diff --git a/.editorconfig b/.editorconfig
index 014c2383bd..449f446a3b 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -10,3 +10,13 @@ indent_style = space
 
 [*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
+
+# ignore python and markdown files
+[*.py]
+indent_style = unset
+
+[**/{CONTRIBUTING,README}.md]
+indent_style = unset
+
+[**/Makefile]
+indent_style = unset
diff --git a/.github/.coveragerc b/.github/.coveragerc
index 522a29eb62..24a419ae07 100644
--- a/.github/.coveragerc
+++ b/.github/.coveragerc
@@ -1,2 +1,5 @@
 [run]
-omit = nf_core/pipeline-template/*
+omit = nf_core/*-template/*
+source = nf_core
+relative_files = True
+
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 75da414db6..04d327bd8c 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -35,45 +35,28 @@ pip install -e .
 
 ## Code formatting
 
-### Black
+### Ruff
 
-All Python code in nf-core/tools must be passed through the [Black Python code formatter](https://black.readthedocs.io/en/stable/).
+All Python code in nf-core/tools must be passed through the [Ruff code linter and formatter](https://github.com/astral-sh/ruff).
 This ensures a harmonised code formatting style throughout the package, from all contributors.
 
-You can run Black on the command line (it's included in `requirements-dev.txt`) - eg. to run recursively on the whole repository:
+You can run Ruff on the command line (it's included in `requirements-dev.txt`) - eg. to run recursively on the whole repository:
 
 ```bash
-black .
+ruff format .
 ```
 
-Alternatively, Black has [integrations for most common editors](https://black.readthedocs.io/en/stable/editor_integration.html)
+Alternatively, Ruff has [integrations for most common editors](https://github.com/astral-sh/ruff-lsp) and VSCode(https://github.com/astral-sh/ruff-vscode)
 to automatically format code when you hit save.
-You can also set it up to run when you [make a commit](https://black.readthedocs.io/en/stable/version_control_integration.html).
 
 There is an automated CI check that runs when you open a pull-request to nf-core/tools that will fail if
-any code does not adhere to Black formatting.
+any code does not adhere to Ruff formatting.
 
-### isort
-
-All Python code must also be passed through [isort](https://pycqa.github.io/isort/index.html).
-This ensures a harmonised imports throughout the package, from all contributors.
-
-To run isort on the command line recursively on the whole repository you can use:
-
-```bash
-isort .
-```
-
-isort also has [plugins for most common editors](https://github.com/pycqa/isort/wiki/isort-Plugins)
-to automatically format code when you hit save.
-Or [version control integration](https://pycqa.github.io/isort/docs/configuration/pre-commit.html) to set it up to run when you make a commit.
-
-There is an automated CI check that runs when you open a pull-request to nf-core/tools that will fail if
-any code does not adhere to isort formatting.
+Ruff has been adopted for linting and formatting in replacement of Black, isort (for imports) and pyupgrade. It also includes Flake8.
 
 ### pre-commit hooks
 
-This repository comes with [pre-commit](https://pre-commit.com/) hooks for black, isort and Prettier. pre-commit automatically runs checks before a commit is committed into the git history. If all checks pass, the commit is made, if files are changed by the pre-commit hooks, the user is informed and has to stage the changes and attempt the commit again.
+This repository comes with [pre-commit](https://pre-commit.com/) hooks for ruff and Prettier. pre-commit automatically runs checks before a commit is committed into the git history. If all checks pass, the commit is made, if files are changed by the pre-commit hooks, the user is informed and has to stage the changes and attempt the commit again.
 
 You can use the pre-commit hooks if you like, but you don't have to. The CI on Github will run the same checks as the tools installed with pre-commit. If the pre-commit checks pass, then the same checks in the CI will pass, too.
 
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index dd64ffa3e5..54dee6df16 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -18,7 +18,7 @@ jobs:
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@v2
         with:
           message: |
             ## This PR is against the `master` branch :x:
diff --git a/.github/workflows/changelog.py b/.github/workflows/changelog.py
new file mode 100644
index 0000000000..2ce14e60b3
--- /dev/null
+++ b/.github/workflows/changelog.py
@@ -0,0 +1,226 @@
+"""
+Taken from https://github.com/MultiQC/MultiQC/blob/main/.github/workflows/changelog.py and updated for nf-core
+
+To be called by a CI action. Assumes the following environment variables are set:
+PR_TITLE, PR_NUMBER, GITHUB_WORKSPACE.
+
+Adds a line into the CHANGELOG.md:
+* Looks for the section to add the line to, based on the PR title, e.g. `Template:`, `Modules:`.
+* All other change will go under the "### General" section.
+* If an entry for the PR is already added, it will not run.
+
+Other assumptions:
+- CHANGELOG.md has a running section for an ongoing "dev" version
+(i.e. titled "## nf-core vX.Ydev").
+"""
+
+import os
+import re
+import subprocess
+import sys
+from pathlib import Path
+from typing import List
+
+REPO_URL = "https://github.com/nf-core/tools"
+
+# Assumes the environment is set by the GitHub action.
+pr_title = os.environ["PR_TITLE"]
+pr_number = os.environ["PR_NUMBER"]
+comment = os.environ.get("COMMENT", "")
+workspace_path = Path(os.environ.get("GITHUB_WORKSPACE", ""))
+
+assert pr_title, pr_title
+assert pr_number, pr_number
+
+# Trim the PR number added when GitHub squashes commits, e.g. "Template: Updated (#2026)"
+pr_title = pr_title.removesuffix(f" (#{pr_number})")
+
+changelog_path = workspace_path / "CHANGELOG.md"
+
+if any(
+    line in pr_title.lower()
+    for line in [
+        "skip changelog",
+        "skip change log",
+        "no changelog",
+        "no change log",
+        "bump version",
+    ]
+):
+    print("Skipping changelog update")
+    sys.exit(0)
+
+
+def _run_cmd(cmd):
+    print(cmd)
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True)
+    if result.returncode != 0:
+        raise RuntimeError(f"Error executing command: {result.stderr}")
+    return result
+
+
+def _determine_change_type(pr_title) -> str:
+    """
+    Determine the type of the PR: Template, Download, Linting, Modules, Subworkflows, or General
+    Returns a tuple of the section name and the module info.
+    """
+    sections = {
+        "Template": "### Template updates",
+        "Download": "### Download updates",
+        "Linting": "### Linting updates",
+        "Modules": "### Modules",
+        "Subworkflows": "### Subworkflows",
+    }
+    current_section = "### General"
+
+    # Check if the PR in any of the sections.
+    for section, section_header in sections.items():
+        # check if the PR title contains any of the section headers, with some loose matching, e.g. removing plural and suffixes
+        if re.sub(r"s$", "", section.lower().replace("ing", "")) in pr_title.lower():
+            current_section = section_header
+
+    return current_section
+
+
+# Determine the type of the PR: new module, module update, or core update.
+section = _determine_change_type(pr_title)
+
+# Remove section indicator from the PR title.
+pr_title = re.sub(rf"{section}[:\s]*", "", pr_title, flags=re.IGNORECASE)
+
+# Prepare the change log entry.
+pr_link = f"([#{pr_number}]({REPO_URL}/pull/{pr_number}))"
+
+# Handle manual changelog entries through comments.
+if comment := comment.removeprefix("@nf-core-bot changelog").strip():
+    pr_title = comment
+new_lines = [
+    f"- {pr_title} {pr_link}\n",
+]
+
+# Finally, updating the changelog.
+# Read the current changelog lines. We will print them back as is, except for one new
+# entry, corresponding to this new PR.
+with changelog_path.open("r") as f:
+    orig_lines = f.readlines()
+updated_lines: List[str] = []
+
+
+def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> str:
+    if line.strip().endswith(pr_link):
+        existing_lines = [line]
+        if new_lines and new_lines == existing_lines and same_section:
+            print(f"Found existing identical entry for this pull request #{pr_number} in the same section:")
+            print("".join(existing_lines))
+            sys.exit(0)  # Just leaving the CHANGELOG intact
+        else:
+            print(
+                f"Found existing entry for this pull request #{pr_number}. It will be replaced and/or moved to proper section"
+            )
+            print("".join(existing_lines))
+            for _ in range(len(existing_lines)):
+                try:
+                    line = orig_lines.pop(0)
+                except IndexError:
+                    break
+    return line
+
+
+# Find the next line in the change log that matches the pattern "## MultiQC v.*dev"
+# If it doesn't exist, exist with code 1 (let's assume that a new section is added
+# manually or by CI when a release is pushed).
+# Else, find the next line that matches the `section` variable, and insert a new line
+# under it (we also assume that section headers are added already).
+inside_version_dev = False
+already_added_entry = False
+while orig_lines:
+    line = orig_lines.pop(0)
+
+    # 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"
+        updated_lines.append(line)
+
+        # Parse version from the line `# v2.12dev` or
+        # `# [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]` ...
+        if not (m := re.match(r".*(v\d+\.\d+(dev)?).*", line)):
+            print(f"Cannot parse version from line {line.strip()}.", file=sys.stderr)
+            sys.exit(1)
+        version = m.group(1)
+
+        if not inside_version_dev:
+            if not version.endswith("dev"):
+                print(
+                    "Can't find a 'dev' version section in the changelog. Make sure "
+                    "it's created, and all the required sections, e.g. `### Template` are created under it .",
+                    file=sys.stderr,
+                )
+                sys.exit(1)
+            inside_version_dev = True
+        else:
+            if version.endswith("dev"):
+                print(
+                    f"Found another 'dev' version section in the changelog, make"
+                    f"sure to change it to a 'release' stable version tag. "
+                    f"Line: {line.strip()}",
+                    file=sys.stderr,
+                )
+                sys.exit(1)
+            # We are past the dev version, so just add back the rest of the lines and break.
+            while orig_lines:
+                line = orig_lines.pop(0)
+                line = _skip_existing_entry_for_this_pr(line, same_section=False)
+                if line:
+                    updated_lines.append(line)
+            break
+        continue
+
+    if inside_version_dev and line.lower().startswith(section.lower()):  # Section of interest header
+        if already_added_entry:
+            print(
+                f"Already added new lines into section {section}, is the section duplicated?",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+        updated_lines.append(line)
+        # Collecting lines until the next section.
+        section_lines: List[str] = []
+        while True:
+            line = orig_lines.pop(0)
+            if line.startswith("#"):
+                # Found the next section header, so need to put all the lines we collected.
+                updated_lines.append("\n")
+                _updated_lines = [_l for _l in section_lines + new_lines if _l.strip()]
+                updated_lines.extend(_updated_lines)
+                updated_lines.append("\n")
+                if new_lines:
+                    print(f"Updated {changelog_path} section '{section}' with lines:\n" + "".join(new_lines))
+                else:
+                    print(f"Removed existing entry from {changelog_path} section '{section}'")
+                already_added_entry = True
+                # Pushing back the next section header line
+                orig_lines.insert(0, line)
+                break
+            # 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=True)
+            section_lines.append(line)
+    else:
+        updated_lines.append(line)
+
+
+def collapse_newlines(lines: List[str]) -> List[str]:
+    updated = []
+    for idx in range(len(lines)):
+        if idx != 0 and not lines[idx].strip() and not lines[idx - 1].strip():
+            continue
+        updated.append(lines[idx])
+    return updated
+
+
+updated_lines = collapse_newlines(updated_lines)
+
+
+# Finally, writing the updated lines back.
+with changelog_path.open("w") as f:
+    f.writelines(updated_lines)
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
new file mode 100644
index 0000000000..4e632fbe4d
--- /dev/null
+++ b/.github/workflows/changelog.yml
@@ -0,0 +1,88 @@
+name: Update CHANGELOG.md
+on:
+  issue_comment:
+    types: [created]
+  pull_request_target:
+    types: [opened]
+
+jobs:
+  update_changelog:
+    runs-on: ubuntu-latest
+    # Run if comment is on a PR with the main repo, and if it contains the magic keywords.
+    # Or run on PR creation, unless asked otherwise in the title.
+    if: |
+      github.repository_owner == 'nf-core' && (
+        github.event_name == 'pull_request_target' ||
+        github.event.issue.pull_request && startsWith(github.event.comment.body, '@nf-core-bot changelog')
+      )
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+
+      # Action runs on the issue comment, so we don't get the PR by default.
+      # Use the GitHub CLI to check out the PR:
+      - name: Checkout Pull Request
+        env:
+          GH_TOKEN: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+        run: |
+          if [[ "${{ github.event_name }}" == "issue_comment" ]]; then
+            PR_NUMBER="${{ github.event.issue.number }}"
+          elif [[ "${{ github.event_name }}" == "pull_request_target" ]]; then
+            PR_NUMBER="${{ github.event.pull_request.number }}"
+          fi
+          gh pr checkout $PR_NUMBER
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install packages
+        run: |
+          python -m pip install --upgrade pip
+          pip install pyyaml
+
+      - name: Update CHANGELOG.md from the PR title
+        env:
+          COMMENT: ${{ github.event.comment.body }}
+          GH_TOKEN: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+        run: |
+          if [[ "${{ github.event_name }}" == "issue_comment" ]]; then
+            export PR_NUMBER='${{ github.event.issue.number }}'
+            export PR_TITLE='${{ github.event.issue.title }}'
+          elif [[ "${{ github.event_name }}" == "pull_request_target" ]]; then
+            export PR_NUMBER='${{ github.event.pull_request.number }}'
+            export PR_TITLE='${{ github.event.pull_request.title }}'
+          fi
+          python ${GITHUB_WORKSPACE}/.github/workflows/changelog.py
+
+      - name: Check if CHANGELOG.md actually changed
+        run: |
+          git diff --exit-code ${GITHUB_WORKSPACE}/CHANGELOG.md || echo "changed=YES" >> $GITHUB_ENV
+          echo "File changed: ${{ env.changed }}"
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: "pip"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit checks
+        if: env.changed == 'YES'
+        run: |
+          pre-commit run --all-files
+
+      - name: Commit and push changes
+        if: env.changed == 'YES'
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add ${GITHUB_WORKSPACE}/CHANGELOG.md
+          git status
+          git commit -m "[automated] Update CHANGELOG.md [no ci]"
+          git push
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 4b55c5e4aa..ff311f9df8 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v7
+      - uses: actions/stale@v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 57dbe86d65..0119efcd41 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -26,15 +26,22 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
+      - name: go to subdirectory and change nextflow workdir
+        run: |
+          mkdir -p create-lint-wf
+          cd create-lint-wf
+          export NXF_WORK=$(pwd)
+
       # Get the repo code
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
+          cache: pip
 
       - name: Install python dependencies
         run: |
@@ -47,14 +54,6 @@ jobs:
         with:
           version: ${{ matrix.NXF_VER }}
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier and editorconfig-checker
-        run: npm install -g prettier editorconfig-checker
-
       # Build a pipeline from the template
       - name: nf-core create
         run: |
@@ -73,11 +72,8 @@ jobs:
         working-directory: create-lint-wf
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-lint-wf/nf-core-testpipeline
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-lint-wf
 
       # Update modules to the latest version
@@ -142,7 +138,11 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: nf-core-log-file
+          name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-lint-wf/log.txt
+
+      - name: Cleanup work directory
+        run: sudo rm -rf create-lint-wf
+        if: always()
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 37cbf65c7d..3805c1a240 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -20,24 +20,37 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.runner }}
     env:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
         TEMPLATE:
-          - "template_skip_all.yml"
           - "template_skip_github_badges.yml"
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
-          - "template_skip_nf_core_configs.yml"
+        runner: ["self-hosted"]
+        profile: ["self_hosted_runner"]
+        include:
+          - TEMPLATE: "template_skip_all.yml"
+            runner: ubuntu-latest
+            profile: "docker"
+          - TEMPLATE: "template_skip_nf_core_configs.yml"
+            runner: ubuntu-latest
+            profile: "docker"
 
     steps:
+      - name: go to working directory
+        run: |
+          mkdir -p create-lint-wf-template
+          cd create-lint-wf-template
+          export NXF_WORK=$(pwd)
+
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -51,18 +64,6 @@ jobs:
         with:
           version: latest-everything
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      # Install the editorconfig linting tools
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
       # Create template files
       - name: Create template skip all (except github)
         run: |
@@ -95,7 +96,7 @@ jobs:
       - name: run the pipeline
         run: |
           cd create-test-lint-wf
-          nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results
+          nextflow run my-prefix-testpipeline -profile test,${{matrix.profile}} --outdir ./results
 
       # Remove results folder before linting
       - name: remove results folder
@@ -107,11 +108,8 @@ jobs:
         run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-test-lint-wf/my-prefix-testpipeline
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: Run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-test-lint-wf
 
       # Remove TODO statements
@@ -145,7 +143,11 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: nf-core-log-file
+          name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar
+
+      - name: Cleanup work directory
+        run: sudo rm -rf create-test-lint-wf
+        if: always()
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 026b0a889b..e128e16a36 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -26,11 +26,17 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
+      - name: go to working directory
+        run: |
+          mkdir -p create-test-wf
+          cd create-test-wf
+          export NXF_WORK=$(pwd)
+
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -49,11 +55,16 @@ jobs:
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
+          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: nf-core-log-file
+          name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt
+
+      - name: Cleanup work directory
+        # cleanup work directory
+        run: sudo rm -rf create-test-wf
+        if: always()
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 62c53508d8..8d3a154d80 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -17,7 +17,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 4184bc5e59..5e857e8dbb 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -10,7 +10,7 @@ jobs:
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
       github.repository == 'nf-core/tools'
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       # Use the @nf-core-bot token to check out so we can push later
       - uses: actions/checkout@v4
@@ -24,31 +24,17 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
-
-      - name: Run 'prettier --write'
-        run: prettier --write ${GITHUB_WORKSPACE}
-
-      - name: Run Black
-        uses: psf/black@stable
-        with:
-          # Override to remove the default --check flag so that we make changes
-          options: "--color"
-
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - name: python-isort
-        uses: isort/isort-action@v1.0.0
-        with:
-          isortVersion: "latest"
-          requirementsFiles: "requirements.txt requirements-dev.txt"
+          cache: "pip"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
       - name: Commit & push changes
         run: |
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 23972c56f6..d9847dd365 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -13,119 +13,21 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  EditorConfig:
-    runs-on: ["self-hosted"]
+  Pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      # Run editor config check only on files not covered by a linter
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
-
-  Prettier:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
-  isort:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-      - name: python-isort
-        uses: isort/isort-action@v1.1.0
-        with:
-          isortVersion: "latest"
-          requirementsFiles: "requirements.txt requirements-dev.txt"
-
-  static-type-check:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: "pip"
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip -r requirements-dev.txt
-          pip install -e .
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
-
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
-
-      - name: Get Python changed files
-        id: changed-py-files
-        uses: tj-actions/changed-files@v23
-        with:
-          files: |
-            *.py
-            **/*.py
-      - name: Run if any of the listed files above is changed
-        if: steps.changed-py-files.outputs.any_changed == 'true'
-        run: mypy ${{ steps.changed-py-files.outputs.all_changed_files }}
+      - name: Run pre-commit
+        run: pre-commit run --all-files
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 1230bfc9d3..169a917d83 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -13,7 +13,7 @@ concurrency:
 jobs:
   push_dockerhub:
     name: Push new Docker image to Docker Hub (dev)
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/tools' }}
     env:
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b6f3592165..8cec6a63d7 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -14,8 +14,9 @@ on:
       - "CHANGELOG.md"
   release:
     types: [published]
+  workflow_dispatch:
 
-# Cancel if a newer run is started
+# Cancel if a newer run with the same workflow name is queued
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
@@ -25,7 +26,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ["ubuntu-latest"]
+    runs-on: "ubuntu-latest"
     strategy:
       matrix:
         python-version: ["3.8", "3.11"]
@@ -44,20 +45,45 @@ jobs:
       runner: ${{ matrix.runner }}
       run-tests: ${{ steps.conditions.outputs.run-tests }}
 
+  # create a test matrix based on all python files in /tests
+  list_tests:
+    name: Get test file matrix
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@v4
+        name: Check out source-code repository
+
+      - name: List tests
+        id: list_tests
+        run: |
+          echo "tests=$(find tests/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+    outputs:
+      tests: ${{ steps.list_tests.outputs.tests }}
+
   test:
-    name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
-    needs: setup
-    if: ${{ needs.setup.outputs.run-tests}}
-    runs-on: ${{ needs.setup.outputs.runner }}
+    name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
+    needs: [setup, list_tests]
+    if: ${{ needs.setup.outputs.run-tests }}
+    runs-on: self-hosted
+    strategy:
+      matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
+      fail-fast: false # run all tests even if one fails
     steps:
-      - uses: actions/checkout@v2
+      - name: go to subdirectory and change nextflow workdir
+        run: |
+          mkdir -p pytest
+          cd pytest
+          export NXF_WORK=$(pwd)
+
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
+          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install dependencies
         run: |
@@ -71,16 +97,25 @@ jobs:
           sudo apt remove -y git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install -y git
+
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
-        with:
-          version: "latest-everything"
+
+      - name: Look if nf-test is already installed and write to env variable
+        id: check-nftest
+        run: |
+          if [ -f /usr/local/bin/nf-test ]; then
+            echo "nftest_installed=true" >> $GITHUB_ENV
+          else
+            echo "nftest_installed=false" >> $GITHUB_ENV
+          fi
 
       - name: Cache nf-test installation
+        if: env.nftest_installed != 'true'
         id: cache-software
         uses: actions/cache@v3
         with:
@@ -90,16 +125,70 @@ jobs:
           key: ${{ runner.os }}-nftest-${{ env.date }}
 
       - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
+        if: steps.cache-software.outputs.cache-hit != 'true' && env.nftest_installed != 'true'
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
+      - name: move coveragerc file up
+        run: |
+          mv .github/.coveragerc .
+
       - name: Test with pytest
-        run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
+        run: |
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
+          # don't fail if no tests were collected, e.g. for test_licence.py
+          if [ "${exit_code}" -eq 5 ]; then
+            echo "No tests were collected"
+            exit 0
+          elif [ "${exit_code}" -ne 0 ]; then
+            echo "Tests failed with exit code ${exit_code}"
+            exit 1
+          fi
+
+      - name: Upload coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage_${{ matrix.test }}
+          path: .coverage
+
+  coverage:
+    needs: test
+    runs-on: self-hosted
+    steps:
+      - name: go to subdirectory
+        run: |
+          mkdir -p pytest
+          cd pytest
+
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        env:
+          AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
+        with:
+          python-version: 3.11
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: move coveragerc file up
+        run: |
+          mv .github/.coveragerc .
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+      - name: Run coverage
+        run: |
+          coverage combine --keep coverage*/.coverage*
+          coverage report
+          coverage xml
 
-      - uses: codecov/codecov-action@v1
-        name: Upload code coverage report
+      - uses: codecov/codecov-action@v3
         with:
-          if: success()
-          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
index f5f289b73e..e0981e8241 100644
--- a/.github/workflows/rich-codex.yml
+++ b/.github/workflows/rich-codex.yml
@@ -8,7 +8,7 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.x
           cache: pip
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 94f8ee54e2..9bbc12cf4b 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -16,7 +16,7 @@ concurrency:
 
 jobs:
   get-pipelines:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
@@ -49,7 +49,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -78,7 +78,7 @@ jobs:
 
       - name: Upload sync log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: sync_log_${{ matrix.pipeline }}
           path: sync_log_${{ matrix.pipeline }}.txt
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index 51c25fa250..91396b2a25 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -20,14 +20,14 @@ concurrency:
 jobs:
   api-docs:
     name: Build & push Sphinx API docs
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
 
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -43,7 +43,7 @@ jobs:
       - name: Sync dev docs
         # Only sync with the website if it was a push from nf-core/tools dev branch
         if: github.repository == 'nf-core/tools' && github.event_name == 'push' && github.event.ref == 'refs/heads/dev'
-        uses: SamKirkland/FTP-Deploy-Action@4.0.0
+        uses: SamKirkland/FTP-Deploy-Action@v4.3.4
         with:
           server: ${{ secrets.ftp_server }}
           username: ${{ secrets.ftp_username}}
diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml
index b0869190d9..2183db3fcf 100644
--- a/.github/workflows/tools-api-docs-release.yml
+++ b/.github/workflows/tools-api-docs-release.yml
@@ -22,7 +22,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -37,7 +37,7 @@ jobs:
 
       - name: Sync release docs
         if: github.repository == 'nf-core/tools'
-        uses: SamKirkland/FTP-Deploy-Action@4.0.0
+        uses: SamKirkland/FTP-Deploy-Action@v4.3.4
         with:
           server: ${{ secrets.ftp_server }}
           username: ${{ secrets.ftp_username}}
diff --git a/.gitpod.yml b/.gitpod.yml
index 3c8b6b5303..39fb530da2 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -9,6 +9,7 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
+
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files
@@ -21,3 +22,4 @@ vscode:
     # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ad23a3c895..fb2a67bace 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,23 +1,23 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.11
     hooks:
-      - id: black
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
+      - id: ruff # linter
+        args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
+      - id: ruff-format # formatter
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
     hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
+      - id: editorconfig-checker
+        alias: ec
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.7.1" # Use the sha / tag you want to point at
+    rev: "v1.8.0"
     hooks:
       - id: mypy
         additional_dependencies:
diff --git a/.prettierignore b/.prettierignore
index 344cafca6e..a55074abfb 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -6,3 +6,7 @@ testing
 nf_core/module-template/meta.yml
 nf_core/module-template/tests/tags.yml
 nf_core/subworkflow-template/tests/tags.yml
+# don't run on things handled by ruff
+*.py
+*.pyc
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c6fd827245..dc96df408f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Template
 
 - Add a Github Action Workflow to the pipeline template that tests a successful download with 'nf-core download' ([#2618](https://github.com/nf-core/tools/pull/2618))
+- Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
 
 ### Download
 
@@ -16,6 +17,13 @@
 
 ### General
 
+- Run CI-pytests for nf-core tools on self-hosted runners ([#2550](https://github.com/nf-core/tools/pull/2550))
+- Add Ruff linter and formatter replacing Black, isort and pyupgrade ([#2620](https://github.com/nf-core/tools/pull/2620))
+- Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([#2630](https://github.com/nf-core/tools/pull/2630))
+- Update mshick/add-pr-comment action to v2 ([#2632](https://github.com/nf-core/tools/pull/2632))
+- update python image version in docker file ([#2636](https://github.com/nf-core/tools/pull/2636))
+- Set pdiff as nf-test differ in Docker image for Gitpod ([#2642](https://github.com/nf-core/tools/pull/2642))
+
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 
 ### Template
diff --git a/Dockerfile b/Dockerfile
index 95d544b26f..9c9770c25f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.11.5-slim
+FROM python:3.11-slim
 LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for the nfcore tools"
 
diff --git a/README.md b/README.md
index 653f5295ea..3a9b31187a 100644
--- a/README.md
+++ b/README.md
@@ -2,9 +2,8 @@
 
 [![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster)
 [![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
-[![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![code style: prettier](https://img.shields.io/badge/code%20style-prettier-ff69b4.svg)](https://github.com/prettier/prettier)
-[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
 
 [![install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/recipes/nf-core/README.html)
 [![install with PyPI](https://img.shields.io/badge/install%20with-PyPI-blue.svg)](https://pypi.org/project/nf-core/)
diff --git a/codecov.yml b/codecov.yml
index 1ecf8960c0..11a63f8bbf 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -4,3 +4,6 @@ coverage:
       default:
         threshold: 5%
     patch: off
+comment:
+  layout: "condensed_header, condensed_files, condensed_footer"
+  require_changes: true
diff --git a/docs/api/Makefile b/docs/api/Makefile
index f961e4ded1..ab30a5051e 100644
--- a/docs/api/Makefile
+++ b/docs/api/Makefile
@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index 27eaf9bcb3..bfdbd7888d 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.
 #
@@ -16,9 +15,10 @@
 import sys
 from typing import Dict
 
-sys.path.insert(0, os.path.abspath("../../../nf_core"))
 import nf_core
 
+sys.path.insert(0, os.path.abspath("../../../nf_core"))
+
 # -- Project information -----------------------------------------------------
 
 project = "nf-core/tools"
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 8cfacf7399..194b2030be 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -934,7 +934,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
     Test modules within a pipeline or a clone of the
     nf-core/modules repository.
     """
-    from nf_core.components.lint import LintException
+    from nf_core.components.lint import LintExceptionError
     from nf_core.modules import ModuleLint
 
     try:
@@ -960,7 +960,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
         )
         if len(module_lint.failed) > 0:
             sys.exit(1)
-    except LintException as e:
+    except LintExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1020,7 +1020,7 @@ def bump_versions(ctx, tool, dir, all, show_all):
     the nf-core/modules repo.
     """
     from nf_core.modules.bump_versions import ModuleVersionBumper
-    from nf_core.modules.modules_utils import ModuleException
+    from nf_core.modules.modules_utils import ModuleExceptionError
 
     try:
         version_bumper = ModuleVersionBumper(
@@ -1030,7 +1030,7 @@ def bump_versions(ctx, tool, dir, all, show_all):
             ctx.obj["modules_repo_no_pull"],
         )
         version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all)
-    except ModuleException as e:
+    except ModuleExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1207,7 +1207,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
     Test subworkflows within a pipeline or a clone of the
     nf-core/modules repository.
     """
-    from nf_core.components.lint import LintException
+    from nf_core.components.lint import LintExceptionError
     from nf_core.subworkflows import SubworkflowLint
 
     try:
@@ -1232,7 +1232,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
         )
         if len(subworkflow_lint.failed) > 0:
             sys.exit(1)
-    except LintException as e:
+    except LintExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1647,7 +1647,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
     the pipeline. It is run automatically for all pipelines when ever a
     new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made.
     """
-    from nf_core.sync import PipelineSync, PullRequestException, SyncException
+    from nf_core.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError
     from nf_core.utils import is_pipeline_directory
 
     # Check if pipeline directory contains necessary files
@@ -1657,7 +1657,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
     sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml)
     try:
         sync_obj.sync()
-    except (SyncException, PullRequestException) as e:
+    except (SyncExceptionError, PullRequestExceptionError) as e:
         log.error(e)
         sys.exit(1)
 
diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py
index 40c8f8984f..c5e8931fbc 100644
--- a/nf_core/bump_version.py
+++ b/nf_core/bump_version.py
@@ -68,7 +68,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
             [
                 (
                     f"/releases/tag/{current_version}",
-                    f"/tree/dev",
+                    "/tree/dev",
                 )
             ],
         )
@@ -78,7 +78,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
             pipeline_obj,
             [
                 (
-                    f"/tree/dev",
+                    "/tree/dev",
                     f"/releases/tag/{multiqc_new_version}",
                 )
             ],
@@ -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..01650a643d 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -53,7 +53,7 @@ def get_repo_info(directory: str, use_prompt: Optional[bool] = True) -> Tuple[st
         raise UserWarning("Repository type could not be established")
 
     # Check if it's a valid answer
-    if not repo_type in ["pipeline", "modules"]:
+    if repo_type not in ["pipeline", "modules"]:
         raise UserWarning(f"Invalid repository type: '{repo_type}'")
 
     # Check for org if modules repo
@@ -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..32f6d1a433 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
@@ -440,12 +439,13 @@ 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:
+                    if "publishDir" not in line and line.strip() != "":
                         config_lines += line
-            if len(config_lines) > 0:
+            # if the nextflow.config file only contained publishDir, non_publish_dir_lines will be 11 characters long (`process {\n}`)
+            if len(config_lines) > 11:
                 log.debug("Copying nextflow.config file from pytest tests")
                 with open(
                     Path(self.directory, self.component_type, self.org, self.component_dir, "tests", "nextflow.config"),
@@ -460,7 +460,7 @@ 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 +475,7 @@ 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..3c2fb9dde3 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
@@ -27,7 +26,7 @@
 log = logging.getLogger(__name__)
 
 
-class LintException(Exception):
+class LintExceptionError(Exception):
     """Exception raised when there was an error with module or subworkflow linting"""
 
     pass
@@ -216,7 +215,7 @@ def _print_results(self, show_passed=False, sort_by="test"):
             try:
                 for lint_result in tests:
                     max_name_len = max(len(lint_result.component_name), max_name_len)
-            except:
+            except Exception:
                 pass
 
         # Helper function to format test links nicely
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 874fa570bc..2f73afe9d3 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:
@@ -168,17 +168,19 @@ def get_inputs_from_main_nf(self):
         input_data = data.split("input:")[1].split("output:")[0]
         regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
         matches = re.finditer(regex, input_data, re.MULTILINE)
-        for matchNum, match in enumerate(matches, start=1):
+        for _, match in enumerate(matches, start=1):
             if match.group(3):
-                inputs.append(match.group(3))
+                input_val = match.group(3).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                inputs.append(input_val)
             elif match.group(4):
-                inputs.append(match.group(4))
+                input_val = match.group(4).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                inputs.append(input_val)
         log.info(f"Found {len(inputs)} inputs in {self.main_nf}")
         self.inputs = inputs
 
     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:
@@ -187,7 +189,7 @@ def get_outputs_from_main_nf(self):
         output_data = data.split("output:")[1].split("when:")[0]
         regex = r"emit:\s*([^)\s,]+)"
         matches = re.finditer(regex, output_data, re.MULTILINE)
-        for matchNum, match in enumerate(matches, start=1):
+        for _, match in enumerate(matches, start=1):
             outputs.append(match.group(1))
         log.info(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 28f2f886b1..55d5747451 100644
--- a/nf_core/components/patch.py
+++ b/nf_core/components/patch.py
@@ -35,7 +35,7 @@ def _parameter_checks(self, component):
         if component is not None and component not in component_names:
             component_dir = [dir for dir, m in components if m == component][0]
             raise UserWarning(
-                f"{self.component_type[:-1].title()} '{Path(self.component_type, component_dir, module)}' does not exist in the pipeline"
+                f"{self.component_type[:-1].title()} '{Path(self.component_type, component_dir, component)}' does not exist in the pipeline"
             )
 
     def patch(self, component=None):
@@ -220,5 +220,5 @@ def remove(self, component):
         ):
             log.error(
                 f"Module files do not appear to match the remote for the commit sha in the 'module.json': {component_version}\n"
-                f"Recommend reinstalling with 'nf-core modules install --force --sha {component_version} {module}' "
+                f"Recommend reinstalling with 'nf-core modules install --force --sha {component_version} {component}' "
             )
diff --git a/nf_core/create.py b/nf_core/create.py
index 56d0912a07..0d5b7e4d7b 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -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..4c0bc97f42 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
@@ -21,7 +20,7 @@
 import rich
 import rich.progress
 from git.exc import GitCommandError, InvalidGitRepositoryError
-from pkg_resources import parse_version as VersionParser
+from pkg_resources import parse_version as version_parser
 
 import nf_core
 import nf_core.list
@@ -551,7 +550,7 @@ def read_remote_containers(self):
                     self.containers_remote = sorted(list(set(self.containers_remote)))
             except (FileNotFoundError, LookupError) as e:
                 log.error(f"[red]Issue with reading the specified remote $NXF_SINGULARITY_CACHE index:[/]\n{e}\n")
-                if stderr.is_interactive and rich.prompt.Confirm.ask(f"[blue]Specify a new index file and try again?"):
+                if stderr.is_interactive and rich.prompt.Confirm.ask("[blue]Specify a new index file and try again?"):
                     self.container_cache_index = None  # reset chosen path to index file.
                     self.prompt_singularity_cachedir_remote()
                 else:
@@ -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.
@@ -853,7 +852,7 @@ def rectify_raw_container_matches(self, raw_findings):
             ['https://depot.galaxyproject.org/singularity/scanpy:1.7.2--pyhdfd78af_0', 'biocontainers/scanpy:1.7.2--pyhdfd78af_0']
             """
             container_value_defs = [
-                capture for _, capture in container_value_defs[:] if not capture in ["singularity", "apptainer"]
+                capture for _, capture in container_value_defs[:] if capture not in ["singularity", "apptainer"]
             ]
 
             """
@@ -1066,10 +1065,10 @@ def get_singularity_images(self, current_revision=""):
                                 self.singularity_pull_image(*container, library, progress)
                                 # Pulling the image was successful, no ContainerError was raised, break the library loop
                                 break
-                            except ContainerError.ImageExists as e:
+                            except ContainerError.ImageExistsError:
                                 # Pulling not required
                                 break
-                            except ContainerError.RegistryNotFound as e:
+                            except ContainerError.RegistryNotFoundError as e:
                                 self.container_library.remove(library)
                                 # The only library was removed
                                 if not self.container_library:
@@ -1079,13 +1078,13 @@ def get_singularity_images(self, current_revision=""):
                                 else:
                                     # Other libraries can be used
                                     continue
-                            except ContainerError.ImageNotFound as e:
+                            except ContainerError.ImageNotFoundError as e:
                                 # Try other registries
                                 if e.error_log.absolute_URI:
                                     break  # there no point in trying other registries if absolute URI was specified.
                                 else:
                                     continue
-                            except ContainerError.InvalidTag as e:
+                            except ContainerError.InvalidTagError:
                                 # Try other registries
                                 continue
                             except ContainerError.OtherError as e:
@@ -1524,7 +1523,7 @@ def tidy_tags_and_branches(self):
                     else:
                         # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns.
                         valid_versions = [
-                            VersionParser(v)
+                            version_parser(v)
                             for v in desired_revisions
                             if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v)
                         ]
@@ -1583,7 +1582,7 @@ def __init__(self, container, registry, address, absolute_URI, out_path, singula
 
         for line in error_msg:
             if re.search(r"dial\stcp.*no\ssuch\shost", line):
-                self.error_type = self.RegistryNotFound(self)
+                self.error_type = self.RegistryNotFoundError(self)
                 break
             elif (
                 re.search(r"requested\saccess\sto\sthe\sresource\sis\sdenied", line)
@@ -1595,13 +1594,13 @@ def __init__(self, container, registry, address, absolute_URI, out_path, singula
                 #                    unauthorized: authentication required
                 # Quay.io: StatusCode: 404,  <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">\n']
                 # ghcr.io: Requesting bearer token: invalid status code from registry 400 (Bad Request)
-                self.error_type = self.ImageNotFound(self)
+                self.error_type = self.ImageNotFoundError(self)
                 break
             elif re.search(r"manifest\sunknown", line):
-                self.error_type = self.InvalidTag(self)
+                self.error_type = self.InvalidTagError(self)
                 break
             elif re.search(r"Image\sfile\salready\sexists", line):
-                self.error_type = self.ImageExists(self)
+                self.error_type = self.ImageExistsError(self)
                 break
             else:
                 continue
@@ -1615,7 +1614,7 @@ def __init__(self, container, registry, address, absolute_URI, out_path, singula
 
         raise self.error_type
 
-    class RegistryNotFound(ConnectionRefusedError):
+    class RegistryNotFoundError(ConnectionRefusedError):
         """The specified registry does not resolve to a valid IP address"""
 
         def __init__(self, error_log):
@@ -1628,7 +1627,7 @@ def __init__(self, error_log):
             )
             super().__init__(self.message, self.helpmessage, self.error_log)
 
-    class ImageNotFound(FileNotFoundError):
+    class ImageNotFoundError(FileNotFoundError):
         """The image can not be found in the registry"""
 
         def __init__(self, error_log):
@@ -1644,7 +1643,7 @@ def __init__(self, error_log):
 
             super().__init__(self.message)
 
-    class InvalidTag(AttributeError):
+    class InvalidTagError(AttributeError):
         """Image and registry are valid, but the (version) tag is not"""
 
         def __init__(self, error_log):
@@ -1653,7 +1652,7 @@ def __init__(self, error_log):
             self.helpmessage = f'Please chose a different library than {self.error_log.registry}\nor try to locate the "{self.error_log.address.split(":")[-1]}" version of "{self.error_log.container}" manually.\nPlease troubleshoot the command \n"{" ".join(self.error_log.singularity_command)}" manually.\n'
             super().__init__(self.message)
 
-    class ImageExists(FileExistsError):
+    class ImageExistsError(FileExistsError):
         """Image already exists in cache/output directory."""
 
         def __init__(self, error_log):
diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index e721f210d0..ad4bed5052 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -47,19 +47,23 @@ RUN conda config --add channels defaults && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --name base \
-        mamba \
-        nextflow \
-        nf-core \
-        nf-test \
-        black \
-        prettier \
-        pre-commit \
-        openjdk \
-        pytest-workflow && \
+    mamba \
+    nextflow \
+    nf-core \
+    nf-test \
+    prettier \
+    pre-commit \
+    ruff \
+    openjdk \
+    pytest-workflow && \
     conda clean --all --force-pkgs-dirs --yes
 
 # Update Nextflow
 RUN nextflow self-update
 
 # Install nf-core
-RUN python -m pip install .
+RUN python -m pip install . --no-cache-dir
+
+# Setup pdiff for nf-test diffs
+RUN export NFT_DIFF="pdiff" && \
+    export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
diff --git a/nf_core/launch.py b/nf_core/launch.py
index 363506c448..25bb4c150c 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
@@ -428,7 +427,7 @@ def prompt_param(self, param_id, param_obj, is_required, answers):
         answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
 
         # If required and got an empty reponse, ask again
-        while type(answer[param_id]) is str and answer[param_id].strip() == "" and is_required:
+        while isinstance(answer[param_id], str) and answer[param_id].strip() == "" and is_required:
             log.error(f"'--{param_id}' is required")
             answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
 
@@ -546,14 +545,14 @@ def single_param_to_questionary(self, param_id, param_obj, answers=None, print_h
         # Start with the default from the param object
         if "default" in param_obj:
             # Boolean default is cast back to a string later - this just normalises all inputs
-            if param_obj["type"] == "boolean" and type(param_obj["default"]) is str:
+            if param_obj["type"] == "boolean" and isinstance(param_obj["default"], str):
                 question["default"] = param_obj["default"].lower() == "true"
             else:
                 question["default"] = param_obj["default"]
 
         # 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 type(self.schema_obj.input_params[param_id]) is str:
+            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()
             else:
                 question["default"] = self.schema_obj.input_params[param_id]
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..a3e7d54b66 100644
--- a/nf_core/lint/actions_ci.py
+++ b/nf_core/lint/actions_ci.py
@@ -1,5 +1,4 @@
 import os
-import re
 
 import yaml
 
@@ -48,7 +47,7 @@ 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}"]}
@@ -62,7 +61,7 @@ def actions_ci(self):
         if not (
             pr_subtree is None
             or ("branches" in pr_subtree and "dev" in pr_subtree["branches"])
-            or ("ignore_branches" in pr_subtree and not "dev" in pr_subtree["ignore_branches"])
+            or ("ignore_branches" in pr_subtree and "dev" not in pr_subtree["ignore_branches"])
         ):
             raise AssertionError()
         if "published" not in ciwf[True]["release"]["types"]:
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..8ef425234b 100644
--- a/nf_core/lint/merge_markers.py
+++ b/nf_core/lint/merge_markers.py
@@ -1,5 +1,4 @@
 import fnmatch
-import io
 import logging
 import os
 
@@ -23,9 +22,9 @@ 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:
-            for l in fh:
-                ignore.append(os.path.basename(l.strip().rstrip("/")))
+        with open(os.path.join(self.wf_path, ".gitignore"), encoding="latin1") as fh:
+            for line in fh:
+                ignore.append(os.path.basename(line.strip().rstrip("/")))
     for root, dirs, files in os.walk(self.wf_path, topdown=True):
         # Ignore files
         for i_base in ignore:
@@ -41,12 +40,12 @@ 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:
-                    for l in fh:
-                        if ">>>>>>>" in l:
-                            failed.append(f"Merge marker '>>>>>>>' in `{os.path.join(root, fname)}`: {l[:30]}")
-                        if "<<<<<<<" in l:
-                            failed.append(f"Merge marker '<<<<<<<' in `{os.path.join(root, fname)}`: {l[:30]}")
+                with open(os.path.join(root, fname), encoding="latin1") as fh:
+                    for line in fh:
+                        if ">>>>>>>" in line:
+                            failed.append(f"Merge marker '>>>>>>>' in `{os.path.join(root, fname)}`: {line[:30]}")
+                        if "<<<<<<<" in line:
+                            failed.append(f"Merge marker '<<<<<<<' in `{os.path.join(root, fname)}`: {line[:30]}")
             except FileNotFoundError:
                 log.debug(f"Could not open file {os.path.join(root, fname)} in merge_markers lint test")
     if len(failed) == 0:
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..328bc03759 100644
--- a/nf_core/lint/nextflow_config.py
+++ b/nf_core/lint/nextflow_config.py
@@ -300,7 +300,7 @@ 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 +320,7 @@ 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..ba6ec79150 100644
--- a/nf_core/lint/pipeline_todos.py
+++ b/nf_core/lint/pipeline_todos.py
@@ -1,5 +1,4 @@
 import fnmatch
-import io
 import logging
 import os
 
@@ -41,9 +40,9 @@ 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:
-            for l in fh:
-                ignore.append(os.path.basename(l.strip().rstrip("/")))
+        with open(os.path.join(root_dir, ".gitignore"), encoding="latin1") as fh:
+            for line in fh:
+                ignore.append(os.path.basename(line.strip().rstrip("/")))
     for root, dirs, files in os.walk(root_dir, topdown=True):
         # Ignore files
         for i_base in ignore:
@@ -52,18 +51,18 @@ 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:
-                    for l in fh:
-                        if "TODO nf-core" in l:
-                            l = (
-                                l.replace("<!--", "")
+                with open(os.path.join(root, fname), encoding="latin1") as fh:
+                    for line in fh:
+                        if "TODO nf-core" in line:
+                            line = (
+                                line.replace("<!--", "")
                                 .replace("-->", "")
                                 .replace("# TODO nf-core: ", "")
                                 .replace("// TODO nf-core: ", "")
                                 .replace("TODO nf-core: ", "")
                                 .strip()
                             )
-                            warned.append(f"TODO string in `{fname}`: _{l}_")
+                            warned.append(f"TODO string in `{fname}`: _{line}_")
                             file_paths.append(os.path.join(root, fname))
             except FileNotFoundError:
                 log.debug(f"Could not open file {fname} in pipeline_todos lint test")
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/system_exit.py b/nf_core/lint/system_exit.py
index 56a526d97b..435a2452d0 100644
--- a/nf_core/lint/system_exit.py
+++ b/nf_core/lint/system_exit.py
@@ -25,9 +25,9 @@ def system_exit(self):
     for file in to_check:
         try:
             with file.open() as fh:
-                for i, l in enumerate(fh.readlines(), start=1):
-                    if "System.exit" in l and not "System.exit(0)" in l:
-                        warned.append(f"`System.exit` in {file.name}: _{l.strip()}_  [line {i}]")
+                for i, line in enumerate(fh.readlines(), start=1):
+                    if "System.exit" in line and "System.exit(0)" not in line:
+                        warned.append(f"`System.exit` in {file.name}: _{line.strip()}_  [line {i}]")
         except FileNotFoundError:
             log.debug(f"Could not open file {file.name} in system_exit lint test")
 
diff --git a/nf_core/lint/template_strings.py b/nf_core/lint/template_strings.py
index fb1f0f32e5..3467229362 100644
--- a/nf_core/lint/template_strings.py
+++ b/nf_core/lint/template_strings.py
@@ -1,4 +1,3 @@
-import io
 import mimetypes
 import re
 
@@ -30,11 +29,11 @@ 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:
+            for line in fh:
                 lnum += 1
-                cc_matches = re.findall(r"[^$]{{[^:}]*}}", l)
+                cc_matches = re.findall(r"[^$]{{[^:}]*}}", 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}")
diff --git a/nf_core/lint/version_consistency.py b/nf_core/lint/version_consistency.py
index fa5b50de01..e396ca9e7a 100644
--- a/nf_core/lint/version_consistency.py
+++ b/nf_core/lint/version_consistency.py
@@ -31,7 +31,7 @@ def version_consistency(self):
     versions["manifest.version"] = self.nf_config.get("manifest.version", "").strip(" '\"")
 
     # Get version from the docker tag
-    if self.nf_config.get("process.container", "") and not ":" in self.nf_config.get("process.container", ""):
+    if self.nf_config.get("process.container", "") and ":" not in self.nf_config.get("process.container", ""):
         failed.append(f"Docker slug seems not to have a version tag: {self.nf_config.get('process.container', '')}")
 
     # Get config container tag (if set; one container per workflow)
@@ -53,8 +53,9 @@ def version_consistency(self):
     # Check if they are consistent
     if len(set(versions.values())) != 1:
         failed.append(
-            "The versioning is not consistent between container, release tag "
-            "and config. Found {}".format(", ".join(["{} = {}".format(k, v) for k, v in versions.items()]))
+            "The versioning is not consistent between container, release tag " "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..d0b59319a3 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
@@ -205,7 +204,7 @@ def print_summary(self):
             def sort_pulled_date(wf):
                 try:
                     return wf.local_wf.last_pull * -1
-                except:
+                except Exception:
                     return 0
 
             filtered_workflows.sort(key=sort_pulled_date)
diff --git a/nf_core/module-template/tests/main.nf.test b/nf_core/module-template/tests/main.nf.test
index 5a2e6cdc63..e1b1dadf12 100644
--- a/nf_core/module-template/tests/main.nf.test
+++ b/nf_core/module-template/tests/main.nf.test
@@ -26,12 +26,12 @@ nextflow_process {
                 """
                 // TODO nf-core: define inputs of the process here. Example:
                 {% if has_meta %}
-                input = [
+                input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
                     ]
                 {%- else %}
-                input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
                 {%- endif %}
                 """
             }
@@ -58,12 +58,12 @@ nextflow_process {
                 """
                 // TODO nf-core: define inputs of the process here. Example:
                 {% if has_meta %}
-                input = [
+                input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
                     ]
                 {%- else %}
-                input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
                 {%- endif %}
                 """
             }
diff --git a/nf_core/modules/__init__.py b/nf_core/modules/__init__.py
index 4b36f302bd..6be871ece8 100644
--- a/nf_core/modules/__init__.py
+++ b/nf_core/modules/__init__.py
@@ -6,7 +6,7 @@
 from .list import ModuleList
 from .modules_json import ModulesJson
 from .modules_repo import ModulesRepo
-from .modules_utils import ModuleException
+from .modules_utils import ModuleExceptionError
 from .patch import ModulePatch
 from .remove import ModuleRemove
 from .update import ModuleUpdate
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 25259f1a16..b9003be974 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
@@ -24,9 +22,8 @@
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.utils import custom_yaml_dumper
+from nf_core.utils import custom_yaml_dumper, rich_force_colors
 from nf_core.utils import plural_s as _s
-from nf_core.utils import rich_force_colors
 
 log = logging.getLogger(__name__)
 
@@ -74,7 +71,7 @@ def bump_versions(
 
         # Verify that this is not a pipeline
         if not self.repo_type == "modules":
-            raise nf_core.modules.modules_utils.ModuleException(
+            raise nf_core.modules.modules_utils.ModuleExceptionError(
                 "This command only works on the nf-core/modules repository, not on pipelines!"
             )
 
@@ -105,12 +102,14 @@ def bump_versions(
         if module:
             self.show_up_to_date = True
             if all_modules:
-                raise nf_core.modules.modules_utils.ModuleException(
+                raise nf_core.modules.modules_utils.ModuleExceptionError(
                     "You cannot specify a tool and request all tools to be bumped."
                 )
             nfcore_modules = [m for m in nfcore_modules if m.component_name == module]
             if len(nfcore_modules) == 0:
-                raise nf_core.modules.modules_utils.ModuleException(f"Could not find the specified module: '{module}'")
+                raise nf_core.modules.modules_utils.ModuleExceptionError(
+                    f"Could not find the specified module: '{module}'"
+                )
 
         progress_bar = Progress(
             "[bold blue]{task.description}",
@@ -146,10 +145,10 @@ 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:
-                    for l in fh:
-                        if "bioconda::" in l:
-                            bioconda_packages = [b for b in l.split() if "bioconda::" in b]
+                with open(module.main_nf) as fh:
+                    for line in fh:
+                        if "bioconda::" in line:
+                            bioconda_packages = [b for b in line.split() if "bioconda::" in b]
             except FileNotFoundError:
                 log.error(
                     f"Neither `environment.yml` nor `main.nf` of {module.component_name} module could be read to get bioconada version of used tools."
@@ -208,7 +207,7 @@ 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 +240,7 @@ 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 +265,7 @@ 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:
@@ -289,7 +288,7 @@ def _print_results(self) -> None:
         for m in [self.up_to_date, self.updated, self.failed]:
             try:
                 max_mod_name_len = max(len(m[2]), max_mod_name_len)
-            except:
+            except Exception:
                 pass
 
         def format_result(module_updates: List[Tuple[str, str]], table: Table) -> Table:
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 68a38cc0cd..866e6312aa 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
@@ -16,7 +15,7 @@
 
 import nf_core.modules.modules_utils
 import nf_core.utils
-from nf_core.components.lint import ComponentLint, LintException, LintResult
+from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult
 from nf_core.lint_utils import console
 
 log = logging.getLogger(__name__)
@@ -119,11 +118,11 @@ def lint(
         # Only lint the given module
         if module:
             if all_modules:
-                raise LintException("You cannot specify a tool and request all tools to be linted.")
+                raise LintExceptionError("You cannot specify a tool and request all tools to be linted.")
             local_modules = []
             remote_modules = [m for m in self.all_remote_components if m.component_name == module]
             if len(remote_modules) == 0:
-                raise LintException(f"Could not find the specified module: '{module}'")
+                raise LintExceptionError(f"Could not find the specified module: '{module}'")
         else:
             local_modules = self.all_local_components
             remote_modules = self.all_remote_components
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..fd4d81f7f2 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:
@@ -81,39 +81,39 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
     script_lines = []
     shell_lines = []
     when_lines = []
-    for l in lines:
-        if re.search(r"^\s*process\s*\w*\s*{", l) and state == "module":
+    for line in lines:
+        if re.search(r"^\s*process\s*\w*\s*{", line) and state == "module":
             state = "process"
-        if re.search(r"input\s*:", l) and state in ["process"]:
+        if re.search(r"input\s*:", line) and state in ["process"]:
             state = "input"
             continue
-        if re.search(r"output\s*:", l) and state in ["input", "process"]:
+        if re.search(r"output\s*:", line) and state in ["input", "process"]:
             state = "output"
             continue
-        if re.search(r"when\s*:", l) and state in ["input", "output", "process"]:
+        if re.search(r"when\s*:", line) and state in ["input", "output", "process"]:
             state = "when"
             continue
-        if re.search(r"script\s*:", l) and state in ["input", "output", "when", "process"]:
+        if re.search(r"script\s*:", line) and state in ["input", "output", "when", "process"]:
             state = "script"
             continue
-        if re.search(r"shell\s*:", l) and state in ["input", "output", "when", "process"]:
+        if re.search(r"shell\s*:", line) and state in ["input", "output", "when", "process"]:
             state = "shell"
             continue
 
         # Perform state-specific linting checks
-        if state == "process" and not _is_empty(l):
-            process_lines.append(l)
-        if state == "input" and not _is_empty(l):
-            inputs.extend(_parse_input(module, l))
-        if state == "output" and not _is_empty(l):
-            outputs += _parse_output(module, l)
+        if state == "process" and not _is_empty(line):
+            process_lines.append(line)
+        if state == "input" and not _is_empty(line):
+            inputs.extend(_parse_input(module, line))
+        if state == "output" and not _is_empty(line):
+            outputs += _parse_output(module, line)
             outputs = list(set(outputs))  # remove duplicate 'meta's
-        if state == "when" and not _is_empty(l):
-            when_lines.append(l)
-        if state == "script" and not _is_empty(l):
-            script_lines.append(l)
-        if state == "shell" and not _is_empty(l):
-            shell_lines.append(l)
+        if state == "when" and not _is_empty(line):
+            when_lines.append(line)
+        if state == "script" and not _is_empty(line):
+            script_lines.append(line)
+        if state == "shell" and not _is_empty(line):
+            shell_lines.append(line)
 
     # Check that we have required sections
     if not len(outputs):
@@ -140,7 +140,7 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
 
     # Check that shell uses a template
     if len(shell_lines):
-        if any("template" in l for l in shell_lines):
+        if any("template" in line for line in shell_lines):
             module.passed.append(("main_nf_shell_template", "`template` found in `shell` block", module.main_nf))
         else:
             module.failed.append(("main_nf_shell_template", "No `template` found in `shell` block", module.main_nf))
@@ -249,21 +249,21 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     # Deprecated enable_conda
     for i, raw_line in enumerate(lines):
         url = None
-        l = raw_line.strip(" \n'\"}:")
+        line = raw_line.strip(" \n'\"}:")
 
         # Catch preceeding "container "
-        if l.startswith("container"):
-            l = l.replace("container", "").strip(" \n'\"}:")
+        if line.startswith("container"):
+            line = line.replace("container", "").strip(" \n'\"}:")
 
-        if _container_type(l) == "conda":
-            if "bioconda::" in l:
-                bioconda_packages = [b for b in l.split() if "bioconda::" in b]
-            match = re.search(r"params\.enable_conda", l)
+        if _container_type(line) == "conda":
+            if "bioconda::" in line:
+                bioconda_packages = [b for b in line.split() if "bioconda::" in b]
+            match = re.search(r"params\.enable_conda", line)
             if match is None:
                 self.passed.append(
                     (
                         "deprecated_enable_conda",
-                        f"Deprecated parameter 'params.enable_conda' correctly not found in the conda definition",
+                        "Deprecated parameter 'params.enable_conda' correctly not found in the conda definition",
                         self.main_nf,
                     )
                 )
@@ -271,35 +271,35 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
                 self.failed.append(
                     (
                         "deprecated_enable_conda",
-                        f"Found deprecated parameter 'params.enable_conda' in the conda definition",
+                        "Found deprecated parameter 'params.enable_conda' in the conda definition",
                         self.main_nf,
                     )
                 )
-        if _container_type(l) == "singularity":
+        if _container_type(line) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 -> 0.11.9--0
             # Please god let's find a better way to do this than regex
-            match = re.search(r"(?:[:.])?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", l)
+            match = re.search(r"(?:[:.])?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", line)
             if match is not None:
                 singularity_tag = match.group(1)
                 self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))
             else:
                 self.failed.append(("singularity_tag", "Unable to parse singularity tag", self.main_nf))
                 singularity_tag = None
-            url = urlparse(l.split("'")[0])
+            url = urlparse(line.split("'")[0])
 
-        if _container_type(l) == "docker":
+        if _container_type(line) == "docker":
             # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5 -> 2.7.1--pl526_5
             # e.g. "biocontainers/biocontainers:v1.2.0_cv1 -> v1.2.0_cv1
-            match = re.search(r":([A-Za-z\d\-_.]+)$", l)
+            match = re.search(r":([A-Za-z\d\-_.]+)$", line)
             if match is not None:
                 docker_tag = match.group(1)
                 self.passed.append(("docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))
             else:
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
                 docker_tag = None
-            if l.startswith(registry):
-                l_stripped = re.sub(r"\W+$", "", l)
+            if line.startswith(registry):
+                l_stripped = re.sub(r"\W+$", "", line)
                 self.failed.append(
                     (
                         "container_links",
@@ -308,15 +308,15 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
                     )
                 )
             else:
-                self.passed.append(("container_links", f"Container prefix is correct", self.main_nf))
+                self.passed.append(("container_links", "Container prefix is correct", self.main_nf))
 
             # Guess if container name is simple one (e.g. nfcore/ubuntu:20.04)
             # If so, add quay.io as default container prefix
-            if l.count("/") == 1 and l.count(":") == 1:
-                l = "/".join([registry, l]).replace("//", "/")
-            url = urlparse(l.split("'")[0])
+            if line.count("/") == 1 and line.count(":") == 1:
+                line = "/".join([registry, line]).replace("//", "/")
+            url = urlparse(line.split("'")[0])
 
-        if l.startswith("container") or _container_type(l) == "docker" or _container_type(l) == "singularity":
+        if line.startswith("container") or _container_type(line) == "docker" or _container_type(line) == "singularity":
             check_container_link_line(self, raw_line, registry)
 
         # Try to connect to container URLs
@@ -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]
@@ -424,7 +424,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
 
 def check_process_labels(self, lines):
     correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long"]
-    all_labels = [l.strip() for l in lines if l.lstrip().startswith("label ")]
+    all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")]
     bad_labels = []
     good_labels = []
     if len(all_labels) > 0:
@@ -475,14 +475,14 @@ def check_process_labels(self, lines):
 def check_container_link_line(self, raw_line, registry):
     """Look for common problems in the container name / URL, for docker and singularity."""
 
-    l = raw_line.strip(" \n'\"}:")
+    line = raw_line.strip(" \n'\"}:")
 
     # lint double quotes
-    if l.count('"') > 2:
+    if line.count('"') > 2:
         self.failed.append(
             (
                 "container_links",
-                f"Too many double quotes found when specifying container: {l.lstrip('container ')}",
+                f"Too many double quotes found when specifying container: {line.lstrip('container ')}",
                 self.main_nf,
             )
         )
@@ -490,7 +490,7 @@ def check_container_link_line(self, raw_line, registry):
         self.passed.append(
             (
                 "container_links",
-                f"Correct number of double quotes found when specifying container: {l.lstrip('container ')}",
+                f"Correct number of double quotes found when specifying container: {line.lstrip('container ')}",
                 self.main_nf,
             )
         )
@@ -524,7 +524,9 @@ def check_container_link_line(self, raw_line, registry):
             )
 
         # lint more than one container in the same line
-        if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or l.startswith(registry)):
+        if ("https://containers" in line or "https://depot" in line) and (
+            "biocontainers/" in line or line.startswith(registry)
+        ):
             self.warned.append(
                 (
                     "container_links",
@@ -576,7 +578,7 @@ def _parse_output(self, line):
     output = []
     if "meta" in line:
         output.append("meta")
-    if not "emit:" in line:
+    if "emit:" not in line:
         self.failed.append(("missing_emit", f"Missing emit statement: {line.strip()}", self.main_nf))
     else:
         output.append(line.split("emit:")[1].strip())
@@ -605,14 +607,14 @@ 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
     new_lines = []
     for line in lines:
-        l = line.strip(" '\"")
-        build_type = _container_type(l)
+        line_stripped = line.strip(" '\"")
+        build_type = _container_type(line_stripped)
         if build_type == "conda":
             new_lines.append(re.sub(rf"{current_version}", f"{latest_version}", line))
         elif build_type in ("singularity", "docker"):
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/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 152ed7b0c0..204c20fd71 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -1,8 +1,6 @@
-import filecmp
 import logging
 import os
 import shutil
-from pathlib import Path
 
 import git
 import rich
diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py
index 3ae01e9eef..ca8993483b 100644
--- a/nf_core/modules/modules_utils.py
+++ b/nf_core/modules/modules_utils.py
@@ -9,7 +9,7 @@
 log = logging.getLogger(__name__)
 
 
-class ModuleException(Exception):
+class ModuleExceptionError(Exception):
     """Exception raised when there was an error with module commands"""
 
     pass
@@ -69,12 +69,12 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis
     if os.path.exists(nfcore_modules_dir):
         for m in sorted([m for m in os.listdir(nfcore_modules_dir) if not m == "lib"]):
             if not os.path.isdir(os.path.join(nfcore_modules_dir, m)):
-                raise ModuleException(
+                raise ModuleExceptionError(
                     f"File found in '{nfcore_modules_dir}': '{m}'! This directory should only contain module directories."
                 )
             m_content = os.listdir(os.path.join(nfcore_modules_dir, m))
             # Not a module, but contains sub-modules
-            if not "main.nf" in m_content:
+            if "main.nf" not in m_content:
                 for tool in m_content:
                     nfcore_modules_names.append(os.path.join(m, tool))
             else:
diff --git a/nf_core/params_file.py b/nf_core/params_file.py
index 5c50c53fb9..51986821b5 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
@@ -9,8 +8,6 @@
 from typing import Literal, Optional
 
 import questionary
-import rich
-import rich.columns
 
 import nf_core.list
 import nf_core.utils
@@ -196,7 +193,7 @@ def format_param(self, name, properties, required_properties=(), show_hidden=Fal
         description = properties.get("description", "")
         self.schema_obj.get_schema_defaults()
         default = properties.get("default")
-        typ = properties.get("type")
+        type = properties.get("type")
         required = name in required_properties
 
         out += _print_wrapped(name, "-", mode="both")
@@ -204,8 +201,11 @@ def format_param(self, name, properties, required_properties=(), show_hidden=Fal
         if description:
             out += _print_wrapped(description + "\n", mode="none", indent=4)
 
-        if typ:
-            out += _print_wrapped(f"Type: {typ}", mode="none", indent=4)
+        if type:
+            out += _print_wrapped(f"Type: {type}", mode="none", indent=4)
+
+        if required:
+            out += _print_wrapped("Required", mode="none", indent=4)
 
         out += _print_wrapped("\n", mode="end")
         out += f"# {name} = {json.dumps(default)}\n"
diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index b6b3190776..9b990088ab 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -22,3 +22,11 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py}]
+indent_style = unset
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 2f83a0962c..4c9fd69fcc 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -31,7 +31,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
index 9a0bf4afbc..25726aa1c9 100644
--- a/nf_core/pipeline-template/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |
diff --git a/nf_core/pipeline-template/.github/workflows/branch.yml b/nf_core/pipeline-template/.github/workflows/branch.yml
index 8edfa540c9..057016e4be 100644
--- a/nf_core/pipeline-template/.github/workflows/branch.yml
+++ b/nf_core/pipeline-template/.github/workflows/branch.yml
@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@v2
         with:
           message: |
             ## This PR is against the `master` branch :x:
diff --git a/nf_core/pipeline-template/.github/workflows/clean-up.yml b/nf_core/pipeline-template/.github/workflows/clean-up.yml
index 427aad5087..8feb3fb017 100644
--- a/nf_core/pipeline-template/.github/workflows/clean-up.yml
+++ b/nf_core/pipeline-template/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v7
+      - uses: actions/stale@v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index 31e8cd2b36..d9986bd30f 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -24,32 +24,25 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: "pip"
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      - name: Run pre-commit
+        run: pre-commit run --all-files || echo "status=fail" >> $GITHUB_ENV
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        if: env.status == 'fail'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix linting with pre-commit"
           git push {%- endraw %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 94aa5278be..a267f1ec14 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -11,61 +11,22 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          python-version: 3.11
+          cache: "pip"
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
@@ -76,7 +37,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -99,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: linting-logs
           path: |
diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml
index 09f8c423e5..e5528b29cf 100644
--- a/nf_core/pipeline-template/.github/workflows/linting_comment.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/nf_core/pipeline-template/.github/workflows/release-announcements.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
index ad497db4e1..1dd48b123f 100644
--- a/nf_core/pipeline-template/.github/workflows/release-announcements.yml
+++ b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -56,7 +56,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@v0.0.2
+      - uses: zentered/bluesky-post-action@v0.1.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
index acf7269536..363d5b1d42 100644
--- a/nf_core/pipeline-template/.gitpod.yml
+++ b/nf_core/pipeline-template/.gitpod.yml
@@ -7,6 +7,7 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
+
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index 0c31cdb99f..984321ff26 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/nf_core/pipeline-template/.pre-commit-config.yaml
@@ -1,5 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
diff --git a/nf_core/pipeline-template/pyproject.toml b/nf_core/pipeline-template/pyproject.toml
index 0d62beb6f9..984c091091 100644
--- a/nf_core/pipeline-template/pyproject.toml
+++ b/nf_core/pipeline-template/pyproject.toml
@@ -1,10 +1,13 @@
-# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Ruff.
 # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.black]
+[tool.ruff]
 line-length = 120
-target_version = ["py37", "py38", "py39", "py310"]
+target-version = "py38"
+select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+cache-dir = "~/.cache/ruff"
 
-[tool.isort]
-profile = "black"
-known_first_party = ["nf_core"]
-multi_line_output = 3
+[tool.ruff.isort]
+known-first-party = ["nf_core"]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
diff --git a/nf_core/refgenie.py b/nf_core/refgenie.py
index 6f09b75532..de9201bcd6 100644
--- a/nf_core/refgenie.py
+++ b/nf_core/refgenie.py
@@ -2,7 +2,6 @@
 Update a nextflow.config file with refgenie genomes
 """
 
-import json
 import logging
 import os
 import re
@@ -86,7 +85,7 @@ 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..b0c5dc04b6 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}")
@@ -317,7 +316,7 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
                     param
                 ] = f"String should not be set to `{config_default}`"
         if schema_param["type"] == "boolean":
-            if not str(config_default) in ["false", "true"]:
+            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}`"
@@ -757,9 +756,7 @@ def prompt_remove_schema_notfound_config(self, p_key):
             if self.no_prompts or self.schema_from_scratch:
                 return True
             if Confirm.ask(
-                ":question: Unrecognised [bold]'params.{}'[/] found in the schema but not in the pipeline config! [yellow]Remove it?".format(
-                    p_key
-                )
+                f":question: Unrecognised [bold]'params.{p_key}'[/] found in the schema but not in the pipeline config! [yellow]Remove it?"
             ):
                 return True
         return False
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index ffba41f9da..3a87190422 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
@@ -16,7 +15,7 @@
 
 import nf_core.modules.modules_utils
 import nf_core.utils
-from nf_core.components.lint import ComponentLint, LintException, LintResult
+from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult
 from nf_core.lint_utils import console
 
 log = logging.getLogger(__name__)
@@ -114,11 +113,11 @@ def lint(
         # Only lint the given module
         if subworkflow:
             if all_subworkflows:
-                raise LintException("You cannot specify a tool and request all tools to be linted.")
+                raise LintExceptionError("You cannot specify a tool and request all tools to be linted.")
             local_subworkflows = []
             remote_subworkflows = [s for s in self.all_remote_components if s.component_name == subworkflow]
             if len(remote_subworkflows) == 0:
-                raise LintException(f"Could not find the specified subworkflow: '{subworkflow}'")
+                raise LintExceptionError(f"Could not find the specified subworkflow: '{subworkflow}'")
         else:
             local_subworkflows = self.all_local_components
             remote_subworkflows = self.all_remote_components
diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
index c7ce77490d..f59e1e4279 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:
@@ -45,30 +45,30 @@ def main_nf(_, subworkflow):
     subworkflow_lines = []
     workflow_lines = []
     main_lines = []
-    for l in lines:
-        if re.search(r"^\s*workflow\s*\w*\s*{", l) and state == "subworkflow":
+    for line in lines:
+        if re.search(r"^\s*workflow\s*\w*\s*{", line) and state == "subworkflow":
             state = "workflow"
-        if re.search(r"take\s*:", l) and state in ["workflow"]:
+        if re.search(r"take\s*:", line) and state in ["workflow"]:
             state = "take"
             continue
-        if re.search(r"main\s*:", l) and state in ["take", "workflow"]:
+        if re.search(r"main\s*:", line) and state in ["take", "workflow"]:
             state = "main"
             continue
-        if re.search(r"emit\s*:", l) and state in ["take", "main", "workflow"]:
+        if re.search(r"emit\s*:", line) and state in ["take", "main", "workflow"]:
             state = "emit"
             continue
 
         # Perform state-specific linting checks
-        if state == "subworkflow" and not _is_empty(l):
-            subworkflow_lines.append(l)
-        if state == "workflow" and not _is_empty(l):
-            workflow_lines.append(l)
-        if state == "take" and not _is_empty(l):
-            inputs.extend(_parse_input(subworkflow, l))
-        if state == "emit" and not _is_empty(l):
-            outputs.extend(_parse_output(subworkflow, l))
-        if state == "main" and not _is_empty(l):
-            main_lines.append(l)
+        if state == "subworkflow" and not _is_empty(line):
+            subworkflow_lines.append(line)
+        if state == "workflow" and not _is_empty(line):
+            workflow_lines.append(line)
+        if state == "take" and not _is_empty(line):
+            inputs.extend(_parse_input(subworkflow, line))
+        if state == "emit" and not _is_empty(line):
+            outputs.extend(_parse_output(subworkflow, line))
+        if state == "main" and not _is_empty(line):
+            main_lines.append(line)
 
     # Check that we have required sections
     if not len(outputs):
@@ -177,9 +177,9 @@ def check_subworkflow_section(self, lines):
     )
 
     includes = []
-    for l in lines:
-        if l.strip().startswith("include"):
-            component_name = l.split("{")[1].split("}")[0].strip()
+    for line in lines:
+        if line.strip().startswith("include"):
+            component_name = line.split("{")[1].split("}")[0].strip()
             if " as " in component_name:
                 component_name = component_name.split(" as ")[1].strip()
             includes.append(component_name)
diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py
index 4944b26188..24e75eddbf 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))
@@ -118,7 +116,7 @@ def meta_yml(subworkflow_lint_object, subworkflow):
             subworkflow.failed.append(
                 (
                     "meta_modules_deprecated",
-                    f"Deprecated section 'modules' found in `meta.yml`, use 'components' instead",
+                    "Deprecated section 'modules' found in `meta.yml`, use 'components' instead",
                     subworkflow.meta_yml,
                 )
             )
@@ -126,7 +124,7 @@ def meta_yml(subworkflow_lint_object, subworkflow):
             subworkflow.passed.append(
                 (
                     "meta_modules_deprecated",
-                    f"Deprecated section 'modules' not found in `meta.yml`",
+                    "Deprecated section 'modules' not found in `meta.yml`",
                     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..995baeacd2 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -23,13 +23,13 @@
 log = logging.getLogger(__name__)
 
 
-class SyncException(Exception):
+class SyncExceptionError(Exception):
     """Exception raised when there was an error with TEMPLATE branch synchronisation"""
 
     pass
 
 
-class PullRequestException(Exception):
+class PullRequestExceptionError(Exception):
     """Exception raised when there was an error creating a Pull-Request on GitHub.com"""
 
     pass
@@ -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)
@@ -138,20 +138,20 @@ def sync(self):
             try:
                 # Check that we have an API auth token
                 if os.environ.get("GITHUB_AUTH_TOKEN", "") == "":
-                    raise PullRequestException("GITHUB_AUTH_TOKEN not set!")
+                    raise PullRequestExceptionError("GITHUB_AUTH_TOKEN not set!")
 
                 # Check that we know the github username and repo name
                 if self.gh_username is None and self.gh_repo is None:
-                    raise PullRequestException("Could not find GitHub username and repo name")
+                    raise PullRequestExceptionError("Could not find GitHub username and repo name")
 
                 self.push_template_branch()
                 self.create_merge_base_branch()
                 self.push_merge_branch()
                 self.make_pull_request()
                 self.close_open_template_merge_prs()
-            except PullRequestException as e:
+            except PullRequestExceptionError as e:
                 self.reset_target_dir()
-                raise PullRequestException(e)
+                raise PullRequestExceptionError(e)
 
         self.reset_target_dir()
 
@@ -170,7 +170,7 @@ def inspect_sync_dir(self):
         try:
             self.repo = git.Repo(self.pipeline_dir)
         except InvalidGitRepositoryError:
-            raise SyncException(f"'{self.pipeline_dir}' does not appear to be a git repository")
+            raise SyncExceptionError(f"'{self.pipeline_dir}' does not appear to be a git repository")
 
         # get current branch so we can switch back later
         self.original_branch = self.repo.active_branch.name
@@ -178,7 +178,7 @@ def inspect_sync_dir(self):
 
         # Check to see if there are uncommitted changes on current branch
         if self.repo.is_dirty(untracked_files=True):
-            raise SyncException(
+            raise SyncExceptionError(
                 "Uncommitted changes found in pipeline directory!\nPlease commit these before running nf-core sync"
             )
 
@@ -192,7 +192,7 @@ def get_wf_config(self):
                 log.info(f"Checking out workflow branch '{self.from_branch}'")
                 self.repo.git.checkout(self.from_branch)
         except GitCommandError:
-            raise SyncException(f"Branch `{self.from_branch}` not found!")
+            raise SyncExceptionError(f"Branch `{self.from_branch}` not found!")
 
         # If not specified, get the name of the active branch
         if not self.from_branch:
@@ -208,7 +208,7 @@ def get_wf_config(self):
         # Check that we have the required variables
         for rvar in self.required_config_vars:
             if rvar not in self.wf_config:
-                raise SyncException(f"Workflow config variable `{rvar}` not found!")
+                raise SyncExceptionError(f"Workflow config variable `{rvar}` not found!")
 
     def checkout_template_branch(self):
         """
@@ -223,7 +223,7 @@ def checkout_template_branch(self):
             try:
                 self.repo.git.checkout("TEMPLATE")
             except GitCommandError:
-                raise SyncException("Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'")
+                raise SyncExceptionError("Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'")
 
     def delete_template_branch_files(self):
         """
@@ -242,7 +242,7 @@ def delete_template_branch_files(self):
                 elif os.path.isdir(file_path):
                     shutil.rmtree(file_path)
             except Exception as e:
-                raise SyncException(e)
+                raise SyncExceptionError(e)
 
     def make_template_pipeline(self):
         """
@@ -272,7 +272,7 @@ 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 SyncException(f"Failed to rebuild pipeline from template with error:\n{err}")
+            raise SyncExceptionError(f"Failed to rebuild pipeline from template with error:\n{err}")
 
     def commit_template_changes(self):
         """If we have any changes with the new template files, make a git commit"""
@@ -287,7 +287,7 @@ def commit_template_changes(self):
             self.made_changes = True
             log.info("Committed changes to 'TEMPLATE' branch")
         except Exception as e:
-            raise SyncException(f"Could not commit changes to TEMPLATE:\n{e}")
+            raise SyncExceptionError(f"Could not commit changes to TEMPLATE:\n{e}")
         return True
 
     def push_template_branch(self):
@@ -299,7 +299,7 @@ def push_template_branch(self):
         try:
             self.repo.git.push()
         except GitCommandError as e:
-            raise PullRequestException(f"Could not push TEMPLATE branch:\n  {e}")
+            raise PullRequestExceptionError(f"Could not push TEMPLATE branch:\n  {e}")
 
     def create_merge_base_branch(self):
         """Create a new branch from the updated TEMPLATE branch
@@ -326,7 +326,7 @@ def create_merge_base_branch(self):
         try:
             self.repo.create_head(self.merge_branch)
         except GitCommandError as e:
-            raise SyncException(f"Could not create new branch '{self.merge_branch}'\n{e}")
+            raise SyncExceptionError(f"Could not create new branch '{self.merge_branch}'\n{e}")
 
     def push_merge_branch(self):
         """Push the newly created merge branch to the remote repository"""
@@ -335,7 +335,7 @@ def push_merge_branch(self):
             origin = self.repo.remote()
             origin.push(self.merge_branch)
         except GitCommandError as e:
-            raise PullRequestException(f"Could not push branch '{self.merge_branch}':\n  {e}")
+            raise PullRequestExceptionError(f"Could not push branch '{self.merge_branch}':\n  {e}")
 
     def make_pull_request(self):
         """Create a pull request to a base branch (default: dev),
@@ -374,7 +374,7 @@ def make_pull_request(self):
                 )
             except Exception as e:
                 stderr.print_exception()
-                raise PullRequestException(f"Something went badly wrong - {e}")
+                raise PullRequestExceptionError(f"Something went badly wrong - {e}")
             else:
                 self.gh_pr_returned_data = r.json()
                 self.pr_url = self.gh_pr_returned_data["html_url"]
@@ -395,7 +395,7 @@ def close_open_template_merge_prs(self):
         try:
             list_prs_json = json.loads(list_prs_request.content)
             list_prs_pp = json.dumps(list_prs_json, indent=4)
-        except:
+        except Exception:
             list_prs_json = list_prs_request.content
             list_prs_pp = list_prs_request.content
 
@@ -438,7 +438,7 @@ def close_open_pr(self, pr):
         try:
             pr_request_json = json.loads(pr_request.content)
             pr_request_pp = json.dumps(pr_request_json, indent=4)
-        except:
+        except Exception:
             pr_request_json = pr_request.content
             pr_request_pp = pr_request.content
 
@@ -462,4 +462,4 @@ def reset_target_dir(self):
         try:
             self.repo.git.checkout(self.original_branch)
         except GitCommandError as e:
-            raise SyncException(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}")
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index a2107f633c..ac0f467e66 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -6,7 +6,6 @@
 from typing import Dict
 
 import git
-import rich.progress
 from git.exc import GitCommandError
 
 from nf_core.utils import load_tools_config
@@ -117,8 +116,6 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
 
         self.remote_url = remote_url
 
-        self.fullname = nf_core.modules.modules_utils.repo_full_name_from_remote(self.remote_url)
-
         self.setup_local_repo(remote_url, branch, hide_progress)
 
         config_fn, repo_config = load_tools_config(self.local_repo_dir)
diff --git a/nf_core/utils.py b/nf_core/utils.py
index bcc8faa3fd..10b21018d2 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -139,7 +139,7 @@ def __init__(self, wf_path):
         try:
             repo = git.Repo(self.wf_path)
             self.git_sha = repo.head.object.hexsha
-        except:
+        except Exception:
             log.debug(f"Could not find git hash for pipeline: {self.wf_path}")
 
         # Overwrite if we have the last commit from the PR - otherwise we get a merge commit hash
@@ -181,14 +181,14 @@ def _load_pipeline_config(self):
 
         self.pipeline_prefix, self.pipeline_name = self.nf_config.get("manifest.name", "").strip("'").split("/")
 
-        nextflowVersionMatch = re.search(r"[0-9\.]+(-edge)?", self.nf_config.get("manifest.nextflowVersion", ""))
-        if nextflowVersionMatch:
-            self.minNextflowVersion = nextflowVersionMatch.group(0)
+        nextflow_version_match = re.search(r"[0-9\.]+(-edge)?", self.nf_config.get("manifest.nextflowVersion", ""))
+        if nextflow_version_match:
+            self.minNextflowVersion = nextflow_version_match.group(0)
 
     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:
@@ -274,8 +274,8 @@ def fetch_wf_config(wf_path, cache_config=True):
     result = run_cmd("nextflow", f"config -flat {wf_path}")
     if result is not None:
         nfconfig_raw, _ = result
-        for l in nfconfig_raw.splitlines():
-            ul = l.decode("utf-8")
+        for line in nfconfig_raw.splitlines():
+            ul = line.decode("utf-8")
             try:
                 k, v = ul.split(" = ", 1)
                 config[k] = v.strip("'\"")
@@ -286,9 +286,9 @@ 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:
-            for l in fh:
-                match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=", l)
+        with open(main_nf) as fh:
+            for line in fh:
+                match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=", line)
                 if match:
                     config[match.group(1)] = "null"
     except FileNotFoundError as e:
@@ -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:
@@ -433,7 +433,7 @@ def poll_nfcore_web_api(api_url, post_data=None):
                 return web_response
 
 
-class GitHub_API_Session(requests_cache.CachedSession):
+class GitHubAPISession(requests_cache.CachedSession):
     """
     Class to provide a single session for interacting with the GitHub API for a run.
     Inherits the requests_cache.CachedSession and adds additional functionality,
@@ -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"]
@@ -590,7 +590,7 @@ def request_retry(self, url, post_data=None):
 
 
 # Single session object to use for entire codebase. Not sure if there's a better way to do this?
-gh_api = GitHub_API_Session()
+gh_api = GitHubAPISession()
 
 
 def anaconda_package(dep, dep_channels=None):
@@ -666,18 +666,18 @@ def parse_anaconda_licence(anaconda_response, version=None):
 
     # Clean up / standardise licence names
     clean_licences = []
-    for l in licences:
-        l = re.sub(r"GNU General Public License v\d \(([^\)]+)\)", r"\1", l)
-        l = re.sub(r"GNU GENERAL PUBLIC LICENSE", "GPL", l, flags=re.IGNORECASE)
-        l = l.replace("GPL-", "GPLv")
-        l = re.sub(r"GPL\s*([\d\.]+)", r"GPL v\1", l)  # Add v prefix to GPL version if none found
-        l = re.sub(r"GPL\s*v(\d).0", r"GPL v\1", l)  # Remove superflous .0 from GPL version
-        l = re.sub(r"GPL \(([^\)]+)\)", r"GPL \1", l)
-        l = re.sub(r"GPL\s*v", "GPL v", l)  # Normalise whitespace to one space between GPL and v
-        l = re.sub(r"\s*(>=?)\s*(\d)", r" \1\2", l)  # Normalise whitespace around >= GPL versions
-        l = l.replace("Clause", "clause")  # BSD capitilisation
-        l = re.sub(r"-only$", "", l)  # Remove superflous GPL "only" version suffixes
-        clean_licences.append(l)
+    for license in licences:
+        license = re.sub(r"GNU General Public License v\d \(([^\)]+)\)", r"\1", license)
+        license = re.sub(r"GNU GENERAL PUBLIC LICENSE", "GPL", license, flags=re.IGNORECASE)
+        license = license.replace("GPL-", "GPLv")
+        license = re.sub(r"GPL\s*([\d\.]+)", r"GPL v\1", license)  # Add v prefix to GPL version if none found
+        license = re.sub(r"GPL\s*v(\d).0", r"GPL v\1", license)  # Remove superflous .0 from GPL version
+        license = re.sub(r"GPL \(([^\)]+)\)", r"GPL \1", license)
+        license = re.sub(r"GPL\s*v", "GPL v", license)  # Normalise whitespace to one space between GPL and v
+        license = re.sub(r"\s*(>=?)\s*(\d)", r" \1\2", license)  # Normalise whitespace around >= GPL versions
+        license = license.replace("Clause", "clause")  # BSD capitilisation
+        license = re.sub(r"-only$", "", license)  # Remove superflous GPL "only" version suffixes
+        clean_licences.append(license)
     return clean_licences
 
 
@@ -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/pyproject.toml b/pyproject.toml
index 2380073107..d75ae89df6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,10 +5,6 @@ requires = [
     "wheel"
 ]
 
-[tool.black]
-line-length = 120
-target_version = ["py37", "py38", "py39", "py310"]
-
 [tool.pytest.ini_options]
 markers = [
     "datafiles: load datafiles"
@@ -16,7 +12,18 @@ markers = [
 testpaths = ["tests"]
 norecursedirs = [ ".*", "build", "dist", "*.egg", "data", "__pycache__", ".github", "nf_core", "docs"]
 
-[tool.isort]
-profile = "black"
-known_first_party = ["nf_core"]
-multi_line_output = 3
+[tool.ruff]
+line-length = 120
+target-version = "py38"
+select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+cache-dir = "~/.cache/ruff"
+
+[tool.ruff.isort]
+known-first-party = ["nf_core"]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+
+[tool.ruff.lint.pep8-naming]
+extend-ignore-names = ["mocked_*", "*allOf", "*URI*"]
+
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 13dba6f30d..6d890f0e1f 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,5 +1,3 @@
-black
-isort
 myst_parser
 pytest-cov
 pytest-datafiles
@@ -8,8 +6,8 @@ Sphinx
 sphinx-rtd-theme
 mypy
 types-PyYAML
-pyupgrade
 types-requests
 types-jsonschema
 types-Markdown
 types-setuptools
+ruff
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..ce8c6dbe11 100644
--- a/tests/modules/bump_versions.py
+++ b/tests/modules/bump_versions.py
@@ -2,17 +2,16 @@
 import re
 
 import pytest
-import yaml
 
 import nf_core.modules
-from nf_core.modules.modules_utils import ModuleException
+from nf_core.modules.modules_utils import ModuleExceptionError
 
 
 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:
@@ -32,7 +31,7 @@ def test_modules_bump_versions_all_modules(self):
 def test_modules_bump_versions_fail(self):
     """Fail updating a module with wrong name"""
     version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
-    with pytest.raises(ModuleException) as excinfo:
+    with pytest.raises(ModuleExceptionError) as excinfo:
         version_bumper.bump_versions(module="no/module")
     assert "Could not find the specified module:" in str(excinfo.value)
 
@@ -41,7 +40,7 @@ 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..460a1439cb 100644
--- a/tests/modules/create.py
+++ b/tests/modules/create.py
@@ -1,4 +1,3 @@
-import filecmp
 import os
 import shutil
 from pathlib import Path
@@ -87,9 +86,9 @@ 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 +96,9 @@ 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..002b889671 100644
--- a/tests/subworkflows/create.py
+++ b/tests/subworkflows/create.py
@@ -1,4 +1,3 @@
-import filecmp
 import os
 import shutil
 from pathlib import Path
@@ -53,9 +52,9 @@ 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 +64,9 @@ 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..b53fef7f0e 100644
--- a/tests/subworkflows/lint.py
+++ b/tests/subworkflows/lint.py
@@ -1,4 +1,3 @@
-import os
 from pathlib import Path
 
 import pytest
@@ -87,9 +86,7 @@ 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/remove.py b/tests/subworkflows/remove.py
index 53a948778b..dec67875bd 100644
--- a/tests/subworkflows/remove.py
+++ b/tests/subworkflows/remove.py
@@ -1,7 +1,5 @@
 from pathlib import Path
 
-from rich.console import Console
-
 from nf_core.modules.modules_json import ModulesJson
 
 
@@ -18,7 +16,7 @@ def test_subworkflows_remove_subworkflow(self):
     bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
     bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
     samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-    mod_json_obj = ModulesJson(self.pipeline_dir)
+    ModulesJson(self.pipeline_dir)
     mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
     assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
     mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 698086e186..32a69ba180 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -8,7 +8,6 @@
 import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
-from nf_core.modules.remove import ModuleRemove
 from nf_core.modules.update import ModuleUpdate
 from nf_core.subworkflows.update import SubworkflowUpdate
 
@@ -73,7 +72,7 @@ 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_download.py b/tests/test_download.py
index 7c9532e977..7f34f7fbc6 100644
--- a/tests/test_download.py
+++ b/tests/test_download.py
@@ -1,7 +1,6 @@
 """Tests for the download subcommand of nf-core tools
 """
 
-import hashlib
 import os
 import re
 import shutil
@@ -16,9 +15,9 @@
 import nf_core.utils
 from nf_core.download import ContainerError, DownloadWorkflow, WorkflowRepo
 from nf_core.synced_repo import SyncedRepo
-from nf_core.utils import NFCORE_CACHE_DIR, NFCORE_DIR, run_cmd
+from nf_core.utils import run_cmd
 
-from .utils import with_temporary_file, with_temporary_folder
+from .utils import with_temporary_folder
 
 
 class DownloadTest(unittest.TestCase):
@@ -160,8 +159,8 @@ def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_co
         if result is not None:
             nfconfig_raw, _ = result
             config = {}
-            for l in nfconfig_raw.splitlines():
-                ul = l.decode("utf-8")
+            for line in nfconfig_raw.splitlines():
+                ul = line.decode("utf-8")
                 try:
                     k, v = ul.split(" = ", 1)
                     config[k] = v.strip("'\"")
@@ -259,7 +258,7 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
         )
 
         # Pull again, but now the image already exists
-        with pytest.raises(ContainerError.ImageExists):
+        with pytest.raises(ContainerError.ImageExistsError):
             download_obj.singularity_pull_image(
                 "hello-world", f"{tmp_dir}/hello-world.sif", None, "docker.io", mock_rich_progress
             )
@@ -269,8 +268,8 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
             "docker.io/bschiffthaler/sed", f"{tmp_dir}/sed.sif", None, "docker.io", mock_rich_progress
         )
 
-        # try to pull from non-existing registry (Name change hello-world_new.sif is needed, otherwise ImageExists is raised before attempting to pull.)
-        with pytest.raises(ContainerError.RegistryNotFound):
+        # try to pull from non-existing registry (Name change hello-world_new.sif is needed, otherwise ImageExistsError is raised before attempting to pull.)
+        with pytest.raises(ContainerError.RegistryNotFoundError):
             download_obj.singularity_pull_image(
                 "hello-world",
                 f"{tmp_dir}/hello-world_new.sif",
@@ -280,23 +279,23 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
             )
 
         # test Image not found for several registries
-        with pytest.raises(ContainerError.ImageNotFound):
+        with pytest.raises(ContainerError.ImageNotFoundError):
             download_obj.singularity_pull_image(
                 "a-container", f"{tmp_dir}/acontainer.sif", None, "quay.io", mock_rich_progress
             )
 
-        with pytest.raises(ContainerError.ImageNotFound):
+        with pytest.raises(ContainerError.ImageNotFoundError):
             download_obj.singularity_pull_image(
                 "a-container", f"{tmp_dir}/acontainer.sif", None, "docker.io", mock_rich_progress
             )
 
-        with pytest.raises(ContainerError.ImageNotFound):
+        with pytest.raises(ContainerError.ImageNotFoundError):
             download_obj.singularity_pull_image(
                 "a-container", f"{tmp_dir}/acontainer.sif", None, "ghcr.io", mock_rich_progress
             )
 
         # test Image not found for absolute URI.
-        with pytest.raises(ContainerError.ImageNotFound):
+        with pytest.raises(ContainerError.ImageNotFoundError):
             download_obj.singularity_pull_image(
                 "docker.io/bschiffthaler/nothingtopullhere",
                 f"{tmp_dir}/nothingtopullhere.sif",
@@ -306,7 +305,7 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
             )
 
         # Traffic from Github Actions to GitHub's Container Registry is unlimited, so no harm should be done here.
-        with pytest.raises(ContainerError.InvalidTag):
+        with pytest.raises(ContainerError.InvalidTagError):
             download_obj.singularity_pull_image(
                 "ewels/multiqc:go-rewrite",
                 f"{tmp_dir}/umi-transfer.sif",
@@ -343,9 +342,8 @@ def test_get_singularity_images(self, tmp_path, mock_fetch_wf_config):
             container_library=("mirage-the-imaginative-registry.io", "quay.io", "ghcr.io", "docker.io"),
         )
         mock_fetch_wf_config.return_value = {
-            "process.mapping.container": "helloworld",
-            "process.mapping.container": "helloworld",
-            "process.mapping.container": "helloooooooworld",
+            "process.helloworld.container": "helloworld",
+            "process.hellooworld.container": "helloooooooworld",
             "process.mapping.container": "ewels/multiqc:gorewrite",
         }
         download_obj.find_container_images("workflow")
diff --git a/tests/test_launch.py b/tests/test_launch.py
index 03c6a8b692..dc8d6b147c 100644
--- a/tests/test_launch.py
+++ b/tests/test_launch.py
@@ -86,7 +86,7 @@ def test_get_pipeline_defaults(self):
         self.launcher.get_pipeline_schema()
         self.launcher.set_schema_inputs()
         assert len(self.launcher.schema_obj.input_params) > 0
-        assert self.launcher.schema_obj.input_params["validate_params"] == True
+        assert self.launcher.schema_obj.input_params["validate_params"] is True
 
     @with_temporary_file
     def test_get_pipeline_defaults_input_params(self, tmp_file):
@@ -119,12 +119,12 @@ def test_ob_to_questionary_string(self):
     @mock.patch("questionary.unsafe_prompt", side_effect=[{"use_web_gui": "Web based"}])
     def test_prompt_web_gui_true(self, mock_prompt):
         """Check the prompt to launch the web schema or use the cli"""
-        assert self.launcher.prompt_web_gui() == True
+        assert self.launcher.prompt_web_gui() is True
 
     @mock.patch("questionary.unsafe_prompt", side_effect=[{"use_web_gui": "Command line"}])
     def test_prompt_web_gui_false(self, mock_prompt):
         """Check the prompt to launch the web schema or use the cli"""
-        assert self.launcher.prompt_web_gui() == False
+        assert self.launcher.prompt_web_gui() is False
 
     @mock.patch("nf_core.utils.poll_nfcore_web_api", side_effect=[{}])
     def test_launch_web_gui_missing_keys(self, mock_poll_nfcore_web_api):
@@ -144,7 +144,7 @@ def test_launch_web_gui(self, mock_poll_nfcore_web_api, mock_webbrowser, mock_wa
         """Check the code that opens the web browser"""
         self.launcher.get_pipeline_schema()
         self.launcher.merge_nxf_flag_schema()
-        assert self.launcher.launch_web_gui() == None
+        assert self.launcher.launch_web_gui() is None
 
     @mock.patch("nf_core.utils.poll_nfcore_web_api", side_effect=[{"status": "error", "message": "foo"}])
     def test_get_web_launch_response_error(self, mock_poll_nfcore_web_api):
@@ -163,7 +163,7 @@ def test_get_web_launch_response_unexpected(self, mock_poll_nfcore_web_api):
     @mock.patch("nf_core.utils.poll_nfcore_web_api", side_effect=[{"status": "waiting_for_user"}])
     def test_get_web_launch_response_waiting(self, mock_poll_nfcore_web_api):
         """Test polling the website for a launch response - status waiting_for_user"""
-        assert self.launcher.get_web_launch_response() == False
+        assert self.launcher.get_web_launch_response() is False
 
     @mock.patch("nf_core.utils.poll_nfcore_web_api", side_effect=[{"status": "launch_params_complete"}])
     def test_get_web_launch_response_missing_keys(self, mock_poll_nfcore_web_api):
@@ -191,7 +191,7 @@ def test_get_web_launch_response_missing_keys(self, mock_poll_nfcore_web_api):
     def test_get_web_launch_response_valid(self, mock_poll_nfcore_web_api, mock_sanitise):
         """Test polling the website for a launch response - complete, valid response"""
         self.launcher.get_pipeline_schema()
-        assert self.launcher.get_web_launch_response() == True
+        assert self.launcher.get_web_launch_response() is True
 
     def test_sanitise_web_response(self):
         """Check that we can properly sanitise results from the web"""
@@ -201,7 +201,7 @@ def test_sanitise_web_response(self):
         self.launcher.schema_obj.input_params["max_cpus"] = "12"
         self.launcher.sanitise_web_response()
         assert "-name" not in self.launcher.nxf_flags
-        assert self.launcher.schema_obj.input_params["igenomes_ignore"] == True
+        assert self.launcher.schema_obj.input_params["igenomes_ignore"] is True
         assert self.launcher.schema_obj.input_params["max_cpus"] == 12
 
     def test_ob_to_questionary_bool(self):
@@ -216,12 +216,12 @@ def test_ob_to_questionary_bool(self):
         assert result["message"] == ""
         assert result["choices"] == ["True", "False"]
         assert result["default"] == "True"
-        assert result["filter"]("True") == True
-        assert result["filter"]("true") == True
-        assert result["filter"](True) == True
-        assert result["filter"]("False") == False
-        assert result["filter"]("false") == False
-        assert result["filter"](False) == False
+        assert result["filter"]("True") is True
+        assert result["filter"]("true") is True
+        assert result["filter"](True) is True
+        assert result["filter"]("False") is False
+        assert result["filter"]("false") is False
+        assert result["filter"](False) is False
 
     def test_ob_to_questionary_number(self):
         """Check converting a python dict to a pyenquirer format - with enum"""
@@ -234,7 +234,7 @@ def test_ob_to_questionary_number(self):
         assert result["validate"]("") is True
         assert result["validate"]("123.56.78") == "Must be a number"
         assert result["validate"]("123.56sdkfjb") == "Must be a number"
-        assert result["filter"]("123.456") == float(123.456)
+        assert result["filter"]("123.456") == 123.456
         assert result["filter"]("") == ""
 
     def test_ob_to_questionary_integer(self):
@@ -248,7 +248,7 @@ def test_ob_to_questionary_integer(self):
         assert result["validate"]("") is True
         assert result["validate"]("123.45") == "Must be an integer"
         assert result["validate"]("123.56sdkfjb") == "Must be an integer"
-        assert result["filter"]("123") == int(123)
+        assert result["filter"]("123") == 123
         assert result["filter"]("") == ""
 
     def test_ob_to_questionary_range(self):
@@ -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..32913bda0d 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -56,9 +56,9 @@ def test_run_linting_function(self):
 
         We don't really check any of this code as it's just a series of function calls
         and we're testing each of those individually. This is mostly to check for syntax errors."""
-        lint_obj = nf_core.lint.run_linting(self.test_pipeline_dir, False)
+        nf_core.lint.run_linting(self.test_pipeline_dir, False)
 
-    def test_init_PipelineLint(self):
+    def test_init_pipeline_lint(self):
         """Simply create a PipelineLint object.
 
         This checks that all of the lint test imports are working properly,
@@ -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..13c82f5188 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
@@ -68,7 +68,7 @@ def test_build_template_file_exists(self, caplog):
 
         # Creates a new empty file
         outfile = Path(self.tmp_dir) / "params-file.yml"
-        with open(outfile, "w") as fp:
+        with open(outfile, "w"):
             pass
 
         res = self.params_template_builder.write_params_file(outfile)
diff --git a/tests/test_refgenie.py b/tests/test_refgenie.py
index 73fbcb863f..5440c1c477 100644
--- a/tests/test_refgenie.py
+++ b/tests/test_refgenie.py
@@ -7,8 +7,6 @@
 import tempfile
 import unittest
 
-import yaml
-
 
 class TestRefgenie(unittest.TestCase):
     """Class for refgenie tests"""
@@ -26,7 +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:
+        except Exception:
             self.NXF_HOME_ORIGINAL = None
         os.environ["NXF_HOME"] = self.NXF_HOME
 
diff --git a/tests/test_schema.py b/tests/test_schema.py
index 105cd9473e..89fcc98b66 100644
--- a/tests/test_schema.py
+++ b/tests/test_schema.py
@@ -305,7 +305,7 @@ def test_build_schema(self):
         Build a new schema param from a pipeline
         Run code to ensure it doesn't crash. Individual functions tested separately.
         """
-        param = self.schema_obj.build_schema(self.template_dir, True, False, None)
+        self.schema_obj.build_schema(self.template_dir, True, False, None)
 
     @with_temporary_folder
     def test_build_schema_from_scratch(self, tmp_dir):
@@ -319,7 +319,7 @@ def test_build_schema_from_scratch(self, tmp_dir):
         shutil.copytree(self.template_dir, test_pipeline_dir)
         os.remove(os.path.join(test_pipeline_dir, "nextflow_schema.json"))
 
-        param = self.schema_obj.build_schema(test_pipeline_dir, True, False, None)
+        self.schema_obj.build_schema(test_pipeline_dir, True, False, None)
 
     @mock.patch("requests.post")
     def test_launch_web_builder_timeout(self, mock_post):
diff --git a/tests/test_sync.py b/tests/test_sync.py
index 597e4375d3..51a27653ab 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -44,7 +44,7 @@ def tearDown(self):
     def test_inspect_sync_dir_notgit(self, tmp_dir):
         """Try syncing an empty directory"""
         psync = nf_core.sync.PipelineSync(tmp_dir)
-        with pytest.raises(nf_core.sync.SyncException) as exc_info:
+        with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info:
             psync.inspect_sync_dir()
         assert "does not appear to be a git repository" in exc_info.value.args[0]
 
@@ -56,7 +56,7 @@ def test_inspect_sync_dir_dirty(self):
         # Try to sync, check we halt with the right error
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         try:
-            with pytest.raises(nf_core.sync.SyncException) as exc_info:
+            with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info:
                 psync.inspect_sync_dir()
             assert exc_info.value.args[0].startswith("Uncommitted changes found in pipeline directory!")
         finally:
@@ -66,7 +66,7 @@ def test_get_wf_config_no_branch(self):
         """Try getting a workflow config when the branch doesn't exist"""
         # Try to sync, check we halt with the right error
         psync = nf_core.sync.PipelineSync(self.pipeline_dir, from_branch="foo")
-        with pytest.raises(nf_core.sync.SyncException) as exc_info:
+        with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info:
             psync.inspect_sync_dir()
             psync.get_wf_config()
         assert exc_info.value.args[0] == "Branch `foo` not found!"
@@ -76,7 +76,7 @@ def test_get_wf_config_missing_required_config(self):
         # Try to sync, check we halt with the right error
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.required_config_vars = ["fakethisdoesnotexist"]
-        with pytest.raises(nf_core.sync.SyncException) as exc_info:
+        with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info:
             psync.inspect_sync_dir()
             psync.get_wf_config()
         # Check that we did actually get some config back
@@ -99,7 +99,7 @@ def test_checkout_template_branch_no_template(self):
 
         psync.repo.delete_head("TEMPLATE")
 
-        with pytest.raises(nf_core.sync.SyncException) as exc_info:
+        with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info:
             psync.checkout_template_branch()
         assert exc_info.value.args[0] == "Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'"
 
@@ -165,7 +165,7 @@ def test_push_template_branch_error(self):
         test_fn.touch()
         psync.commit_template_changes()
         # Try to push changes
-        with pytest.raises(nf_core.sync.PullRequestException) as exc_info:
+        with pytest.raises(nf_core.sync.PullRequestExceptionError) as exc_info:
             psync.push_template_branch()
         assert exc_info.value.args[0].startswith("Could not push TEMPLATE branch")
 
@@ -220,7 +220,7 @@ def test_push_merge_branch_without_create_branch(self):
         psync.get_wf_config()
         psync.repo.create_remote("origin", self.remote_path)
 
-        with pytest.raises(nf_core.sync.PullRequestException) as exc_info:
+        with pytest.raises(nf_core.sync.PullRequestExceptionError) as exc_info:
             psync.push_merge_branch()
         assert exc_info.value.args[0].startswith(f"Could not push branch '{psync.merge_branch}'")
 
@@ -329,7 +329,7 @@ def test_make_pull_request_bad_response(self, mock_post, mock_get):
         psync.gh_username = "bad_url"
         psync.gh_repo = "bad_url/response"
         os.environ["GITHUB_AUTH_TOKEN"] = "test"
-        with pytest.raises(nf_core.sync.PullRequestException) as exc_info:
+        with pytest.raises(nf_core.sync.PullRequestExceptionError) as exc_info:
             psync.make_pull_request()
         assert exc_info.value.args[0].startswith(
             "Something went badly wrong - GitHub API PR failed - got return code 404"
@@ -420,6 +420,6 @@ def test_reset_target_dir_fake_branch(self):
 
         psync.original_branch = "fake_branch"
 
-        with pytest.raises(nf_core.sync.SyncException) as exc_info:
+        with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info:
             psync.reset_target_dir()
         assert exc_info.value.args[0].startswith("Could not reset to original branch `fake_branch`")
diff --git a/tests/test_test_utils.py b/tests/test_test_utils.py
index 154a31fca6..c7088b9282 100644
--- a/tests/test_test_utils.py
+++ b/tests/test_test_utils.py
@@ -1,8 +1,5 @@
-import tempfile
 from pathlib import Path
 
-import pytest
-
 from .utils import with_temporary_file, with_temporary_folder
 
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 90d1886dbd..3079d75808 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -134,7 +134,7 @@ def test_request_cant_create_cache(self, mock_mkd, mock_exists):
 
     def test_pip_package_pass(self):
         result = nf_core.utils.pip_package("multiqc=1.10")
-        assert type(result) == dict
+        assert isinstance(result, dict)
 
     @mock.patch("requests.get")
     def test_pip_package_timeout(self, mock_get):
diff --git a/tests/utils.py b/tests/utils.py
index 198ac3d583..89c1328818 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -5,9 +5,7 @@
 import functools
 import os
 import tempfile
-from contextlib import contextmanager
-from pathlib import Path
-from typing import Any, Callable, Generator, Tuple
+from typing import Any, Callable, Tuple
 
 import responses
 
@@ -27,7 +25,7 @@
 GITLAB_BRANCH_ORG_PATH_BRANCH = "org-path"
 GITLAB_BRANCH_TEST_OLD_SHA = "e772abc22c1ff26afdf377845c323172fb3c19ca"
 GITLAB_BRANCH_TEST_NEW_SHA = "7d73e21f30041297ea44367f2b4fd4e045c0b991"
-GITLAB_NFTEST_BRANCH = "nf-test-tests"
+GITLAB_NFTEST_BRANCH = "nf-test-tests-self-hosted-runners"
 
 
 def with_temporary_folder(func: Callable[..., Any]) -> Callable[..., Any]: