diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index 27eaf9bcb3..8304775d5f 100644
--- a/docs/api/_src/conf.py
+++ b/docs/api/_src/conf.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py
index 40c8f8984f..8472f78494 100644
--- a/nf_core/bump_version.py
+++ b/nf_core/bump_version.py
@@ -187,7 +187,7 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt
     fn = pipeline_obj._fp(filename)
     content = ""
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             content = fh.read()
     except FileNotFoundError:
         log.warning(f"File not found: '{fn}'")
diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 44924a2704..8332429835 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -227,7 +227,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
         if patch_path.exists():
             log.info(f"Modules {module_name} contains a patch file.")
             rewrite = False
-            with open(patch_path, "r") as fh:
+            with open(patch_path) as fh:
                 lines = fh.readlines()
                 for index, line in enumerate(lines):
                     # Check if there are old paths in the patch file and replace
@@ -264,7 +264,7 @@ def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[
         if self.repo_type == "pipeline":
             workflow_files = Path(self.dir, "workflows").glob("*.nf")
             for workflow_file in workflow_files:
-                with open(workflow_file, "r") as fh:
+                with open(workflow_file) as fh:
                     # 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:
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index eec533ce60..2dc5bf4fc1 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -138,7 +138,7 @@ def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str
     """
     modules = []
     subworkflows = []
-    with open(Path(subworkflow_dir, "main.nf"), "r") as fh:
+    with open(Path(subworkflow_dir, "main.nf")) as fh:
         for line in fh:
             regex = re.compile(
                 r"include(?: *{ *)([a-zA-Z\_0-9]*)(?: *as *)?(?:[a-zA-Z\_0-9]*)?(?: *})(?: *from *)(?:'|\")(.*)(?:'|\")"
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 568ca22af5..8ccd83b594 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
 """
 
-from __future__ import print_function
 
 import glob
 import json
@@ -440,7 +439,7 @@ def _copy_old_files(self, component_old_path):
         pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir)
         nextflow_config = pytest_dir / "nextflow.config"
         if nextflow_config.is_file():
-            with open(nextflow_config, "r") as fh:
+            with open(nextflow_config) as fh:
                 config_lines = ""
                 for line in fh:
                     if "publishDir" not in line:
@@ -460,7 +459,7 @@ def _print_and_delete_pytest_files(self):
             "[violet]Do you want to delete the pytest files?[/]\nPytest file 'main.nf' will be printed to standard output to allow migrating the tests manually to 'main.nf.test'.",
             default=False,
         ):
-            with open(pytest_dir / "main.nf", "r") as fh:
+            with open(pytest_dir / "main.nf") as fh:
                 log.info(fh.read())
             shutil.rmtree(pytest_dir)
             log.info(
@@ -475,7 +474,7 @@ def _print_and_delete_pytest_files(self):
             )
         # Delete tags from pytest_modules.yml
         modules_yml = Path(self.directory, "tests", "config", "pytest_modules.yml")
-        with open(modules_yml, "r") as fh:
+        with open(modules_yml) as fh:
             yml_file = yaml.safe_load(fh)
         yml_key = str(self.component_dir) if self.component_type == "modules" else f"subworkflows/{self.component_dir}"
         if yml_key in yml_file:
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index e4d8038b87..54fc0004dc 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -184,7 +184,7 @@ def get_local_yaml(self):
                 meta_fn = Path(comp_dir, "meta.yml")
                 if meta_fn.exists():
                     log.debug(f"Found local file: {meta_fn}")
-                    with open(meta_fn, "r") as fh:
+                    with open(meta_fn) as fh:
                         self.local_path = comp_dir
                         return yaml.safe_load(fh)
 
@@ -196,7 +196,7 @@ def get_local_yaml(self):
                 meta_fn = Path(comp_dir, "meta.yml")
                 if meta_fn.exists():
                     log.debug(f"Found local file: {meta_fn}")
-                    with open(meta_fn, "r") as fh:
+                    with open(meta_fn) as fh:
                         self.local_path = comp_dir
                         return yaml.safe_load(fh)
             log.debug(f"{self.component_type[:-1].title()} '{self.component}' meta.yml not found locally")
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index efffc28e85..ea8299cf7c 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -3,7 +3,6 @@
 in nf-core pipelines
 """
 
-from __future__ import print_function
 
 import logging
 import operator
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 874fa570bc..e7e12c7837 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -81,7 +81,7 @@ def __init__(
     def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
         """Collect all tags from the main.nf.test file."""
         tags = []
-        with open(test_main_nf, "r") as fh:
+        with open(test_main_nf) as fh:
             for line in fh:
                 if line.strip().startswith("tag"):
                     tags.append(line.strip().split()[1].strip('"'))
@@ -90,7 +90,7 @@ def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
     def _get_included_components(self, main_nf: Union[Path, str]):
         """Collect all included components from the main.nf file."""
         included_components = []
-        with open(main_nf, "r") as fh:
+        with open(main_nf) as fh:
             for line in fh:
                 if line.strip().startswith("include"):
                     # get tool/subtool or subworkflow name from include statement, can be in the form
@@ -107,7 +107,7 @@ def _get_included_components(self, main_nf: Union[Path, str]):
     def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, str]):
         """Collect all included components from the main.nf file."""
         included_components = []
-        with open(main_nf_test, "r") as fh:
+        with open(main_nf_test) as fh:
             for line in fh:
                 if line.strip().startswith("script"):
                     # get tool/subtool or subworkflow name from script statement, can be:
@@ -151,7 +151,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
     def get_inputs_from_main_nf(self):
         """Collect all inputs from the main.nf file."""
         inputs = []
-        with open(self.main_nf, "r") as f:
+        with open(self.main_nf) as f:
             data = f.read()
         # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
         # regex matches:
@@ -178,7 +178,7 @@ def get_inputs_from_main_nf(self):
 
     def get_outputs_from_main_nf(self):
         outputs = []
-        with open(self.main_nf, "r") as f:
+        with open(self.main_nf) as f:
             data = f.read()
         # get output values from main.nf after "output:". the names are always after "emit:"
         if "output:" not in data:
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 077cb2b840..1664ec1b4c 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -499,7 +499,7 @@ def get_all_components_info(self, branch=None):
                         ]
             elif 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]
diff --git a/nf_core/create.py b/nf_core/create.py
index 56d0912a07..7971eb919b 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -75,7 +75,7 @@ def __init__(
             ],
         }
         # Get list of files we're skipping with the supplied skip keys
-        self.skip_paths = set(sp for k in skip_paths_keys for sp in skippable_paths[k])
+        self.skip_paths = {sp for k in skip_paths_keys for sp in skippable_paths[k]}
 
         # Set convenience variables
         self.name = self.template_params["name"]
@@ -108,7 +108,7 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         # Obtain template customization info from template yaml file or `.nf-core.yml` config file
         try:
             if template_yaml_path is not None:
-                with open(template_yaml_path, "r") as f:
+                with open(template_yaml_path) as f:
                     template_yaml = yaml.safe_load(f)
             elif "template" in config_yml:
                 template_yaml = config_yml["template"]
@@ -395,7 +395,7 @@ def remove_nf_core_in_bug_report_template(self):
         """
         bug_report_path = self.outdir / ".github" / "ISSUE_TEMPLATE" / "bug_report.yml"
 
-        with open(bug_report_path, "r") as fh:
+        with open(bug_report_path) as fh:
             contents = yaml.load(fh, Loader=yaml.FullLoader)
 
         # Remove the first item in the body, which is the information about the docs
diff --git a/nf_core/download.py b/nf_core/download.py
index 08bef935ba..f8cad8152f 100644
--- a/nf_core/download.py
+++ b/nf_core/download.py
@@ -1,6 +1,5 @@
 """Downloads a nf-core pipeline to the local file system."""
 
-from __future__ import print_function
 
 import concurrent.futures
 import io
@@ -640,7 +639,7 @@ def wf_use_local_configs(self, revision_dirname):
         log.debug(f"Editing 'params.custom_config_base' in '{nfconfig_fn}'")
 
         # Load the nextflow.config file into memory
-        with open(nfconfig_fn, "r") as nfconfig_fh:
+        with open(nfconfig_fn) as nfconfig_fh:
             nfconfig = nfconfig_fh.read()
 
         # Replace the target string
@@ -700,7 +699,7 @@ def find_container_images(self, workflow_directory):
                 if bool(config_findings_dsl2):
                     # finding fill always be a tuple of length 2, first the quote used and second the enquoted value.
                     for finding in config_findings_dsl2:
-                        config_findings.append((finding + (self.nf_config, "Nextflow configs")))
+                        config_findings.append(finding + (self.nf_config, "Nextflow configs"))
                 else:  # no regex match, likely just plain string
                     """
                     Append string also as finding-like tuple for consistency
@@ -719,7 +718,7 @@ def find_container_images(self, workflow_directory):
             for file in files:
                 if file.endswith(".nf"):
                     file_path = os.path.join(subdir, file)
-                    with open(file_path, "r") as fh:
+                    with open(file_path) as fh:
                         # Look for any lines with container "xxx" or container 'xxx'
                         search_space = fh.read()
                         """
@@ -744,7 +743,7 @@ def find_container_images(self, workflow_directory):
                         for finding in local_module_findings:
                             # append finding since we want to collect them from all modules
                             # also append search_space because we need to start over later if nothing was found.
-                            module_findings.append((finding + (search_space, file_path)))
+                            module_findings.append(finding + (search_space, file_path))
 
         # Not sure if there will ever be multiple container definitions per module, but beware DSL3.
         # Like above run on shallow copy, because length may change at runtime.
diff --git a/nf_core/launch.py b/nf_core/launch.py
index 363506c448..4174812d6e 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -1,6 +1,5 @@
 """ Launch a pipeline, interactively collecting params """
 
-from __future__ import print_function
 
 import copy
 import json
diff --git a/nf_core/licences.py b/nf_core/licences.py
index d686a56178..a8a35334dd 100644
--- a/nf_core/licences.py
+++ b/nf_core/licences.py
@@ -1,6 +1,5 @@
 """Lists software licences for a given workflow."""
 
-from __future__ import print_function
 
 import json
 import logging
diff --git a/nf_core/lint/actions_awsfulltest.py b/nf_core/lint/actions_awsfulltest.py
index e8e1c951b1..66aa3f99bf 100644
--- a/nf_core/lint/actions_awsfulltest.py
+++ b/nf_core/lint/actions_awsfulltest.py
@@ -32,7 +32,7 @@ def actions_awsfulltest(self):
     fn = os.path.join(self.wf_path, ".github", "workflows", "awsfulltest.yml")
     if os.path.isfile(fn):
         try:
-            with open(fn, "r") as fh:
+            with open(fn) as fh:
                 wf = yaml.safe_load(fh)
         except Exception as e:
             return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
diff --git a/nf_core/lint/actions_awstest.py b/nf_core/lint/actions_awstest.py
index ccdf0abf6a..7c55998944 100644
--- a/nf_core/lint/actions_awstest.py
+++ b/nf_core/lint/actions_awstest.py
@@ -27,7 +27,7 @@ def actions_awstest(self):
         return {"ignored": [f"'awstest.yml' workflow not found: `{fn}`"]}
 
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             wf = yaml.safe_load(fh)
     except Exception as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
diff --git a/nf_core/lint/actions_ci.py b/nf_core/lint/actions_ci.py
index e669eceb8c..9eee03a0d3 100644
--- a/nf_core/lint/actions_ci.py
+++ b/nf_core/lint/actions_ci.py
@@ -48,7 +48,7 @@ def actions_ci(self):
         return {"ignored": ["'.github/workflows/ci.yml' not found"]}
 
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             ciwf = yaml.safe_load(fh)
     except Exception as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
diff --git a/nf_core/lint/actions_schema_validation.py b/nf_core/lint/actions_schema_validation.py
index 9d49b84c6b..fa4471d98c 100644
--- a/nf_core/lint/actions_schema_validation.py
+++ b/nf_core/lint/actions_schema_validation.py
@@ -36,7 +36,7 @@ def actions_schema_validation(self):
 
         # load workflow
         try:
-            with open(wf_path, "r") as fh:
+            with open(wf_path) as fh:
                 wf_json = yaml.safe_load(fh)
         except Exception as e:
             failed.append(f"Could not parse yaml file: {wf}, {e}")
diff --git a/nf_core/lint/files_unchanged.py b/nf_core/lint/files_unchanged.py
index 2b64d62638..82b286fb44 100644
--- a/nf_core/lint/files_unchanged.py
+++ b/nf_core/lint/files_unchanged.py
@@ -187,16 +187,16 @@ def _tf(file_path):
         else:
             for f in files:
                 try:
-                    with open(_pf(f), "r") as fh:
+                    with open(_pf(f)) as fh:
                         pipeline_file = fh.read()
-                    with open(_tf(f), "r") as fh:
+                    with open(_tf(f)) as fh:
                         template_file = fh.read()
                     if template_file in pipeline_file:
                         passed.append(f"`{f}` matches the template")
                     else:
                         if "files_unchanged" in self.fix:
                             # Try to fix the problem by overwriting the pipeline file
-                            with open(_tf(f), "r") as fh:
+                            with open(_tf(f)) as fh:
                                 template_file = fh.read()
                             with open(_pf(f), "w") as fh:
                                 fh.write(template_file)
diff --git a/nf_core/lint/merge_markers.py b/nf_core/lint/merge_markers.py
index f33a5095d8..144d4990f1 100644
--- a/nf_core/lint/merge_markers.py
+++ b/nf_core/lint/merge_markers.py
@@ -23,7 +23,7 @@ def merge_markers(self):
 
     ignore = [".git"]
     if os.path.isfile(os.path.join(self.wf_path, ".gitignore")):
-        with io.open(os.path.join(self.wf_path, ".gitignore"), "rt", encoding="latin1") as fh:
+        with open(os.path.join(self.wf_path, ".gitignore"), encoding="latin1") as fh:
             for l in fh:
                 ignore.append(os.path.basename(l.strip().rstrip("/")))
     for root, dirs, files in os.walk(self.wf_path, topdown=True):
@@ -41,7 +41,7 @@ def merge_markers(self):
             if nf_core.utils.is_file_binary(os.path.join(root, fname)):
                 continue
             try:
-                with io.open(os.path.join(root, fname), "rt", encoding="latin1") as fh:
+                with open(os.path.join(root, fname), encoding="latin1") as fh:
                     for l in fh:
                         if ">>>>>>>" in l:
                             failed.append(f"Merge marker '>>>>>>>' in `{os.path.join(root, fname)}`: {l[:30]}")
diff --git a/nf_core/lint/multiqc_config.py b/nf_core/lint/multiqc_config.py
index cbbeae07a8..b2f1a89a1b 100644
--- a/nf_core/lint/multiqc_config.py
+++ b/nf_core/lint/multiqc_config.py
@@ -34,7 +34,7 @@ def multiqc_config(self) -> Dict[str, List[str]]:
         return {"ignored": ["'assets/multiqc_config.yml' not found"]}
 
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             mqc_yml = yaml.safe_load(fh)
     except Exception as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
index 24f1e5c12f..7648c107b2 100644
--- a/nf_core/lint/nextflow_config.py
+++ b/nf_core/lint/nextflow_config.py
@@ -190,13 +190,11 @@ def nextflow_config(self):
 
     # Check and warn if the process configuration is done with deprecated syntax
     process_with_deprecated_syntax = list(
-        set(
-            [
-                re.search(r"^(process\.\$.*?)\.+.*$", ck).group(1)
-                for ck in self.nf_config.keys()
-                if re.match(r"^(process\.\$.*?)\.+.*$", ck)
-            ]
-        )
+        {
+            re.search(r"^(process\.\$.*?)\.+.*$", ck).group(1)
+            for ck in self.nf_config.keys()
+            if re.match(r"^(process\.\$.*?)\.+.*$", ck)
+        }
     )
     for pd in process_with_deprecated_syntax:
         warned.append(f"Process configuration is done with deprecated_syntax: {pd}")
@@ -300,7 +298,7 @@ def nextflow_config(self):
         ]
         path = os.path.join(self.wf_path, "nextflow.config")
         i = 0
-        with open(path, "r") as f:
+        with open(path) as f:
             for line in f:
                 if lines[i] in line:
                     i += 1
@@ -320,7 +318,7 @@ def nextflow_config(self):
             )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
-    with open(os.path.join(self.wf_path, "nextflow.config"), "r") as f:
+    with open(os.path.join(self.wf_path, "nextflow.config")) as f:
         content = f.read()
 
         # Remove comments
diff --git a/nf_core/lint/pipeline_todos.py b/nf_core/lint/pipeline_todos.py
index 890e227fa1..ed2f1fb94e 100644
--- a/nf_core/lint/pipeline_todos.py
+++ b/nf_core/lint/pipeline_todos.py
@@ -41,7 +41,7 @@ def pipeline_todos(self, root_dir=None):
 
     ignore = [".git"]
     if os.path.isfile(os.path.join(root_dir, ".gitignore")):
-        with io.open(os.path.join(root_dir, ".gitignore"), "rt", encoding="latin1") as fh:
+        with open(os.path.join(root_dir, ".gitignore"), encoding="latin1") as fh:
             for l in fh:
                 ignore.append(os.path.basename(l.strip().rstrip("/")))
     for root, dirs, files in os.walk(root_dir, topdown=True):
@@ -52,7 +52,7 @@ def pipeline_todos(self, root_dir=None):
             files[:] = [f for f in files if not fnmatch.fnmatch(os.path.join(root, f), i)]
         for fname in files:
             try:
-                with io.open(os.path.join(root, fname), "rt", encoding="latin1") as fh:
+                with open(os.path.join(root, fname), encoding="latin1") as fh:
                     for l in fh:
                         if "TODO nf-core" in l:
                             l = (
diff --git a/nf_core/lint/readme.py b/nf_core/lint/readme.py
index 55060442b1..cade9ca3ea 100644
--- a/nf_core/lint/readme.py
+++ b/nf_core/lint/readme.py
@@ -31,7 +31,7 @@ def readme(self):
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("readme", [])
 
-    with open(os.path.join(self.wf_path, "README.md"), "r") as fh:
+    with open(os.path.join(self.wf_path, "README.md")) as fh:
         content = fh.read()
 
     if "nextflow_badge" not in ignore_configs:
diff --git a/nf_core/lint/template_strings.py b/nf_core/lint/template_strings.py
index fb1f0f32e5..0665675c97 100644
--- a/nf_core/lint/template_strings.py
+++ b/nf_core/lint/template_strings.py
@@ -30,7 +30,7 @@ def template_strings(self):
         if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
             continue
 
-        with io.open(fn, "r", encoding="latin1") as fh:
+        with open(fn, encoding="latin1") as fh:
             lnum = 0
             for l in fh:
                 lnum += 1
diff --git a/nf_core/lint/version_consistency.py b/nf_core/lint/version_consistency.py
index fa5b50de01..2336db4a42 100644
--- a/nf_core/lint/version_consistency.py
+++ b/nf_core/lint/version_consistency.py
@@ -54,7 +54,7 @@ def version_consistency(self):
     if len(set(versions.values())) != 1:
         failed.append(
             "The versioning is not consistent between container, release tag "
-            "and config. Found {}".format(", ".join(["{} = {}".format(k, v) for k, v in versions.items()]))
+            "and config. Found {}".format(", ".join([f"{k} = {v}" for k, v in versions.items()]))
         )
 
     passed.append("Version tags are numeric and consistent between container, release tag and config.")
diff --git a/nf_core/list.py b/nf_core/list.py
index 94d9d8e043..38bfb3f938 100644
--- a/nf_core/list.py
+++ b/nf_core/list.py
@@ -1,6 +1,5 @@
 """Lists available nf-core pipelines and versions."""
 
-from __future__ import print_function
 
 import json
 import logging
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 25259f1a16..17774ac410 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -4,8 +4,6 @@
 """
 
 
-from __future__ import print_function
-
 import logging
 import os
 import re
@@ -146,7 +144,7 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
         except FileNotFoundError:
             # try it in the main.nf instead
             try:
-                with open(module.main_nf, "r") as fh:
+                with open(module.main_nf) as fh:
                     for l in fh:
                         if "bioconda::" in l:
                             bioconda_packages = [b for b in l.split() if "bioconda::" in b]
@@ -208,7 +206,7 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
                 ),
             ]
 
-            with open(module.main_nf, "r") as fh:
+            with open(module.main_nf) as fh:
                 content = fh.read()
 
             # Go over file content of main.nf and find replacements
@@ -241,7 +239,7 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
                 fh.write(content)
 
             # change version in environment.yml
-            with open(module.environment_yml, "r") as fh:
+            with open(module.environment_yml) as fh:
                 env_yml = yaml.safe_load(fh)
             re.sub(bioconda_packages[0], f"'bioconda::{bioconda_tool_name}={last_ver}'", env_yml["dependencies"])
             with open(module.environment_yml, "w") as fh:
@@ -266,7 +264,7 @@ def get_bioconda_version(self, module: NFCoreComponent) -> List[str]:
         # Check whether file exists and load it
         bioconda_packages = []
         try:
-            with open(module.environment_yml, "r") as fh:
+            with open(module.environment_yml) as fh:
                 env_yml = yaml.safe_load(fh)
             bioconda_packages = env_yml.get("dependencies", [])
         except FileNotFoundError:
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 68a38cc0cd..75d2d830b8 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -6,7 +6,6 @@
 nf-core modules lint
 """
 
-from __future__ import print_function
 
 import logging
 import os
diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index a052425539..c2fc9384e5 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -23,14 +23,14 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
     env_yml = None
     #  load the environment.yml file
     try:
-        with open(Path(module.component_dir, "environment.yml"), "r") as fh:
+        with open(Path(module.component_dir, "environment.yml")) as fh:
             env_yml = yaml.safe_load(fh)
 
         module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml))
 
     except FileNotFoundError:
         # check if the module's main.nf requires a conda environment
-        with open(Path(module.component_dir, "main.nf"), "r") as fh:
+        with open(Path(module.component_dir, "main.nf")) as fh:
             main_nf = fh.read()
             if 'conda "${moduleDir}/environment.yml"' in main_nf:
                 module.failed.append(
@@ -49,9 +49,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
     if env_yml:
         valid_env_yml = False
         try:
-            with open(
-                Path(module_lint_object.modules_repo.local_repo_dir, "modules/environment-schema.json"), "r"
-            ) as fh:
+            with open(Path(module_lint_object.modules_repo.local_repo_dir, "modules/environment-schema.json")) as fh:
                 schema = json.load(fh)
             validators.validate(instance=env_yml, schema=schema)
             module.passed.append(
@@ -92,7 +90,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
                     yaml.dump(env_yml, fh, Dumper=custom_yaml_dumper())
 
             # Check that the name in the environment.yml file matches the name in the meta.yml file
-            with open(Path(module.component_dir, "meta.yml"), "r") as fh:
+            with open(Path(module.component_dir, "meta.yml")) as fh:
                 meta_yml = yaml.safe_load(fh)
 
             if env_yml["name"] == meta_yml["name"]:
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 56a9e99925..52ee0151ed 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -55,7 +55,7 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
     if lines is None:
         try:
             # Check whether file exists and load it
-            with open(module.main_nf, "r") as fh:
+            with open(module.main_nf) as fh:
                 lines = fh.readlines()
             module.passed.append(("main_nf_exists", "Module file exists", module.main_nf))
         except FileNotFoundError:
@@ -348,7 +348,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
 
     # Get bioconda packages from environment.yml
     try:
-        with open(Path(self.component_dir, "environment.yml"), "r") as fh:
+        with open(Path(self.component_dir, "environment.yml")) as fh:
             env_yml = yaml.safe_load(fh)
         if "dependencies" in env_yml:
             bioconda_packages = [x for x in env_yml["dependencies"] if isinstance(x, str) and "bioconda::" in x]
@@ -605,7 +605,7 @@ def _fix_module_version(self, current_version, latest_version, singularity_tag,
     # Get latest build
     build = _get_build(response)
 
-    with open(self.main_nf, "r") as source:
+    with open(self.main_nf) as source:
         lines = source.readlines()
 
     # Check if the new version + build exist and replace
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 7552c1ceae..551a978f4d 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -54,7 +54,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
             meta_yaml = yaml.safe_load("".join(lines))
     if meta_yaml is None:
         try:
-            with open(module.meta_yml, "r") as fh:
+            with open(module.meta_yml) as fh:
                 meta_yaml = yaml.safe_load(fh)
             module.passed.append(("meta_yml_exists", "Module `meta.yml` exists", module.meta_yml))
         except FileNotFoundError:
@@ -64,7 +64,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
     # Confirm that the meta.yml file is valid according to the JSON schema
     valid_meta_yml = False
     try:
-        with open(Path(module_lint_object.modules_repo.local_repo_dir, "modules/meta-schema.json"), "r") as fh:
+        with open(Path(module_lint_object.modules_repo.local_repo_dir, "modules/meta-schema.json")) as fh:
             schema = json.load(fh)
         validators.validate(instance=meta_yaml, schema=schema)
         module.passed.append(("meta_yml_valid", "Module `meta.yml` is valid", module.meta_yml))
diff --git a/nf_core/modules/lint/module_patch.py b/nf_core/modules/lint/module_patch.py
index d52962eabb..29bf78a66b 100644
--- a/nf_core/modules/lint/module_patch.py
+++ b/nf_core/modules/lint/module_patch.py
@@ -40,7 +40,7 @@ def check_patch_valid(module, patch_path):
     Returns:
         (bool): False if any test failed, True otherwise
     """
-    with open(patch_path, "r") as fh:
+    with open(patch_path) as fh:
         patch_lines = fh.readlines()
 
     # Check that the file contains a patch for at least one file
@@ -170,8 +170,8 @@ def patch_reversible(module_lint_object, module, patch_path):
         )
     except LookupError:
         # Patch failed. Save the patch file by moving to the install dir
-        module.failed.append((("patch_reversible", "Patch file is outdated or edited", patch_path)))
+        module.failed.append(("patch_reversible", "Patch file is outdated or edited", patch_path))
         return False
 
-    module.passed.append((("patch_reversible", "Patch agrees with module files", patch_path)))
+    module.passed.append(("patch_reversible", "Patch agrees with module files", patch_path))
     return True
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 87033e3f49..520f8cf0a2 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -44,7 +44,7 @@ def module_tests(_, module: NFCoreComponent):
 
     if module.nftest_main_nf.is_file():
         # Check if main.nf.test.snap file exists, if 'snap(' is inside main.nf.test
-        with open(module.nftest_main_nf, "r") as fh:
+        with open(module.nftest_main_nf) as fh:
             if "snapshot(" in fh.read():
                 snap_file = module.nftest_testdir / "main.nf.test.snap"
                 if snap_file.is_file():
@@ -52,7 +52,7 @@ def module_tests(_, module: NFCoreComponent):
                         ("test_snapshot_exists", "snapshot file `main.nf.test.snap` exists", snap_file)
                     )
                     # Validate no empty files
-                    with open(snap_file, "r") as snap_fh:
+                    with open(snap_file) as snap_fh:
                         try:
                             snap_content = json.load(snap_fh)
                             for test_name in snap_content.keys():
@@ -145,7 +145,7 @@ def module_tests(_, module: NFCoreComponent):
     pytest_yml_path = module.base_dir / "tests" / "config" / "pytest_modules.yml"
     if pytest_yml_path.is_file() and not is_pytest:
         try:
-            with open(pytest_yml_path, "r") as fh:
+            with open(pytest_yml_path) as fh:
                 pytest_yml = yaml.safe_load(fh)
                 if module.component_name in pytest_yml.keys():
                     module.failed.append(
@@ -165,7 +165,7 @@ def module_tests(_, module: NFCoreComponent):
     if module.tags_yml.is_file():
         # Check that tags.yml exists and it has the correct entry
         module.passed.append(("test_tags_yml_exists", "file `tags.yml` exists", module.tags_yml))
-        with open(module.tags_yml, "r") as fh:
+        with open(module.tags_yml) as fh:
             tags_yml = yaml.safe_load(fh)
             if module.component_name in tags_yml.keys():
                 module.passed.append(("test_tags_yml", "correct entry in tags.yml", module.tags_yml))
diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index efce3868e5..a97229ff62 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -74,9 +74,9 @@ def get_module_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_to_d
             temp_path = Path(to_dir, file)
             curr_path = Path(from_dir, file)
             if temp_path.exists() and curr_path.exists() and temp_path.is_file():
-                with open(temp_path, "r") as fh:
+                with open(temp_path) as fh:
                     new_lines = fh.readlines()
-                with open(curr_path, "r") as fh:
+                with open(curr_path) as fh:
                     old_lines = fh.readlines()
 
                 if new_lines == old_lines:
@@ -93,7 +93,7 @@ def get_module_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_to_d
                     diffs[file] = (ModulesDiffer.DiffEnum.CHANGED, diff)
 
             elif temp_path.exists():
-                with open(temp_path, "r") as fh:
+                with open(temp_path) as fh:
                     new_lines = fh.readlines()
                 # The file was created
                 # Show file against /dev/null
@@ -108,7 +108,7 @@ def get_module_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_to_d
             elif curr_path.exists():
                 # The file was removed
                 # Show file against /dev/null
-                with open(curr_path, "r") as fh:
+                with open(curr_path) as fh:
                     old_lines = fh.readlines()
                 diff = difflib.unified_diff(
                     old_lines,
@@ -279,7 +279,7 @@ def per_file_patch(patch_fn):
             dict[str, str]: A dictionary indexed by the filenames with the
                             file patches as values
         """
-        with open(patch_fn, "r") as fh:
+        with open(patch_fn) as fh:
             lines = fh.readlines()
 
         patches = {}
@@ -447,7 +447,7 @@ def try_apply_patch(module, repo_path, patch_path, module_dir, reverse=False):
             log.debug(f"Applying patch to {file}")
             fn = Path(file).relative_to(module_relpath)
             file_path = module_dir / fn
-            with open(file_path, "r") as fh:
+            with open(file_path) as fh:
                 file_lines = fh.readlines()
             patched_new_lines = ModulesDiffer.try_apply_single_patch(file_lines, patch, reverse=reverse)
             new_files[str(fn)] = patched_new_lines
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 32eb8736d6..f68c27b2d8 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -637,7 +637,7 @@ def load(self):
             UserWarning: If the modules.json file is not found
         """
         try:
-            with open(self.modules_json_path, "r") as fh:
+            with open(self.modules_json_path) as fh:
                 try:
                     self.modules_json = json.load(fh)
                 except json.JSONDecodeError as e:
diff --git a/nf_core/params_file.py b/nf_core/params_file.py
index 5c50c53fb9..d9db5a3fd7 100644
--- a/nf_core/params_file.py
+++ b/nf_core/params_file.py
@@ -1,6 +1,5 @@
 """ Create a YAML parameter file """
 
-from __future__ import print_function
 
 import json
 import logging
diff --git a/nf_core/refgenie.py b/nf_core/refgenie.py
index 6f09b75532..d52c9c5554 100644
--- a/nf_core/refgenie.py
+++ b/nf_core/refgenie.py
@@ -86,7 +86,7 @@ def _update_nextflow_home_config(refgenie_genomes_config_file, nxf_home):
     if os.path.exists(nxf_home_config):
         # look for include statement in config
         has_include_statement = False
-        with open(nxf_home_config, "r") as fh:
+        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):
diff --git a/nf_core/schema.py b/nf_core/schema.py
index 7e4726f189..32ced148a8 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -1,6 +1,5 @@
 """ Code to deal with pipeline JSON Schema """
 
-from __future__ import print_function
 
 import copy
 import json
@@ -107,7 +106,7 @@ def load_lint_schema(self):
 
     def load_schema(self):
         """Load a pipeline schema from a file"""
-        with open(self.schema_filename, "r") as fh:
+        with open(self.schema_filename) as fh:
             self.schema = json.load(fh)
         self.schema_defaults = {}
         self.schema_params = {}
@@ -189,7 +188,7 @@ def load_input_params(self, params_path):
         """
         # First, try to load as JSON
         try:
-            with open(params_path, "r") as fh:
+            with open(params_path) as fh:
                 try:
                     params = json.load(fh)
                 except json.JSONDecodeError as e:
@@ -200,7 +199,7 @@ def load_input_params(self, params_path):
             log.debug(f"Could not load input params as JSON: {json_e}")
             # This failed, try to load as YAML
             try:
-                with open(params_path, "r") as fh:
+                with open(params_path) as fh:
                     params = yaml.safe_load(fh)
                     self.input_params.update(params)
                     log.debug(f"Loaded YAML input params: {params_path}")
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index ffba41f9da..dc8fa68c30 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -6,7 +6,6 @@
 nf-core subworkflows lint
 """
 
-from __future__ import print_function
 
 import logging
 import os
diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
index c7ce77490d..f52b7846c3 100644
--- a/nf_core/subworkflows/lint/main_nf.py
+++ b/nf_core/subworkflows/lint/main_nf.py
@@ -32,7 +32,7 @@ def main_nf(_, subworkflow):
     if lines is None:
         try:
             # Check whether file exists and load it
-            with open(subworkflow.main_nf, "r") as fh:
+            with open(subworkflow.main_nf) as fh:
                 lines = fh.readlines()
             subworkflow.passed.append(("main_nf_exists", "Subworkflow file exists", subworkflow.main_nf))
         except FileNotFoundError:
diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py
index 4944b26188..c5f544a597 100644
--- a/nf_core/subworkflows/lint/meta_yml.py
+++ b/nf_core/subworkflows/lint/meta_yml.py
@@ -26,7 +26,7 @@ def meta_yml(subworkflow_lint_object, subworkflow):
     """
     # Read the meta.yml file
     try:
-        with open(subworkflow.meta_yml, "r") as fh:
+        with open(subworkflow.meta_yml) as fh:
             meta_yaml = yaml.safe_load(fh)
         subworkflow.passed.append(("meta_yml_exists", "Subworkflow `meta.yml` exists", subworkflow.meta_yml))
     except FileNotFoundError:
@@ -36,9 +36,7 @@ def meta_yml(subworkflow_lint_object, subworkflow):
     # Confirm that the meta.yml file is valid according to the JSON schema
     valid_meta_yml = True
     try:
-        with open(
-            Path(subworkflow_lint_object.modules_repo.local_repo_dir, "subworkflows/yaml-schema.json"), "r"
-        ) as fh:
+        with open(Path(subworkflow_lint_object.modules_repo.local_repo_dir, "subworkflows/yaml-schema.json")) as fh:
             schema = json.load(fh)
         jsonschema.validators.validate(instance=meta_yaml, schema=schema)
         subworkflow.passed.append(("meta_yml_valid", "Subworkflow `meta.yml` is valid", subworkflow.meta_yml))
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index 1ebced6d42..f7284320ea 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -52,14 +52,14 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
             )
 
     if subworkflow.nftest_main_nf.is_file():
-        with open(subworkflow.nftest_main_nf, "r") as fh:
+        with open(subworkflow.nftest_main_nf) as fh:
             # Check if main.nf.test.snap file exists, if 'snap(' is inside main.nf.test
             if "snapshot(" in fh.read():
                 snap_file = subworkflow.nftest_testdir / "main.nf.test.snap"
                 if snap_file.is_file():
                     subworkflow.passed.append(("test_snapshot_exists", "test `main.nf.test.snap` exists", snap_file))
                     # Validate no empty files
-                    with open(snap_file, "r") as snap_fh:
+                    with open(snap_file) as snap_fh:
                         try:
                             snap_content = json.load(snap_fh)
                             for test_name in snap_content.keys():
@@ -158,7 +158,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
     pytest_yml_path = subworkflow.base_dir / "tests" / "config" / "pytest_modules.yml"
     if pytest_yml_path.is_file() and not is_pytest:
         try:
-            with open(pytest_yml_path, "r") as fh:
+            with open(pytest_yml_path) as fh:
                 pytest_yml = yaml.safe_load(fh)
                 if "subworkflows/" + subworkflow.component_name in pytest_yml.keys():
                     subworkflow.failed.append(
@@ -178,7 +178,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
     if subworkflow.tags_yml.is_file():
         # Check tags.yml exists and it has the correct entry
         subworkflow.passed.append(("test_tags_yml_exists", "file `tags.yml` exists", subworkflow.tags_yml))
-        with open(subworkflow.tags_yml, "r") as fh:
+        with open(subworkflow.tags_yml) as fh:
             tags_yml = yaml.safe_load(fh)
             if "subworkflows/" + subworkflow.component_name in tags_yml.keys():
                 subworkflow.passed.append(("test_tags_yml", "correct entry in tags.yml", subworkflow.tags_yml))
diff --git a/nf_core/sync.py b/nf_core/sync.py
index 5402a6121d..085a6e6d65 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -96,7 +96,7 @@ def __init__(
                     default=False,
                 ).unsafe_ask()
             if overwrite_template or "template" not in self.config_yml:
-                with open(template_yaml_path, "r") as f:
+                with open(template_yaml_path) as f:
                     self.config_yml["template"] = yaml.safe_load(f)
                 with open(self.config_yml_path, "w") as fh:
                     yaml.safe_dump(self.config_yml, fh)
diff --git a/nf_core/utils.py b/nf_core/utils.py
index bcc8faa3fd..e790e37d8a 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -188,7 +188,7 @@ def _load_pipeline_config(self):
     def _load_conda_environment(self):
         """Try to load the pipeline environment.yml file, if it exists"""
         try:
-            with open(os.path.join(self.wf_path, "environment.yml"), "r") as fh:
+            with open(os.path.join(self.wf_path, "environment.yml")) as fh:
                 self.conda_config = yaml.safe_load(fh)
         except FileNotFoundError:
             log.debug("No conda `environment.yml` file found.")
@@ -262,7 +262,7 @@ def fetch_wf_config(wf_path, cache_config=True):
         cache_path = os.path.join(cache_basedir, cache_fn)
         if os.path.isfile(cache_path) and cache_config is True:
             log.debug(f"Found a config cache, loading: {cache_path}")
-            with open(cache_path, "r") as fh:
+            with open(cache_path) as fh:
                 try:
                     config = json.load(fh)
                 except json.JSONDecodeError as e:
@@ -286,7 +286,7 @@ def fetch_wf_config(wf_path, cache_config=True):
     # Values in this file are likely to be complex, so don't both trying to capture them. Just get the param name.
     try:
         main_nf = os.path.join(wf_path, "main.nf")
-        with open(main_nf, "r") as fh:
+        with open(main_nf) as fh:
             for l in fh:
                 match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=", l)
                 if match:
@@ -312,7 +312,7 @@ def run_cmd(executable: str, cmd: str) -> Union[Tuple[bytes, bytes], None]:
     full_cmd = f"{executable} {cmd}"
     log.debug(f"Running command: {full_cmd}")
     try:
-        proc = subprocess.run(shlex.split(full_cmd), stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
+        proc = subprocess.run(shlex.split(full_cmd), capture_output=True, check=True)
         return (proc.stdout, proc.stderr)
     except OSError as e:
         if e.errno == errno.ENOENT:
@@ -480,7 +480,7 @@ def __call__(self, r):
         gh_cli_config_fn = os.path.expanduser("~/.config/gh/hosts.yml")
         if self.auth is None and os.path.exists(gh_cli_config_fn):
             try:
-                with open(gh_cli_config_fn, "r") as fh:
+                with open(gh_cli_config_fn) as fh:
                     gh_cli_config = yaml.safe_load(fh)
                     self.auth = requests.auth.HTTPBasicAuth(
                         gh_cli_config["github.com"]["user"], gh_cli_config["github.com"]["oauth_token"]
@@ -792,7 +792,7 @@ def increase_indent(self, flow=False, indentless=False):
 
             See https://github.com/yaml/pyyaml/issues/234#issuecomment-765894586
             """
-            return super(CustomDumper, self).increase_indent(flow=flow, indentless=False)
+            return super().increase_indent(flow=flow, indentless=False)
 
         # HACK: insert blank lines between top-level objects
         # inspired by https://stackoverflow.com/a/44284819/3786245
@@ -1025,7 +1025,7 @@ def load_tools_config(directory: Union[str, Path] = "."):
             log.debug(f"No tools config file found: {CONFIG_PATHS[0]}")
         return Path(directory, CONFIG_PATHS[0]), {}
 
-    with open(config_fn, "r") as fh:
+    with open(config_fn) as fh:
         tools_config = yaml.safe_load(fh)
 
     # If the file is empty
@@ -1145,7 +1145,7 @@ def validate_file_md5(file_name, expected_md5hex):
     if file_md5hex.upper() == expected_md5hex.upper():
         log.debug(f"md5 sum of image matches expected: {expected_md5hex}")
     else:
-        raise IOError(f"{file_name} md5 does not match remote: {expected_md5hex} - {file_md5hex}")
+        raise OSError(f"{file_name} md5 does not match remote: {expected_md5hex} - {file_md5hex}")
 
     return True
 
diff --git a/tests/components/generate_snapshot.py b/tests/components/generate_snapshot.py
index 46fd63fe3f..c5067d7210 100644
--- a/tests/components/generate_snapshot.py
+++ b/tests/components/generate_snapshot.py
@@ -26,7 +26,7 @@ def test_generate_snapshot_module(self):
         snap_path = Path("modules", "nf-core-test", "fastqc", "tests", "main.nf.test.snap")
         assert snap_path.exists()
 
-        with open(snap_path, "r") as fh:
+        with open(snap_path) as fh:
             snap_content = json.load(fh)
         assert "versions" in snap_content
         assert "content" in snap_content["versions"]
@@ -48,7 +48,7 @@ def test_generate_snapshot_subworkflow(self):
         snap_path = Path("subworkflows", "nf-core-test", "bam_sort_stats_samtools", "tests", "main.nf.test.snap")
         assert snap_path.exists()
 
-        with open(snap_path, "r") as fh:
+        with open(snap_path) as fh:
             snap_content = json.load(fh)
         assert "test_bam_sort_stats_samtools_paired_end_flagstats" in snap_content
         assert (
@@ -86,7 +86,7 @@ def test_update_snapshot_module(self):
 
     with set_wd(self.nfcore_modules):
         snap_path = Path("modules", "nf-core-test", "bwa", "mem", "tests", "main.nf.test.snap")
-        with open(snap_path, "r") as fh:
+        with open(snap_path) as fh:
             snap_content = json.load(fh)
         original_timestamp = snap_content["Single-End"]["timestamp"]
         # delete the timestamp in json
@@ -103,7 +103,7 @@ def test_update_snapshot_module(self):
         )
         snap_generator.run()
 
-        with open(snap_path, "r") as fh:
+        with open(snap_path) as fh:
             snap_content = json.load(fh)
         assert "Single-End" in snap_content
         assert snap_content["Single-End"]["timestamp"] != original_timestamp
diff --git a/tests/lint/actions_awsfulltest.py b/tests/lint/actions_awsfulltest.py
index 30293e31a4..bbda92a4d1 100644
--- a/tests/lint/actions_awsfulltest.py
+++ b/tests/lint/actions_awsfulltest.py
@@ -19,7 +19,7 @@ def test_actions_awsfulltest_pass(self):
 
     # Edit .github/workflows/awsfulltest.yml to use -profile test_full
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "r") as fh:
+    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
         awsfulltest_yml = fh.read()
     awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ")
     with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
@@ -44,7 +44,7 @@ def test_actions_awsfulltest_fail(self):
 
     # Edit .github/workflows/awsfulltest.yml to use -profile test_full
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "r") as fh:
+    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
         awsfulltest_yml = yaml.safe_load(fh)
     del awsfulltest_yml[True]["release"]
     with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
diff --git a/tests/lint/actions_awstest.py b/tests/lint/actions_awstest.py
index 0e19f781aa..7bfa6052f8 100644
--- a/tests/lint/actions_awstest.py
+++ b/tests/lint/actions_awstest.py
@@ -20,7 +20,7 @@ def test_actions_awstest_fail(self):
 
     # Edit .github/workflows/awsfulltest.yml to use -profile test_full
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "r") as fh:
+    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
         awstest_yml = yaml.safe_load(fh)
     awstest_yml[True]["push"] = ["master"]
     with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
diff --git a/tests/lint/actions_ci.py b/tests/lint/actions_ci.py
index d44dbb73b5..8734b2f78b 100644
--- a/tests/lint/actions_ci.py
+++ b/tests/lint/actions_ci.py
@@ -31,7 +31,7 @@ def test_actions_ci_fail_wrong_trigger(self):
 
     # Edit .github/workflows/actions_ci.yml to mess stuff up!
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml"), "r") as fh:
+    with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml")) as fh:
         ci_yml = yaml.safe_load(fh)
     ci_yml[True]["push"] = ["dev", "patch"]
     ci_yml["jobs"]["test"]["strategy"]["matrix"] = {"nxf_versionnn": ["foo", ""]}
diff --git a/tests/lint/actions_schema_validation.py b/tests/lint/actions_schema_validation.py
index 48bb07e4dd..ad65d90018 100644
--- a/tests/lint/actions_schema_validation.py
+++ b/tests/lint/actions_schema_validation.py
@@ -9,7 +9,7 @@ def test_actions_schema_validation_missing_jobs(self):
     """Missing 'jobs' field should result in failure"""
     new_pipeline = self._make_pipeline_copy()
 
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "r") as fh:
+    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
         awstest_yml = yaml.safe_load(fh)
     awstest_yml.pop("jobs")
     with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
@@ -27,7 +27,7 @@ def test_actions_schema_validation_missing_on(self):
     """Missing 'on' field should result in failure"""
     new_pipeline = self._make_pipeline_copy()
 
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "r") as fh:
+    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
         awstest_yml = yaml.safe_load(fh)
     awstest_yml.pop(True)
     with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
@@ -46,7 +46,7 @@ def test_actions_schema_validation_fails_for_additional_property(self):
     """Missing 'jobs' field should result in failure"""
     new_pipeline = self._make_pipeline_copy()
 
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "r") as fh:
+    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
         awstest_yml = yaml.safe_load(fh)
     awstest_yml["not_jobs"] = awstest_yml["jobs"]
     with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
diff --git a/tests/lint/merge_markers.py b/tests/lint/merge_markers.py
index be0d076757..64a62e25c3 100644
--- a/tests/lint/merge_markers.py
+++ b/tests/lint/merge_markers.py
@@ -7,7 +7,7 @@ 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"), "r") as fh:
+    with open(os.path.join(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:
diff --git a/tests/lint/multiqc_config.py b/tests/lint/multiqc_config.py
index 446b4378b0..721560ce81 100644
--- a/tests/lint/multiqc_config.py
+++ b/tests/lint/multiqc_config.py
@@ -18,7 +18,7 @@ def test_multiqc_config_exists_ignore(self):
 def test_multiqc_config_missing_report_section_order(self):
     """Test that linting fails if the multiqc_config.yml file is missing the report_section_order"""
     new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
         mqc_yml = yaml.safe_load(fh)
     mqc_yml_tmp = mqc_yml
     mqc_yml.pop("report_section_order")
@@ -36,7 +36,7 @@ def test_multiqc_config_missing_report_section_order(self):
 def test_multiqc_incorrect_export_plots(self):
     """Test that linting fails if the multiqc_config.yml file has an incorrect value for export_plots"""
     new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
         mqc_yml = yaml.safe_load(fh)
     mqc_yml_tmp = mqc_yml
     mqc_yml["export_plots"] = False
@@ -54,7 +54,7 @@ def test_multiqc_incorrect_export_plots(self):
 def test_multiqc_config_report_comment_fail(self):
     """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment"""
     new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
         mqc_yml = yaml.safe_load(fh)
     mqc_yml_tmp = mqc_yml
     mqc_yml["report_comment"] = "This is a test"
@@ -73,7 +73,7 @@ def test_multiqc_config_report_comment_fail(self):
 def test_multiqc_config_report_comment_release_fail(self):
     """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment for a release version"""
     new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
         mqc_yml = yaml.safe_load(fh)
     mqc_yml_tmp = mqc_yml
     with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py
index 1542b8cf65..5d5f8e7345 100644
--- a/tests/lint/nextflow_config.py
+++ b/tests/lint/nextflow_config.py
@@ -43,7 +43,7 @@ def test_nextflow_config_missing_test_profile_failed(self):
     new_pipeline = self._make_pipeline_copy()
     # Change the name of the test profile so there is no such profile
     nf_conf_file = os.path.join(new_pipeline, "nextflow.config")
-    with open(nf_conf_file, "r") as f:
+    with open(nf_conf_file) as f:
         content = f.read()
         fail_content = re.sub(r"\btest\b", "testfail", content)
     with open(nf_conf_file, "w") as f:
diff --git a/tests/modules/bump_versions.py b/tests/modules/bump_versions.py
index 3c19041f63..99900e7509 100644
--- a/tests/modules/bump_versions.py
+++ b/tests/modules/bump_versions.py
@@ -12,7 +12,7 @@ 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")
-    with open(env_yml_path, "r") as fh:
+    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)
     with open(env_yml_path, "w") as fh:
@@ -41,7 +41,7 @@ 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")
-    with open(env_yml_path, "r") as fh:
+    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)
     with open(env_yml_path, "w") as fh:
diff --git a/tests/modules/create.py b/tests/modules/create.py
index 74e5ec3896..47f541a417 100644
--- a/tests/modules/create.py
+++ b/tests/modules/create.py
@@ -87,9 +87,9 @@ def test_modules_migrate(self, mock_rich_ask):
     # Clone modules repo with pytests
     shutil.rmtree(self.nfcore_modules)
     Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
-    with open(module_dir / "main.nf", "r") as fh:
+    with open(module_dir / "main.nf") as fh:
         old_main_nf = fh.read()
-    with open(module_dir / "meta.yml", "r") as fh:
+    with open(module_dir / "meta.yml") as fh:
         old_meta_yml = fh.read()
 
     # Create a module with --migrate-pytest
@@ -97,9 +97,9 @@ def test_modules_migrate(self, mock_rich_ask):
     module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
     module_create.create()
 
-    with open(module_dir / "main.nf", "r") as fh:
+    with open(module_dir / "main.nf") as fh:
         new_main_nf = fh.read()
-    with open(module_dir / "meta.yml", "r") as fh:
+    with open(module_dir / "meta.yml") as fh:
         new_meta_yml = fh.read()
     nextflow_config = module_dir / "tests" / "nextflow.config"
 
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index a8a775e6f6..a5d8567b76 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -333,7 +333,7 @@ def test_modules_lint_snapshot_file_missing_fail(self):
 
 def test_modules_lint_snapshot_file_not_needed(self):
     """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "r") as fh:
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test")) as fh:
         content = fh.read()
         new_content = content.replace("snapshot(", "snap (")
     with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "w") as fh:
@@ -372,7 +372,7 @@ def test_modules_environment_yml_file_sorted_correctly(self):
 
 def test_modules_environment_yml_file_sorted_incorrectly(self):
     """Test linting a module with an incorrectly sorted environment.yml file"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "r") as fh:
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")) as fh:
         yaml_content = yaml.safe_load(fh)
     # Add a new dependency to the environment.yml file and reverse the order
     yaml_content["dependencies"].append("z")
@@ -548,7 +548,7 @@ def test_modules_missing_test_main_nf(self):
 
 def test_modules_missing_required_tag(self):
     """Test linting a module with a missing required tag"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "r") as fh:
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test")) as fh:
         content = fh.read()
         new_content = content.replace("modules_nfcore", "foo")
     with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "w") as fh:
@@ -581,7 +581,7 @@ def test_modules_missing_tags_yml(self):
 
 def test_modules_incorrect_tags_yml_key(self):
     """Test linting a module with an incorrect key in tags.yml file"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "r") as fh:
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml")) as fh:
         content = fh.read()
         new_content = content.replace("bpipe/test:", "bpipe_test:")
     with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "w") as fh:
@@ -598,7 +598,7 @@ def test_modules_incorrect_tags_yml_key(self):
 
 def test_modules_incorrect_tags_yml_values(self):
     """Test linting a module with an incorrect path in tags.yml file"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "r") as fh:
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml")) as fh:
         content = fh.read()
         new_content = content.replace("modules/nf-core/bpipe/test/**", "foo")
     with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "w") as fh:
diff --git a/tests/modules/modules_json.py b/tests/modules/modules_json.py
index 63ee4e743d..a054b6b131 100644
--- a/tests/modules/modules_json.py
+++ b/tests/modules/modules_json.py
@@ -17,7 +17,7 @@
 def test_get_modules_json(self):
     """Checks that the get_modules_json function returns the correct result"""
     mod_json_path = os.path.join(self.pipeline_dir, "modules.json")
-    with open(mod_json_path, "r") as fh:
+    with open(mod_json_path) as fh:
         try:
             mod_json_sb = json.load(fh)
         except json.JSONDecodeError as e:
@@ -73,7 +73,7 @@ def test_mod_json_create(self):
 
 def modify_main_nf(path):
     """Modify a file to test patch creation"""
-    with open(path, "r") as fh:
+    with open(path) as fh:
         lines = fh.readlines()
     # Modify $meta.id to $meta.single_end
     lines[1] = '    tag "$meta.single_end"\n'
@@ -112,7 +112,7 @@ def test_mod_json_create_with_patch(self):
     assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]
 
     # Check that fastqc/main.nf maintains the changes
-    with open(module_path / "main.nf", "r") as fh:
+    with open(module_path / "main.nf") as fh:
         lines = fh.readlines()
     assert lines[1] == '    tag "$meta.single_end"\n'
 
@@ -214,7 +214,7 @@ def test_mod_json_dump(self):
     assert os.path.exists(mod_json_path)
 
     # Check that the dump function writes the correct content
-    with open(mod_json_path, "r") as f:
+    with open(mod_json_path) as f:
         try:
             mod_json_new = json.load(f)
         except json.JSONDecodeError as e:
diff --git a/tests/modules/patch.py b/tests/modules/patch.py
index 338d890f2f..dc939c7ea7 100644
--- a/tests/modules/patch.py
+++ b/tests/modules/patch.py
@@ -43,7 +43,7 @@ def setup_patch(pipeline_dir, modify_module):
 
 def modify_main_nf(path):
     """Modify a file to test patch creation"""
-    with open(path, "r") as fh:
+    with open(path) as fh:
         lines = fh.readlines()
     # We want a patch file that looks something like:
     # -    tuple val(meta), path(reads)
@@ -99,7 +99,7 @@ def test_create_patch_change(self):
     )
 
     # Check that the correct lines are in the patch file
-    with open(module_path / patch_fn, "r") as fh:
+    with open(module_path / patch_fn) as fh:
         patch_lines = fh.readlines()
     module_relpath = module_path.relative_to(self.pipeline_dir)
     assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines, module_relpath / "main.nf"
@@ -157,7 +157,7 @@ def test_create_patch_try_apply_successful(self):
     )
 
     # Check that the correct lines are in the patch file
-    with open(module_path / patch_fn, "r") as fh:
+    with open(module_path / patch_fn) as fh:
         patch_lines = fh.readlines()
     module_relpath = module_path.relative_to(self.pipeline_dir)
     assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
@@ -167,7 +167,7 @@ def test_create_patch_try_apply_successful(self):
     assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
     # Check that 'main.nf' is updated correctly
-    with open(module_path / "main.nf", "r") as fh:
+    with open(module_path / "main.nf") as fh:
         main_nf_lines = fh.readlines()
     # These lines should have been removed by the patch
     assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
@@ -258,7 +258,7 @@ def test_create_patch_update_success(self):
     ), modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME)
 
     # Check that the correct lines are in the patch file
-    with open(module_path / patch_fn, "r") as fh:
+    with open(module_path / patch_fn) as fh:
         patch_lines = fh.readlines()
     module_relpath = module_path.relative_to(self.pipeline_dir)
     assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
@@ -268,7 +268,7 @@ def test_create_patch_update_success(self):
     assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
     # Check that 'main.nf' is updated correctly
-    with open(module_path / "main.nf", "r") as fh:
+    with open(module_path / "main.nf") as fh:
         main_nf_lines = fh.readlines()
     # These lines should have been removed by the patch
     assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
@@ -300,7 +300,7 @@ def test_create_patch_update_fail(self):
     )
 
     # Save the file contents for downstream comparison
-    with open(module_path / patch_fn, "r") as fh:
+    with open(module_path / patch_fn) as fh:
         patch_contents = fh.read()
 
     update_obj = nf_core.modules.ModuleUpdate(
@@ -317,14 +317,14 @@ def test_create_patch_update_fail(self):
     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, "r") as fh:
+        with open(module_path / file) as fh:
             installed = fh.read()
-        with open(temp_module_dir / file, "r") as fh:
+        with open(temp_module_dir / file) as fh:
             shouldbe = fh.read()
         assert installed == shouldbe
 
     # Check that the patch file is unaffected
-    with open(module_path / patch_fn, "r") as fh:
+    with open(module_path / patch_fn) as fh:
         new_patch_contents = fh.read()
     assert patch_contents == new_patch_contents
 
diff --git a/tests/modules/update.py b/tests/modules/update.py
index 399e9cc12c..5208070fa5 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -345,7 +345,7 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions)
     module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")
     main_path = Path(module_path, "main.nf")
-    with open(main_path, "r") as fh:
+    with open(main_path) as fh:
         lines = fh.readlines()
     for line_index in range(len(lines)):
         if lines[line_index] == "    label 'process_medium'\n":
diff --git a/tests/subworkflows/create.py b/tests/subworkflows/create.py
index fc628df34f..03a2fe1aaf 100644
--- a/tests/subworkflows/create.py
+++ b/tests/subworkflows/create.py
@@ -53,9 +53,9 @@ def test_subworkflows_migrate(self, mock_rich_ask):
     # Clone modules repo with pytests
     shutil.rmtree(self.nfcore_modules)
     Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
-    with open(subworkflow_dir / "main.nf", "r") as fh:
+    with open(subworkflow_dir / "main.nf") as fh:
         old_main_nf = fh.read()
-    with open(subworkflow_dir / "meta.yml", "r") as fh:
+    with open(subworkflow_dir / "meta.yml") as fh:
         old_meta_yml = fh.read()
 
     # Create a subworkflow with --migrate-pytest
@@ -65,9 +65,9 @@ def test_subworkflows_migrate(self, mock_rich_ask):
     )
     subworkflow_create.create()
 
-    with open(subworkflow_dir / "main.nf", "r") as fh:
+    with open(subworkflow_dir / "main.nf") as fh:
         new_main_nf = fh.read()
-    with open(subworkflow_dir / "meta.yml", "r") as fh:
+    with open(subworkflow_dir / "meta.yml") as fh:
         new_meta_yml = fh.read()
     nextflow_config = subworkflow_dir / "tests" / "nextflow.config"
 
diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py
index 1380db2260..9f690cb234 100644
--- a/tests/subworkflows/lint.py
+++ b/tests/subworkflows/lint.py
@@ -87,9 +87,7 @@ def test_subworkflows_lint_snapshot_file_missing_fail(self):
 
 def test_subworkflows_lint_snapshot_file_not_needed(self):
     """Test linting a subworkflow which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file"""
-    with open(
-        Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test"), "r"
-    ) as fh:
+    with open(Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test")) as fh:
         content = fh.read()
         new_content = content.replace("snapshot(", "snap (")
     with open(
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 698086e186..a615f55f8f 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -73,7 +73,7 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
     assert update_obj.update("fastq_align_bowtie2") is True
     assert cmp_component(tmpdir, sw_path) is True
 
-    with open(patch_path, "r") as fh:
+    with open(patch_path) as fh:
         line = fh.readline()
         assert line.startswith(
             "Changes in module 'nf-core/fastq_align_bowtie2' between (f3c078809a2513f1c95de14f6633fe1f03572fdb) and"
diff --git a/tests/test_launch.py b/tests/test_launch.py
index 03c6a8b692..a2e02f2ae7 100644
--- a/tests/test_launch.py
+++ b/tests/test_launch.py
@@ -321,7 +321,7 @@ def test_build_command_params(self):
             == f'nextflow run {self.pipeline_dir} -params-file "{os.path.relpath(self.nf_params_fn)}"'
         )
         # Check saved parameters file
-        with open(self.nf_params_fn, "r") as fh:
+        with open(self.nf_params_fn) as fh:
             try:
                 saved_json = json.load(fh)
             except json.JSONDecodeError as e:
diff --git a/tests/test_lint.py b/tests/test_lint.py
index b2e7f3b574..6b62173d6e 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -134,7 +134,7 @@ def test_json_output(self, tmp_dir):
         self.lint_obj._save_json_results(json_fn)
 
         # Load created JSON file and check its contents
-        with open(json_fn, "r") as fh:
+        with open(json_fn) as fh:
             try:
                 saved_json = json.load(fh)
             except json.JSONDecodeError as e:
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 92c8dfda3f..f7ada2a483 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -47,7 +47,7 @@ def create_modules_repo_dummy(tmp_dir):
     # Remove doi from meta.yml which makes lint fail
     meta_yml_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "meta.yml")
 
-    with open(meta_yml_path, "r") as fh:
+    with open(meta_yml_path) as fh:
         meta_yml = yaml.safe_load(fh)
     del meta_yml["tools"][0]["bpipe"]["doi"]
     with open(meta_yml_path, "w") as fh:
@@ -60,7 +60,7 @@ def create_modules_repo_dummy(tmp_dir):
 
     # remove "TODO" statements from main.nf
     main_nf_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "main.nf")
-    with open(main_nf_path, "r") as fh:
+    with open(main_nf_path) as fh:
         main_nf = fh.read()
     main_nf = main_nf.replace("TODO", "")
     with open(main_nf_path, "w") as fh:
@@ -68,7 +68,7 @@ def create_modules_repo_dummy(tmp_dir):
 
     # remove "TODO" statements from main.nf.test
     main_nf_test_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test")
-    with open(main_nf_test_path, "r") as fh:
+    with open(main_nf_test_path) as fh:
         main_nf_test = fh.read()
     main_nf_test = main_nf_test.replace("TODO", "")
     with open(main_nf_test_path, "w") as fh:
diff --git a/tests/test_params_file.py b/tests/test_params_file.py
index 824e8fe345..e1777a0a96 100644
--- a/tests/test_params_file.py
+++ b/tests/test_params_file.py
@@ -31,7 +31,7 @@ def setup_class(cls):
         cls.invalid_template_schema = os.path.join(cls.template_dir, "nextflow_schema_invalid.json")
 
         # Remove the allOf section to make the schema invalid
-        with open(cls.template_schema, "r") as fh:
+        with open(cls.template_schema) as fh:
             o = json.load(fh)
             del o["allOf"]
 
@@ -49,7 +49,7 @@ def test_build_template(self):
 
         assert os.path.exists(outfile)
 
-        with open(outfile, "r") as fh:
+        with open(outfile) as fh:
             out = fh.read()
 
         assert "nf-core/testpipeline" in out