diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
index 51bf2ae5f7..1741b934f2 100644
--- a/.github/actions/create-lint-wf/action.yml
+++ b/.github/actions/create-lint-wf/action.yml
@@ -17,7 +17,7 @@ runs:
 
     # Set up Nextflow
     - name: Install Nextflow
-      uses: nf-core/setup-nextflow@v1
+      uses: nf-core/setup-nextflow@v2
       with:
         version: ${{ matrix.NXF_VER }}
 
diff --git a/.github/workflows/changelog.py b/.github/workflows/changelog.py
index 4835b0d0f0..471665e4b1 100644
--- a/.github/workflows/changelog.py
+++ b/.github/workflows/changelog.py
@@ -79,7 +79,7 @@ def _determine_change_type(pr_title) -> tuple[str, str]:
 section, section_header = _determine_change_type(pr_title)
 
 # Remove section indicator from the PR title.
-pr_title = re.sub(rf"{section}[:\s]*", "", pr_title, flags=re.IGNORECASE)
+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}))"
@@ -91,7 +91,6 @@ def _determine_change_type(pr_title) -> tuple[str, str]:
 new_lines = [
     f"- {pr_title} {pr_link}\n",
 ]
-
 print(f"Adding new lines into section '{section}':\n" + "".join(new_lines))
 
 # Finally, updating the changelog.
@@ -144,10 +143,11 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
 
         # 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)):
+        if not (m := re.match(r".*(v\d+\.\d+.\d*(dev)?).*", line)):
             print(f"Cannot parse version from line {line.strip()}.", file=sys.stderr)
             sys.exit(1)
         version = m.group(1)
+        print(f"Found version: {version}")
 
         if not inside_version_dev:
             if not version.endswith("dev"):
@@ -209,6 +209,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
             # If the line already contains a link to the PR, don't add it again.
             line = _skip_existing_entry_for_this_pr(line, same_section=True)
             section_lines.append(line)
+
     else:
         updated_lines.append(line)
 
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index e69229c051..7a72e18d22 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -7,6 +7,9 @@ on:
       - "docs/**"
       - "CHANGELOG.md"
   pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
   release:
     types: [published]
   workflow_dispatch:
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 188cccfd75..0d65c40b07 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -6,6 +6,9 @@ on:
     paths:
       - nf_core/pipeline-template/**
   pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
   release:
     types: [published]
   workflow_dispatch:
@@ -72,7 +75,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: latest-everything
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index cd36d4e62d..9800ac1910 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -7,6 +7,9 @@ on:
       - "docs/**"
       - "CHANGELOG.md"
   pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
   release:
     types: [published]
   workflow_dispatch:
@@ -59,7 +62,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.NXF_VER }}
 
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index eec676a746..2aed1752ff 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -12,7 +12,9 @@ on:
     paths-ignore:
       - "docs/**"
       - "CHANGELOG.md"
+      # ignore github workflows except for the current one
       - ".github/**"
+      - "!.github/workflows/pytest.yml"
   release:
     types: [published]
   workflow_dispatch:
@@ -119,32 +121,10 @@ jobs:
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-
-      - 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@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-nftest-${{ env.date }}
+        uses: nf-core/setup-nextflow@v2
 
       - name: Install nf-test
-        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/
+        uses: nf-core/setup-nf-test@v1
 
       - name: move coveragerc file up
         run: |
@@ -197,7 +177,7 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@87c55149d96e628cc2ef7e6fc2aab372015aec85 # v4
+        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*
diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
index 8748f3d7b3..13fd71a883 100644
--- a/.github/workflows/rich-codex.yml
+++ b/.github/workflows/rich-codex.yml
@@ -15,22 +15,10 @@ jobs:
           cache-dependency-path: setup.py
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-nftest-${{ env.date }}
+        uses: nf-core/setup-nextflow@v2
 
       - 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/
+        uses: nf-core/setup-nf-test@v1
 
       - name: Install nf-core/tools
         run: pip install git+https://github.com/nf-core/tools.git@dev
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index c998552ddd..19e895f452 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -67,7 +67,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-everything"
 
diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml
index f357bed03b..0fa3adaf20 100644
--- a/.github/workflows/update_components_template.yml
+++ b/.github/workflows/update_components_template.yml
@@ -23,11 +23,11 @@ jobs:
 
       - name: Update modules
         run: nf-core modules update --all
-        working-directory: nf-core/pipeline-template
+        working-directory: nf_core/pipeline-template
 
       - name: Update subworkflows
         run: nf-core subworkflows update --all
-        working-directory: nf-core/pipeline-template
+        working-directory: nf_core/pipeline-template
 
       # Commit the changes
       - name: Commit changes
diff --git a/.gitpod.yml b/.gitpod.yml
index 445cb35706..b2fbb73133 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -1,4 +1,4 @@
-image: nfcore/gitpod:latest
+image: nfcore/gitpod:dev
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 03fbb7bedf..d0d5381b9f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.2
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -9,6 +9,8 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
@@ -17,7 +19,7 @@ repos:
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.8.0"
+    rev: "v1.9.0"
     hooks:
       - id: mypy
         additional_dependencies:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e3189edaa..6bb9843197 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,34 @@
 # nf-core/tools: Changelog
 
+## v2.13.2dev
+
+### Template
+
+- Remove fasta default from nextflow.config ([#2828](https://github.com/nf-core/tools/pull/2828))
+- Update templates to use nf-core/setup-nextflow v2
+- Link to troubleshooting docs when pipeline fails ([#2845](https://github.com/nf-core/tools/pull/2845))
+- Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))
+
+### Linting
+
+- Only match assignments of params in `main.nf` and not references like `params.aligner == <something>` ([#2833](https://github.com/nf-core/tools/pull/2833))
+
+### Components
+
+### General
+
+- Update CI to use nf-core/setup-nextflow v2
+- Changelog bot: handle also patch version before dev suffix ([#2820](https://github.com/nf-core/tools/pull/2820))
+- Fix path in component update script ([#2823](https://github.com/nf-core/tools/pull/2823))
+- Update prettier to 3.2.5 ([#2830](https://github.com/nf-core/tools/pull/2830))
+- Update GitHub Actions ([#2827](https://github.com/nf-core/tools/pull/2827))
+- Switch to setup-nf-test ([#2834](https://github.com/nf-core/tools/pull/2834))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.2 ([#2836](https://github.com/nf-core/tools/pull/2836))
+- Add tests for assignment and referencing of params in main.nf ([#2841](https://github.com/nf-core/tools/pull/2841))
+- Optimize layers in dockerfile ([#2842](https://github.com/nf-core/tools/pull/2842))
+- Update gitpod/workspace-base Docker digest to 1e133e5 ([#2843](https://github.com/nf-core/tools/pull/2843))
+- Update python:3.11-slim Docker digest to a2eb07f ([#2847](https://github.com/nf-core/tools/pull/2847))
+
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 
 ### Template
diff --git a/Dockerfile b/Dockerfile
index 62431be140..60768499a1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.11-slim@sha256:ce81dc539f0aedc9114cae640f8352fad83d37461c24a3615b01f081d0c0583a
+FROM python:3.11-slim@sha256:a2eb07f336e4f194358382611b4fea136c632b40baa6314cb27a366deeaf0144
 LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for the nfcore tools"
 
diff --git a/docs/api/requirements.txt b/docs/api/requirements.txt
index fc5184b95f..abffe30740 100644
--- a/docs/api/requirements.txt
+++ b/docs/api/requirements.txt
@@ -1,4 +1,5 @@
 Sphinx>=3.3.1
 sphinxcontrib-napoleon
+sphinx-markdown-builder
 sphinx_rtd_theme>=0.5.0
 myst-parser
diff --git a/nf_core/__init__.py b/nf_core/__init__.py
index d96be73f3d..2d4fe45a0a 100644
--- a/nf_core/__init__.py
+++ b/nf_core/__init__.py
@@ -1,4 +1,4 @@
-""" Main nf_core module file.
+"""Main nf_core module file.
 
 Shouldn't do much, as everything is under subcommands.
 """
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 7d2d083fa9..d6f6077be9 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
-""" nf-core: Helper tools for use with nf-core Nextflow pipelines. """
+"""nf-core: Helper tools for use with nf-core Nextflow pipelines."""
+
 import logging
 import os
 import sys
diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index f1a9e7c401..9b81f54f06 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -2,7 +2,6 @@
 The ComponentsTest class handles the generation and testing of nf-test snapshots.
 """
 
-
 import logging
 import os
 import re
@@ -91,9 +90,9 @@ def run(self) -> None:
         """Run build steps"""
         self.check_inputs()
         os.environ["NFT_DIFF"] = "pdiff"  # set nf-test differ to pdiff to get a better diff output
-        os.environ[
-            "NFT_DIFF_ARGS"
-        ] = "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        os.environ["NFT_DIFF_ARGS"] = (
+            "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        )
         with nf_core.utils.set_wd(Path(self.dir)):
             self.check_snapshot_stability()
         if len(self.errors) > 0:
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index c4b477a0ab..d2169e3a72 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -2,7 +2,6 @@
 The ComponentCreate class handles generating of module and subworkflow templates
 """
 
-
 import glob
 import json
 import logging
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index 3c2fb9dde3..c99934bca3 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -3,7 +3,6 @@
 in nf-core pipelines
 """
 
-
 import logging
 import operator
 import os
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 2f73afe9d3..d9731ba7c9 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -1,6 +1,7 @@
 """
 The NFCoreComponent class holds information and utility functions for a single module or subworkflow
 """
+
 import logging
 import re
 from pathlib import Path
diff --git a/nf_core/create.py b/nf_core/create.py
index c094d33a22..b420b1c86d 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -1,6 +1,7 @@
 """Creates a nf-core pipeline matching the current
 organization's specification based on a template.
 """
+
 import configparser
 import logging
 import os
diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index f04c7dcd04..3136d02e97 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -1,14 +1,14 @@
 # Test build locally before making a PR
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
-FROM gitpod/workspace-base@sha256:c15ee2f4de8902421ccbfbd77329a9e8e4abf18477e1b5ae8a1a572790254647
+FROM gitpod/workspace-base@sha256:1e133e5691add6c19443672594b9f3d7d9c3372ead4c86a4490c2701dbfa32e3
 
 USER root
 
 # Install util tools.
 # software-properties-common is needed to add ppa support for Apptainer installation
 RUN apt-get update --quiet && \
-    apt-get install --quiet --yes \
+    apt-get install --quiet --yes --no-install-recommends \
     apt-transport-https \
     apt-utils \
     sudo \
@@ -18,18 +18,17 @@ RUN apt-get update --quiet && \
     curl \
     tree \
     graphviz \
-    software-properties-common
-
-# Install Apptainer (Singularity)
-RUN add-apt-repository -y ppa:apptainer/ppa && \
+    software-properties-common && \
+    add-apt-repository -y ppa:apptainer/ppa && \
     apt-get update --quiet && \
-    apt install -y apptainer
-
-# Install Conda
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    apt-get install --quiet --yes apptainer && \
+    wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
     bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
-    rm Miniconda3-latest-Linux-x86_64.sh
+    rm Miniconda3-latest-Linux-x86_64.sh && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
+# Set PATH for Conda
 ENV PATH="/opt/conda/bin:$PATH"
 
 # Add the nf-core source files to the image
@@ -47,23 +46,20 @@ 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 \
     prettier \
     pre-commit \
     ruff \
+    mypy \
     openjdk \
     pytest-workflow && \
     conda clean --all --force-pkgs-dirs --yes
 
-# Update Nextflow
-RUN nextflow self-update
-
-# Install nf-core
-RUN python -m pip install . --no-cache-dir
+# Update Nextflow and Install nf-core
+RUN nextflow self-update && \
+    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"
+ENV NFT_DIFF="pdiff"
+ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
diff --git a/nf_core/launch.py b/nf_core/launch.py
index 25bb4c150c..bc0cd58aec 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -1,5 +1,4 @@
-""" Launch a pipeline, interactively collecting params """
-
+"""Launch a pipeline, interactively collecting params"""
 
 import copy
 import json
diff --git a/nf_core/licences.py b/nf_core/licences.py
index a8a35334dd..be737280f8 100644
--- a/nf_core/licences.py
+++ b/nf_core/licences.py
@@ -1,6 +1,5 @@
 """Lists software licences for a given workflow."""
 
-
 import json
 import logging
 import os
diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
index d3e29d2363..47b7d78f5e 100644
--- a/nf_core/lint/nextflow_config.py
+++ b/nf_core/lint/nextflow_config.py
@@ -245,10 +245,9 @@ def nextflow_config(self):
                 raise AssertionError()
         except (AssertionError, IndexError):
             failed.append(
-                "Config variable ``manifest.homePage`` did not begin with https://github.com/nf-core/:\n    {}".format(
-                    manifest_homepage
-                )
+                f"Config variable ``manifest.homePage`` did not begin with https://github.com/nf-core/:\n    {manifest_homepage}"
             )
+
         else:
             passed.append("Config variable ``manifest.homePage`` began with https://github.com/nf-core/")
 
@@ -375,7 +374,6 @@ def nextflow_config(self):
     schema.load_schema()
     schema.get_schema_defaults()  # Get default values from schema
     schema.get_schema_types()  # Get types from schema
-    self.nf_config.keys()  # Params in nextflow.config
     for param_name in schema.schema_defaults.keys():
         param = "params." + param_name
         if param in ignore_defaults:
diff --git a/nf_core/list.py b/nf_core/list.py
index 67d1a76878..658f4dc6d2 100644
--- a/nf_core/list.py
+++ b/nf_core/list.py
@@ -1,6 +1,5 @@
 """Lists available nf-core pipelines and versions."""
 
-
 import json
 import logging
 import os
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index b9003be974..9b54174d5a 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -3,7 +3,6 @@
 or for a single module
 """
 
-
 import logging
 import os
 import re
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 866e6312aa..b2816dab6a 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -6,7 +6,6 @@
 nf-core modules lint
 """
 
-
 import logging
 import os
 
diff --git a/nf_core/modules/lint/module_changes.py b/nf_core/modules/lint/module_changes.py
index ee8cabebe1..eb76f4b88b 100644
--- a/nf_core/modules/lint/module_changes.py
+++ b/nf_core/modules/lint/module_changes.py
@@ -1,6 +1,7 @@
 """
 Check whether the content of a module has changed compared to the original repository
 """
+
 import shutil
 import tempfile
 from pathlib import Path
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 520f8cf0a2..b1a611d70a 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -1,6 +1,7 @@
 """
 Lint the tests of a module in nf-core/modules
 """
+
 import json
 import logging
 from pathlib import Path
diff --git a/nf_core/params_file.py b/nf_core/params_file.py
index 267fe7086a..78798b065e 100644
--- a/nf_core/params_file.py
+++ b/nf_core/params_file.py
@@ -1,5 +1,4 @@
-""" Create a YAML parameter file """
-
+"""Create a YAML parameter file"""
 
 import json
 import logging
diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
index d04335275a..ca0687733e 100644
--- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
+++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
@@ -20,7 +20,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
 - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
       {%- endif %}
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nf-test test tests/ --verbose --profile +docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 84c727f60d..3880b2c4dc 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}"
 
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index b53a427e06..44d06c0cd5 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,7 +30,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
@@ -68,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results{% endraw %}
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 59b85f95fc..612467ff6e 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -35,7 +35,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index af57081f60..4dc0f1dcd7 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/nf_core/pipeline-template/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 17e75f18a4..2f9b349916 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -18,7 +18,6 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-    fasta                      = null
     {%- endif -%}
 
     // MultiQC options
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 5bc51caab8..e02a113755 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -143,6 +143,10 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
     }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
 }
 
 /*
diff --git a/nf_core/schema.py b/nf_core/schema.py
index df04dc5a1e..373f8bbaa1 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -1,5 +1,4 @@
-""" Code to deal with pipeline JSON Schema """
-
+"""Code to deal with pipeline JSON Schema"""
 
 import copy
 import json
@@ -84,16 +83,13 @@ def load_lint_schema(self):
             self.get_schema_defaults()
             self.validate_default_params()
             if len(self.invalid_nextflow_config_default_parameters) > 0:
+                params = "\n --".join(
+                    [f"{param}: {msg}" for param, msg in self.invalid_nextflow_config_default_parameters.items()]
+                )
                 log.info(
-                    "[red][✗] Invalid default parameters found:\n  --{}\n\nNOTE: Use null in config for no default.".format(
-                        "\n  --".join(
-                            [
-                                f"{param}: {msg}"
-                                for param, msg in self.invalid_nextflow_config_default_parameters.items()
-                            ]
-                        )
-                    )
+                    f"[red][✗] Invalid default parameters found:\n {params} \n\nNOTE: Use null in config for no default."
                 )
+
             else:
                 log.info(f"[green][✓] Pipeline schema looks valid[/] [dim](found {num_params} params)")
         except json.decoder.JSONDecodeError as e:
@@ -282,9 +278,9 @@ def validate_default_params(self):
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(param, group_properties[param], self.pipeline_params[param])
                 else:
-                    self.invalid_nextflow_config_default_parameters[
-                        param
-                    ] = "Not in pipeline parameters. Check `nextflow.config`."
+                    self.invalid_nextflow_config_default_parameters[param] = (
+                        "Not in pipeline parameters. Check `nextflow.config`."
+                    )
 
         # Go over ungrouped params if any exist
         ungrouped_properties = self.schema.get("properties")
@@ -297,9 +293,9 @@ def validate_default_params(self):
                         param, ungrouped_properties[param], self.pipeline_params[param]
                     )
                 else:
-                    self.invalid_nextflow_config_default_parameters[
-                        param
-                    ] = "Not in pipeline parameters. Check `nextflow.config`."
+                    self.invalid_nextflow_config_default_parameters[param] = (
+                        "Not in pipeline parameters. Check `nextflow.config`."
+                    )
 
     def validate_config_default_parameter(self, param, schema_param, config_default):
         """
@@ -314,9 +310,9 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
         ):
             # Check that we are not deferring the execution of this parameter in the schema default with squiggly brakcets
             if schema_param["type"] != "string" or "{" not in schema_param["default"]:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Schema default (`{schema_param['default']}`) does not match the config default (`{config_default}`)"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Schema default (`{schema_param['default']}`) does not match the config default (`{config_default}`)"
+                )
                 return
 
         # if default is null, we're good
@@ -326,28 +322,28 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
         # Check variable types in nextflow.config
         if schema_param["type"] == "string":
             if str(config_default) in ["false", "true", "''"]:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"String should not be set to `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"String should not be set to `{config_default}`"
+                )
         if schema_param["type"] == "boolean":
             if str(config_default) not in ["false", "true"]:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Booleans should only be true or false, not `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Booleans should only be true or false, not `{config_default}`"
+                )
         if schema_param["type"] == "integer":
             try:
                 int(config_default)
             except ValueError:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Does not look like an integer: `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Does not look like an integer: `{config_default}`"
+                )
         if schema_param["type"] == "number":
             try:
                 float(config_default)
             except ValueError:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Does not look like a number (float): `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Does not look like a number (float): `{config_default}`"
+                )
 
     def validate_schema(self, schema=None):
         """
@@ -647,17 +643,13 @@ def build_schema(self, pipeline_dir, no_prompts, web_only, url):
                     # Extra help for people running offline
                     if "Could not connect" in e.args[0]:
                         log.info(
-                            "If you're working offline, now copy your schema ({}) and paste at https://nf-co.re/pipeline_schema_builder".format(
-                                self.schema_filename
-                            )
+                            f"If you're working offline, now copy your schema ({self.schema_filename}) and paste at https://nf-co.re/pipeline_schema_builder"
                         )
                         log.info("When you're finished, you can paste the edited schema back into the same file")
                     if self.web_schema_build_web_url:
                         log.info(
                             "To save your work, open {}\n"
-                            "Click the blue 'Finished' button, copy the schema and paste into this file: {}".format(
-                                self.web_schema_build_web_url, self.schema_filename
-                            )
+                            f"Click the blue 'Finished' button, copy the schema and paste into this file: { self.web_schema_build_web_url, self.schema_filename}"
                         )
                     return False
 
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index 3a87190422..96d2e0ab92 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -6,7 +6,6 @@
 nf-core subworkflows lint
 """
 
-
 import logging
 import os
 
diff --git a/nf_core/subworkflows/lint/subworkflow_changes.py b/nf_core/subworkflows/lint/subworkflow_changes.py
index b7fa13d931..a9c9616a21 100644
--- a/nf_core/subworkflows/lint/subworkflow_changes.py
+++ b/nf_core/subworkflows/lint/subworkflow_changes.py
@@ -1,6 +1,7 @@
 """
 Check whether the content of a subworkflow has changed compared to the original repository
 """
+
 from pathlib import Path
 
 import nf_core.modules.modules_repo
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index f7284320ea..796a56d018 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -1,6 +1,7 @@
 """
 Lint the tests of a subworkflow in nf-core/modules
 """
+
 import json
 import logging
 from pathlib import Path
diff --git a/nf_core/sync.py b/nf_core/sync.py
index 995baeacd2..93a79c3d50 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -1,5 +1,4 @@
-"""Synchronise a pipeline TEMPLATE branch with the template.
-"""
+"""Synchronise a pipeline TEMPLATE branch with the template."""
 
 import json
 import logging
diff --git a/nf_core/utils.py b/nf_core/utils.py
index e1778b55b3..9261388a39 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1,6 +1,7 @@
 """
 Common utility functions for the nf-core python package.
 """
+
 import concurrent.futures
 import datetime
 import errno
@@ -288,7 +289,7 @@ def fetch_wf_config(wf_path, cache_config=True):
         main_nf = os.path.join(wf_path, "main.nf")
         with open(main_nf) as fh:
             for line in fh:
-                match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=", line)
+                match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=(?!=)", line)
                 if match:
                     config[match.group(1)] = "null"
     except FileNotFoundError as e:
diff --git a/pytest.ini b/pytest.ini
index 652bdf8e53..cf37159478 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,6 +1,4 @@
 [pytest]
-filterwarnings =
-    ignore::pytest.PytestRemovedIn8Warning:_pytest.nodes:140
 testpaths =
     tests
 python_files = test_*.py
diff --git a/requirements.txt b/requirements.txt
index e4319d2352..6b5b3ab57d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,7 +9,7 @@ pillow
 pdiff
 pre-commit
 prompt_toolkit>=3.0.3
-pytest-workflow>=1.6.0
+pytest-workflow>=2.0.0
 pytest>=7.0.0
 pyyaml
 questionary>=1.8.0
diff --git a/setup.py b/setup.py
index c7f3fa41c6..fc7b69ac1e 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "2.13.1"
+version = "2.13.2dev"
 
 with open("README.md") as f:
     readme = f.read()
diff --git a/tests/components/generate_snapshot.py b/tests/components/generate_snapshot.py
index c5067d7210..50024a8ebb 100644
--- a/tests/components/generate_snapshot.py
+++ b/tests/components/generate_snapshot.py
@@ -1,4 +1,5 @@
 """Test generate a snapshot"""
+
 import json
 from pathlib import Path
 from unittest.mock import MagicMock
diff --git a/tests/components/snapshot_test.py b/tests/components/snapshot_test.py
index d774618476..b3fc259770 100644
--- a/tests/components/snapshot_test.py
+++ b/tests/components/snapshot_test.py
@@ -1,4 +1,5 @@
 """Test the 'modules test' or 'subworkflows test' command which runs nf-test test."""
+
 import shutil
 from pathlib import Path
 
diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py
index fa85568f14..06af8c4fb8 100644
--- a/tests/lint/nextflow_config.py
+++ b/tests/lint/nextflow_config.py
@@ -83,7 +83,6 @@ def test_default_values_fail(self):
     with open(nf_schema_file) as f:
         content = f.read()
         fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content)
-        print(fail_content)
     with open(nf_schema_file, "w") as f:
         f.write(fail_content)
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
@@ -100,6 +99,36 @@ def test_default_values_fail(self):
     )
 
 
+def test_catch_params_assignment_in_main_nf(self):
+    """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add parameter assignment in main.nf
+    main_nf_file = Path(new_pipeline) / "main.nf"
+    with open(main_nf_file, "a") as f:
+        f.write("params.max_time = 42")
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 1
+    assert (
+        result["failed"][0]
+        == "Config default value incorrect: `params.max_time` is set as `240.h` in `nextflow_schema.json` but is `null` in `nextflow.config`."
+    )
+
+
+def test_allow_params_reference_in_main_nf(self):
+    """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add parameter reference in main.nf
+    main_nf_file = Path(new_pipeline) / "main.nf"
+    with open(main_nf_file, "a") as f:
+        f.write("params.max_time == 42")
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+
+
 def test_default_values_ignored(self):
     """Test ignoring linting of default values."""
     new_pipeline = self._make_pipeline_copy()
diff --git a/tests/test_bump_version.py b/tests/test_bump_version.py
index 658a2339d4..c697d34287 100644
--- a/tests/test_bump_version.py
+++ b/tests/test_bump_version.py
@@ -1,5 +1,5 @@
-"""Some tests covering the bump_version code.
-"""
+"""Some tests covering the bump_version code."""
+
 import os
 
 import yaml
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 1261e3a9e9..d1dff0fe7b 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,4 +1,4 @@
-""" Tests covering the command-line code.
+"""Tests covering the command-line code.
 
 Most tests check the cli arguments are passed along and that some action is
 taken.
diff --git a/tests/test_components.py b/tests/test_components.py
index b7f67eb51d..eaf999c3c3 100644
--- a/tests/test_components.py
+++ b/tests/test_components.py
@@ -1,5 +1,4 @@
-""" Tests covering the modules commands
-"""
+"""Tests covering the modules commands"""
 
 import os
 import shutil
diff --git a/tests/test_create.py b/tests/test_create.py
index 1cc073cb54..e2672499cd 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -1,5 +1,5 @@
-"""Some tests covering the pipeline creation sub command.
-"""
+"""Some tests covering the pipeline creation sub command."""
+
 import os
 import unittest
 from pathlib import Path
diff --git a/tests/test_download.py b/tests/test_download.py
index d823040247..621379842b 100644
--- a/tests/test_download.py
+++ b/tests/test_download.py
@@ -1,5 +1,4 @@
-"""Tests for the download subcommand of nf-core tools
-"""
+"""Tests for the download subcommand of nf-core tools"""
 
 import os
 import re
diff --git a/tests/test_launch.py b/tests/test_launch.py
index dc8d6b147c..79dbe3fb97 100644
--- a/tests/test_launch.py
+++ b/tests/test_launch.py
@@ -1,5 +1,4 @@
-""" Tests covering the pipeline launch code.
-"""
+"""Tests covering the pipeline launch code."""
 
 import json
 import os
diff --git a/tests/test_licenses.py b/tests/test_licenses.py
index 4fb58a107c..8023c9e891 100644
--- a/tests/test_licenses.py
+++ b/tests/test_licenses.py
@@ -1,5 +1,4 @@
-"""Some tests covering the pipeline creation sub command.
-"""
+"""Some tests covering the pipeline creation sub command."""
 # import json
 # import os
 # import tempfile
diff --git a/tests/test_lint.py b/tests/test_lint.py
index 9839265892..d10cef37e4 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -1,5 +1,5 @@
-"""Some tests covering the linting code.
-"""
+"""Some tests covering the linting code."""
+
 import fnmatch
 import json
 import os
@@ -221,6 +221,8 @@ def test_sphinx_md_files(self):
         test_multiqc_incorrect_export_plots,
     )
     from .lint.nextflow_config import (  # type: ignore[misc]
+        test_allow_params_reference_in_main_nf,
+        test_catch_params_assignment_in_main_nf,
         test_default_values_fail,
         test_default_values_float,
         test_default_values_float_fail,
diff --git a/tests/test_list.py b/tests/test_list.py
index c1f51e03e0..c78276b41d 100644
--- a/tests/test_list.py
+++ b/tests/test_list.py
@@ -1,5 +1,4 @@
-""" Tests covering the workflow listing code.
-"""
+"""Tests covering the workflow listing code."""
 
 import json
 import os
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 539d3dcc57..944a09f670 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -1,5 +1,4 @@
-""" Tests covering the modules commands
-"""
+"""Tests covering the modules commands"""
 
 import os
 import shutil
diff --git a/tests/test_refgenie.py b/tests/test_refgenie.py
index 5440c1c477..23cc0dd14a 100644
--- a/tests/test_refgenie.py
+++ b/tests/test_refgenie.py
@@ -1,5 +1,4 @@
-""" Tests covering the refgenie integration code
-"""
+"""Tests covering the refgenie integration code"""
 
 import os
 import shlex
diff --git a/tests/test_schema.py b/tests/test_schema.py
index 89fcc98b66..29f4921985 100644
--- a/tests/test_schema.py
+++ b/tests/test_schema.py
@@ -1,5 +1,4 @@
-""" Tests covering the pipeline schema code.
-"""
+"""Tests covering the pipeline schema code."""
 
 import json
 import os
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index cd0bd21146..6163faa7a9 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -1,5 +1,4 @@
-""" Tests covering the subworkflows commands
-"""
+"""Tests covering the subworkflows commands"""
 
 import os
 import shutil
diff --git a/tests/test_sync.py b/tests/test_sync.py
index 51a27653ab..6f0e502e8b 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -1,5 +1,4 @@
-""" Tests covering the sync command
-"""
+"""Tests covering the sync command"""
 
 import json
 import os
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 4b5ab19fce..145060450f 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,5 +1,4 @@
-""" Tests covering for utility functions.
-"""
+"""Tests covering for utility functions."""
 
 import os
 import shutil