/test_remove.py b/tests/subworkflows/test_remove.py
index 94cd64d0c1..88ea58acf8 100644
--- a/tests/subworkflows/test_remove.py
+++ b/tests/subworkflows/test_remove.py
@@ -30,11 +30,9 @@ def test_subworkflows_remove_subworkflow(self):
         # assert subworkflows key is removed from modules.json
         assert (
             "bam_sort_stats_samtools"
-            not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
-        )
-        assert (
-            "samtools/index" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"].keys()
+            not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]
         )
+        assert "samtools/index" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]
 
     def test_subworkflows_remove_subworkflow_keep_installed_module(self):
         """Test removing subworkflow and all it's dependencies after installing it, except for a separately installed module"""
@@ -57,11 +55,10 @@ def test_subworkflows_remove_subworkflow_keep_installed_module(self):
         # assert subworkflows key is removed from modules.json
         assert (
             "bam_sort_stats_samtools"
-            not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
+            not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]
         )
         assert (
-            "samtools/index"
-            in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys()
+            "samtools/index" in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]
         )
 
     def test_subworkflows_remove_one_of_two_subworkflow(self):
@@ -120,11 +117,6 @@ def test_subworkflows_remove_subworkflow_keep_installed_cross_org_module(self):
         assert Path.exists(nfcore_fastqc_path) is True
         assert mod_json_before != mod_json_after
         # assert subworkflows key is removed from modules.json
-        assert CROSS_ORGANIZATION_URL not in mod_json_after["repos"].keys()
-        assert (
-            "fastqc" in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys()
-        )
-        assert (
-            "fastp"
-            not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys()
-        )
+        assert CROSS_ORGANIZATION_URL not in mod_json_after["repos"]
+        assert "fastqc" in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]
+        assert "fastp" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]
diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py
index 7d2f78f041..936b61c782 100644
--- a/tests/subworkflows/test_update.py
+++ b/tests/subworkflows/test_update.py
@@ -157,7 +157,7 @@ def test_update_with_config_fixed_version(self):
         # Fix the subworkflow version in the .nf-core.yml to an old version
         update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": OLD_SUBWORKFLOWS_SHA}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
@@ -188,7 +188,7 @@ def test_update_with_config_dont_update(self):
         # Set the fastq_align_bowtie2 field to no update in the .nf-core.yml
         update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": False}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
@@ -219,7 +219,7 @@ def test_update_with_config_fix_all(self):
         # Fix the version of all nf-core subworkflows in the .nf-core.yml to an old version
         update_config = {NF_CORE_MODULES_REMOTE: OLD_SUBWORKFLOWS_SHA}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
@@ -250,7 +250,7 @@ def test_update_with_config_no_updates(self):
         # Set all repository updates to False
         update_config = {NF_CORE_MODULES_REMOTE: False}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        setattr(tools_config, "update", update_config)
+        tools_config.update = update_config
         assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
             yaml.dump(tools_config.model_dump(), f)
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 10727c3828..31f6c691aa 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -101,35 +101,35 @@ def test_cli_launch(self, mock_launcher):
         """Test nf-core pipeline is launched and cli parameters are passed on."""
         mock_launcher.return_value.launch_pipeline.return_value = True
 
-        temp_params_in = tempfile.NamedTemporaryFile()
-        params = {
-            "revision": "abcdef",
-            "id": "idgui",
-            "command-only": None,
-            "params-out": "/path/params/out",
-            "params-in": temp_params_in.name,
-            "save-all": None,
-            "show-hidden": None,
-            "url": "builder_url",
-        }
-        cmd = ["pipelines", "launch"] + self.assemble_params(params) + ["pipeline_name"]
-        result = self.invoke_cli(cmd)
+        with tempfile.NamedTemporaryFile() as temp_params_in:
+            params = {
+                "revision": "abcdef",
+                "id": "idgui",
+                "command-only": None,
+                "params-out": "/path/params/out",
+                "params-in": temp_params_in.name,
+                "save-all": None,
+                "show-hidden": None,
+                "url": "builder_url",
+            }
+            cmd = ["pipelines", "launch"] + self.assemble_params(params) + ["pipeline_name"]
+            result = self.invoke_cli(cmd)
 
-        assert result.exit_code == 0
+            assert result.exit_code == 0
 
-        mock_launcher.assert_called_once_with(
-            cmd[-1],
-            params["revision"],
-            "command-only" in params,
-            params["params-in"],
-            params["params-out"],
-            "save-all" in params,
-            "show-hidden" in params,
-            params["url"],
-            params["id"],
-        )
+            mock_launcher.assert_called_once_with(
+                cmd[-1],
+                params["revision"],
+                "command-only" in params,
+                params["params-in"],
+                params["params-out"],
+                "save-all" in params,
+                "show-hidden" in params,
+                params["url"],
+                params["id"],
+            )
 
-        mock_launcher.return_value.launch_pipeline.assert_called_once()
+            mock_launcher.return_value.launch_pipeline.assert_called_once()
 
     @mock.patch("nf_core.pipelines.launch.Launch")
     def test_cli_launch_no_params_in(self, mock_launcher):
@@ -267,37 +267,37 @@ def test_lint(self, mock_lint, mock_is_pipeline):
         mock_lint_results[2].failed = []
         mock_lint.return_value = mock_lint_results
 
-        temp_pipeline_dir = tempfile.NamedTemporaryFile()
-        params = {
-            "dir": temp_pipeline_dir.name,
-            "release": None,
-            "fix": "fix test",
-            "key": "key test",
-            "show-passed": None,
-            "fail-ignored": None,
-            "fail-warned": None,
-            "markdown": "output_file.md",
-            "json": "output_file.json",
-        }
-
-        cmd = ["pipelines", "lint"] + self.assemble_params(params)
-        result = self.invoke_cli(cmd)
+        with tempfile.NamedTemporaryFile() as temp_pipeline_dir:
+            params = {
+                "dir": temp_pipeline_dir.name,
+                "release": None,
+                "fix": "fix test",
+                "key": "key test",
+                "show-passed": None,
+                "fail-ignored": None,
+                "fail-warned": None,
+                "markdown": "output_file.md",
+                "json": "output_file.json",
+            }
+
+            cmd = ["pipelines", "lint"] + self.assemble_params(params)
+            result = self.invoke_cli(cmd)
 
-        assert result.exit_code == 0
-        mock_lint.assert_called_once_with(
-            params["dir"],
-            "release" in params,
-            (params["fix"],),
-            (params["key"],),
-            "show-passed" in params,
-            "fail-ignored" in params,
-            "fail-warned" in params,
-            "test",
-            params["markdown"],
-            params["json"],
-            "hide-progress" in params,
-            False,  # plain_text
-        )
+            assert result.exit_code == 0
+            mock_lint.assert_called_once_with(
+                params["dir"],
+                "release" in params,
+                (params["fix"],),
+                (params["key"],),
+                "show-passed" in params,
+                "fail-ignored" in params,
+                "fail-warned" in params,
+                "test",
+                params["markdown"],
+                params["json"],
+                "hide-progress" in params,
+                False,  # plain_text
+            )
 
     def test_lint_no_dir(self):
         """Test nf-core pipelines lint fails if --dir does not exist"""
diff --git a/tests/test_utils.py b/tests/test_utils.py
index f72de515c1..c7f5f37ed9 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -144,7 +144,7 @@ def test_get_repo_releases_branches_nf_core(self):
                 break
         else:
             raise AssertionError("Release 1.6 not found")
-        assert "dev" in wf_branches.keys()
+        assert "dev" in wf_branches
 
     def test_get_repo_releases_branches_not_nf_core(self):
         wfs = nf_core.pipelines.list.Workflows()
@@ -155,7 +155,7 @@ def test_get_repo_releases_branches_not_nf_core(self):
                 break
         else:
             raise AssertionError("MultiQC release v1.32 not found")
-        assert "main" in wf_branches.keys()
+        assert "main" in wf_branches
 
     def test_get_repo_releases_branches_not_exists(self):
         wfs = nf_core.pipelines.list.Workflows()
@@ -212,9 +212,8 @@ def test_set_wd(self):
 
     def test_set_wd_revert_on_raise(self):
         wd_before_context = Path().resolve()
-        with pytest.raises(Exception):
-            with nf_core.utils.set_wd(self.tmp_dir):
-                raise Exception
+        with pytest.raises(RuntimeError), nf_core.utils.set_wd(self.tmp_dir):
+            raise RuntimeError
         assert wd_before_context == Path().resolve()
 
     @mock.patch("nf_core.utils.run_cmd")