diff --git a/.editorconfig b/.editorconfig
index 72dda28..6d9b74c 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -31,3 +31,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 37f8c98..a27b873 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# nf-core/variantbenchmarking: Contributing Guidelines
+# `nf-core/variantbenchmarking`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving nf-core/variantbenchmarking.
@@ -55,9 +55,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Getting help
 
@@ -65,13 +65,13 @@ For further information/help, please consult the [nf-core/variantbenchmarking do
 
 ## Pipeline contribution conventions
 
-To make the nf-core/variantbenchmarking code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/variantbenchmarking` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
 Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 094f013..7bcf0bb 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -9,7 +9,6 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/variantbenchmarking pipeline documentation](https://nf-co.re/variantbenchmarking/usage)
-
   - type: textarea
     id: description
     attributes:
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 6289350..9b0eeaf 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,11 +1,12 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on PRs opened against the master branch.
+# This workflow is triggered on PRs opened against the main/master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   pull_request:
     branches:
+      - main
       - master
   workflow_dispatch:
   pull_request_review:
@@ -18,18 +19,30 @@ jobs:
     if: github.repository == 'nf-core/variantbenchmarking' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - uses: octokit/request-action@v2.x
+      - name: Get PR reviews
+        uses: octokit/request-action@v2.x
+        if: github.event_name != 'workflow_dispatch'
         id: check_approvals
+        continue-on-error: true
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
         if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 58404c3..9d2c4e6 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -1,15 +1,17 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/variantbenchmarking'
         run: |
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 161cf12..fe5cfe5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,8 +33,9 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-stable"
+          - "latest-everything"
         profile:
+          - "conda"
           - "docker"
           - "singularity"
         isMaster:
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 713dc3e..ab06316 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main/master branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,17 +17,34 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:
   NXF_ANSI_LOG: false
 
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    outputs:
+      REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+      REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+      REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
   download:
     runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -35,7 +52,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -50,12 +67,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
@@ -64,24 +75,27 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
-          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
@@ -89,30 +103,31 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.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() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Post-pipeline run container image count: $image_count"
-          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
         run: |
-          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
-            final_count=${{ env.IMAGE_COUNT_AFTER }}
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 4d278c6..56988a5 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index a502573..dbd52d5 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 42e519b..95b6b6a 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index c6ba35d..76a9e67 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
index d01fb43..537529b 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template_version_comment.yml
@@ -9,10 +9,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -24,20 +26,21 @@ jobs:
 
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated | grep nf-core
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
           message: |
-            ## :warning: Newer version of the nf-core template is available.
-
-            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            Please update your pipeline to the latest version.
-
-            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
           #
diff --git a/.gitpod.yml b/.gitpod.yml
index 4611863..83599f6 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -6,12 +6,5 @@ tasks:
       nextflow self-update
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
-    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    - 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
+  extensions:
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index 79752ea..c398cf4 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,17 +1,15 @@
-bump_version: null
 lint:
   actions_ci: false
-nf_core_version: 3.0.1
-org_path: null
+  files_unchanged:
+    - .gitignore
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
-  author: kuebra.narci@dkfz.de
+  author: kuebra.narci@dkfz-heidelberg.de
   description: "Benchmarking pipeline for germline and somatic variant callers "
   force: false
   is_nfcore: true
   name: variantbenchmarking
   org: nf-core
   outdir: .
-  skip_features: null
   version: 1.0dev
-update: null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9e9f0e1..1dec865 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/.prettierignore b/.prettierignore
index 437d763..edd29f0 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..a33b527
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/LICENSE b/LICENSE
index 0aefc2e..d9ef4e5 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) kuebra.narci@dkfz.de
+Copyright (c) The nf-core/variantbenchmarking team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index e68c04e..4f75533 100644
--- a/README.md
+++ b/README.md
@@ -104,6 +104,7 @@ The generation of comprehensive report that consolidates all benchmarking result
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
diff --git a/conf/base.config b/conf/base.config
index 135e755..f5c60d6 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -20,7 +20,7 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
+    // NOTE - Please try and reuse the labels below as much as possible.
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
diff --git a/docs/usage.md b/docs/usage.md
index 9c7e7d5..691a8b8 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -186,9 +186,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-:::warning
-Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-:::
+> [!WARNING]
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -219,23 +218,21 @@ nextflow pull nf-core/variantbenchmarking
 
 ### Reproducibility
 
-It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
 First, go to the [nf-core/variantbenchmarking releases page](https://github.com/nf-core/variantbenchmarking/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
-To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-:::tip
-If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-:::
+> [!TIP]
+> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
-:::note
-These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
-:::
+> [!NOTE]
+> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen)
 
 ### `-profile`
 
@@ -243,16 +240,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-:::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-:::
+> [!IMPORTANT]
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment.
 
 - `test`
   - A profile with a complete configuration for automated testing
@@ -312,13 +308,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 ### Resource requests
 
-Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
 ### Custom Containers
 
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
 
 To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
 
diff --git a/modules.json b/modules.json
index ac2a4b9..faee1cb 100644
--- a/modules.json
+++ b/modules.json
@@ -22,12 +22,7 @@
                     },
                     "bcftools/norm": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
-                    },
-                    "bcftools/query": {
-                        "branch": "master",
-                        "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
+                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
                     "bcftools/reheader": {
@@ -166,17 +161,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 6f5b867..a27122c 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.25.1
+  - bioconda::multiqc=1.27
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index cc0643e..58d9313 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 2fcbb5f..7b7c132 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:51:46.317523"
+        "timestamp": "2025-01-27T09:29:57.631982377"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:52:20.680978"
+        "timestamp": "2025-01-27T09:30:34.743726958"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:52:09.185842"
+        "timestamp": "2025-01-27T09:30:21.44383553"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 2badde6..200178a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -71,8 +71,7 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-
-    // Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
     config_profile_name        = null
     config_profile_description = null
 
@@ -185,6 +184,13 @@ profiles {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
+        process {
+            resourceLimits = [
+                memory: 8.GB,
+                cpus  : 4,
+                time  : 1.h
+            ]
+        }
     }
     test           { includeConfig 'conf/test.config'                }
     test_full      { includeConfig 'conf/test_full.config'           }
@@ -229,50 +235,61 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
 
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
 }
 report {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
 }
 trace {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
 }
 prov {
     enabled = true
     formats {
         bco {
-            file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json"
+            file = "${params.outdir}/pipeline_info/manifest_${params.trace_report_suffix}.bco.json"
         }
     }
 }
 
 manifest {
     name            = 'nf-core/variantbenchmarking'
-    author          = """kuebra.narci@dkfz.de"""
+    author          = """kuebra.narci@dkfz.de""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
+    contributors    = [
+        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
+        [
+            name: 'kuebra.narci@dkfz.de',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+    ]
     homePage        = 'https://github.com/nf-core/variantbenchmarking'
     description     = """Benchmarking pipeline for germline and somatic variant callers """
     mainScript      = 'main.nf'
+    defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
     version         = '1.0dev'
     doi             = ''
@@ -280,15 +297,16 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
     id 'nf-prov@1.2.2'   // Provenance reports for pipeline runs
 }
 
 validation {
     defaultIgnoreParams = ["genomes"]
+    monochromeLogs = params.monochrome_logs
     help {
         enabled = true
-        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        command = "nextflow run nf-core/variantbenchmarking -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
         beforeText = """
@@ -298,15 +316,15 @@ validation {
 \033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
 \033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                         \033[0;32m`._,._,\'\033[0m
-\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+\033[0;35m  nf-core/variantbenchmarking ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
-https://doi.org/10.1038/s41587-020-0439-x
+    https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-https://github.com/${manifest.name}/blob/master/CITATIONS.md
+    https://github.com/nf-core/variantbenchmarking/blob/master/CITATIONS.md
 """
     }
     summary {
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5dd3d26..28738e8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -376,6 +376,12 @@
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
+                },
+                "trace_report_suffix": {
+                    "type": "string",
+                    "fa_icon": "far calendar",
+                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
+                    "hidden": true
                 }
             }
         }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
new file mode 100644
index 0000000..4d6651d
--- /dev/null
+++ b/ro-crate-metadata.json
@@ -0,0 +1,295 @@
+{
+    "@context": [
+        "https://w3id.org/ro/crate/1.1/context",
+        {
+            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+            "TestService": "https://w3id.org/ro/terms/test#TestService",
+            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+            "definition": "https://w3id.org/ro/terms/test#definition",
+            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
+            "instance": "https://w3id.org/ro/terms/test#instance",
+            "resource": "https://w3id.org/ro/terms/test#resource",
+            "runsOn": "https://w3id.org/ro/terms/test#runsOn"
+        }
+    ],
+    "@graph": [
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2025-01-27T14:49:17+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-variantbenchmarking_logo_dark.png\">\n    <img alt=\"nf-core/variantbenchmarking\" src=\"docs/images/nf-core-variantbenchmarking_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/variantbenchmarking)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23variantbenchmarking-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantbenchmarking)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/variantbenchmarking** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/variantbenchmarking \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/variantbenchmarking/usage) and the [parameter documentation](https://nf-co.re/variantbenchmarking/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/variantbenchmarking/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/variantbenchmarking/output).\n\n## Credits\n\nnf-core/variantbenchmarking was originally written by kuebra.narci@dkfz.de.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#variantbenchmarking` channel](https://nfcore.slack.com/channels/variantbenchmarking) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/variantbenchmarking for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "hasPart": [
+                {
+                    "@id": "main.nf"
+                },
+                {
+                    "@id": "assets/"
+                },
+                {
+                    "@id": "conf/"
+                },
+                {
+                    "@id": "docs/"
+                },
+                {
+                    "@id": "docs/images/"
+                },
+                {
+                    "@id": "modules/"
+                },
+                {
+                    "@id": "modules/nf-core/"
+                },
+                {
+                    "@id": "workflows/"
+                },
+                {
+                    "@id": "subworkflows/"
+                },
+                {
+                    "@id": "nextflow.config"
+                },
+                {
+                    "@id": "README.md"
+                },
+                {
+                    "@id": "nextflow_schema.json"
+                },
+                {
+                    "@id": "CHANGELOG.md"
+                },
+                {
+                    "@id": "LICENSE"
+                },
+                {
+                    "@id": "CODE_OF_CONDUCT.md"
+                },
+                {
+                    "@id": "CITATIONS.md"
+                },
+                {
+                    "@id": "modules.json"
+                },
+                {
+                    "@id": "docs/usage.md"
+                },
+                {
+                    "@id": "docs/output.md"
+                },
+                {
+                    "@id": ".nf-core.yml"
+                },
+                {
+                    "@id": ".pre-commit-config.yaml"
+                },
+                {
+                    "@id": ".prettierignore"
+                }
+            ],
+            "isBasedOn": "https://github.com/nf-core/variantbenchmarking",
+            "license": "MIT",
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "mentions": [
+                {
+                    "@id": "#ae45bd39-5f9e-4b26-b5c0-9ca6bc1fa200"
+                }
+            ],
+            "name": "nf-core/variantbenchmarking"
+        },
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": [
+                {
+                    "@id": "https://w3id.org/ro/crate/1.1"
+                },
+                {
+                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+                }
+            ]
+        },
+        {
+            "@id": "main.nf",
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "dateCreated": "",
+            "dateModified": "2025-01-27T14:49:17Z",
+            "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
+            "keywords": ["nf-core", "nextflow", "benchmark", "draft", "structural-variants", "variant-calling"],
+            "license": ["MIT"],
+            "name": ["nf-core/variantbenchmarking"],
+            "programmingLanguage": {
+                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+            },
+            "sdPublisher": {
+                "@id": "https://nf-co.re/"
+            },
+            "url": ["https://github.com/nf-core/variantbenchmarking", "https://nf-co.re/variantbenchmarking/dev/"],
+            "version": ["1.0dev"]
+        },
+        {
+            "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
+            "@type": "ComputerLanguage",
+            "identifier": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "name": "Nextflow",
+            "url": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "version": "!>=24.04.2"
+        },
+        {
+            "@id": "#ae45bd39-5f9e-4b26-b5c0-9ca6bc1fa200",
+            "@type": "TestSuite",
+            "instance": [
+                {
+                    "@id": "#5b391f3e-435e-4c5f-8beb-cb6dc0854d4f"
+                }
+            ],
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "name": "Test suite for nf-core/variantbenchmarking"
+        },
+        {
+            "@id": "#5b391f3e-435e-4c5f-8beb-cb6dc0854d4f",
+            "@type": "TestInstance",
+            "name": "GitHub Actions workflow for testing nf-core/variantbenchmarking",
+            "resource": "repos/nf-core/variantbenchmarking/actions/workflows/ci.yml",
+            "runsOn": {
+                "@id": "https://w3id.org/ro/terms/test#GithubService"
+            },
+            "url": "https://api.github.com"
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#GithubService",
+            "@type": "TestService",
+            "name": "Github Actions",
+            "url": {
+                "@id": "https://github.com"
+            }
+        },
+        {
+            "@id": "assets/",
+            "@type": "Dataset",
+            "description": "Additional files"
+        },
+        {
+            "@id": "conf/",
+            "@type": "Dataset",
+            "description": "Configuration files"
+        },
+        {
+            "@id": "docs/",
+            "@type": "Dataset",
+            "description": "Markdown files for documenting the pipeline"
+        },
+        {
+            "@id": "docs/images/",
+            "@type": "Dataset",
+            "description": "Images for the documentation files"
+        },
+        {
+            "@id": "modules/",
+            "@type": "Dataset",
+            "description": "Modules used by the pipeline"
+        },
+        {
+            "@id": "modules/nf-core/",
+            "@type": "Dataset",
+            "description": "nf-core modules"
+        },
+        {
+            "@id": "workflows/",
+            "@type": "Dataset",
+            "description": "Main pipeline workflows to be executed in main.nf"
+        },
+        {
+            "@id": "subworkflows/",
+            "@type": "Dataset",
+            "description": "Smaller subworkflows"
+        },
+        {
+            "@id": "nextflow.config",
+            "@type": "File",
+            "description": "Main Nextflow configuration file"
+        },
+        {
+            "@id": "README.md",
+            "@type": "File",
+            "description": "Basic pipeline usage information"
+        },
+        {
+            "@id": "nextflow_schema.json",
+            "@type": "File",
+            "description": "JSON schema for pipeline parameter specification"
+        },
+        {
+            "@id": "CHANGELOG.md",
+            "@type": "File",
+            "description": "Information on changes made to the pipeline"
+        },
+        {
+            "@id": "LICENSE",
+            "@type": "File",
+            "description": "The license - should be MIT"
+        },
+        {
+            "@id": "CODE_OF_CONDUCT.md",
+            "@type": "File",
+            "description": "The nf-core code of conduct"
+        },
+        {
+            "@id": "CITATIONS.md",
+            "@type": "File",
+            "description": "Citations needed when using the pipeline"
+        },
+        {
+            "@id": "modules.json",
+            "@type": "File",
+            "description": "Version information for modules from nf-core/modules"
+        },
+        {
+            "@id": "docs/usage.md",
+            "@type": "File",
+            "description": "Usage documentation"
+        },
+        {
+            "@id": "docs/output.md",
+            "@type": "File",
+            "description": "Output documentation"
+        },
+        {
+            "@id": ".nf-core.yml",
+            "@type": "File",
+            "description": "nf-core configuration file, configuring template features and linting rules"
+        },
+        {
+            "@id": ".pre-commit-config.yaml",
+            "@type": "File",
+            "description": "Configuration file for pre-commit hooks"
+        },
+        {
+            "@id": ".prettierignore",
+            "@type": "File",
+            "description": "Ignore file for prettier"
+        },
+        {
+            "@id": "https://nf-co.re/",
+            "@type": "Organization",
+            "name": "nf-core",
+            "url": "https://nf-co.re/"
+        }
+    ]
+}
diff --git a/subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf b/subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf
index 4d516ea..fe60950 100644
--- a/subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf
@@ -47,7 +47,6 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -57,13 +56,13 @@ workflow PIPELINE_INITIALISATION {
         null
     )
 
-
     //
     // Check config provided to the pipeline
     //
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
+
     //
     // Custom validation for pipeline parameters
     //
@@ -94,7 +93,6 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
@@ -102,6 +100,7 @@ workflow PIPELINE_COMPLETION {
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    def multiqc_reports = multiqc_report.toList()
 
     //
     // Completion email and summary
@@ -115,7 +114,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                multiqc_report.toList()
+                multiqc_reports.getVal(),
             )
         }
 
@@ -197,7 +196,7 @@ def toolBibliographyText() {
 }
 
 def methodsDescriptionText(mqc_methods_yaml) {
-    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    // Convert  to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file
     def meta = [:]
     meta.workflow = workflow.toMap()
     meta["manifest_map"] = workflow.manifest.toMap()
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 2b0dc67..d6e593e 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
@@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -92,10 +92,12 @@ def checkCondaChannels() {
         channels = config.channels
     }
     catch (NullPointerException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
     catch (IOException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
@@ -106,17 +108,19 @@ def checkCondaChannels() {
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
-    def channel_priority_violation = false
-
-    required_channels_in_order.eachWithIndex { channel, index ->
-        if (index < required_channels_in_order.size() - 1) {
-            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
-        }
-    }
+    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn(
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  There is a problem with your Conda configuration!\n\n" + "  You will need to set-up the conda-forge and bioconda channels correctly.\n" + "  Please refer to https://bioconda.github.io/\n" + "  The observed channel order is \n" + "  ${channels}\n" + "  but the following channel order is required:\n" + "  ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        )
+        log.warn """\
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            There is a problem with your Conda configuration!
+            You will need to set-up the conda-forge and bioconda channels correctly.
+            Please refer to https://bioconda.github.io/
+            The observed channel order is
+            ${channels}
+            but the following channel order is required:
+            ${required_channels_in_order}
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        """.stripIndent(true)
     }
 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce..02dbf09 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index b78273c..bfd2587 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
@@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    def manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    manifest_doi.each { doi_ref ->
-        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
 //
 // Generate workflow version string
 //
@@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
@@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) {
     return colorcodes
 }
 
-//
-// Attach the multiqc report to email
-//
-def attachMultiqcReport(multiqc_report) {
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
-                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-                }
-                mqc_report = mqc_report[0]
-            }
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+            return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
         }
+    } else {
+        return null
     }
-    catch (Exception all) {
-        if (multiqc_report) {
-            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
-        }
-    }
-    return mqc_report
 }
 
 //
@@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = attachMultiqcReport(multiqc_report)
+    def mqc_report = getSingleReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // Render the sendmail template
-    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
     def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
@@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     if (email_address) {
         try {
             if (plaintext_email) {
-new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
             ['sendmail', '-t'].execute() << sendmail_html
             log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
         }
-        catch (Exception all) {
+        catch (Exception msg) {
+            log.debug(msg.toString())
+            log.debug("Trying with mail instead of sendmail")
             // Catch failures and try with plaintext
             def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 1dc317f..f117040 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -41,26 +41,14 @@ nextflow_function {
         }
     }
 
-    test("Test Function workflowCitation") {
-
-        function "workflowCitation"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function nfCoreLogo") {
+    test("Test Function without logColours") {
 
-        function "nfCoreLogo"
+        function "logColours"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = true
                 """
             }
         }
@@ -73,9 +61,8 @@ nextflow_function {
         }
     }
 
-    test("Test Function dashedLine") {
-
-        function "dashedLine"
+    test("Test Function with logColours") {
+        function "logColours"
 
         when {
             function {
@@ -93,14 +80,13 @@ nextflow_function {
         }
     }
 
-    test("Test Function without logColours") {
-
-        function "logColours"
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = true
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
                 """
             }
         }
@@ -108,18 +94,22 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") }
             )
         }
     }
 
-    test("Test Function with logColours") {
-        function "logColours"
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
                 """
             }
         }
@@ -127,7 +117,9 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
             )
         }
     }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 1037232..02c6701 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -17,26 +17,6 @@
         },
         "timestamp": "2024-02-28T12:02:59.729647"
     },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:10.562934"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:07.019761"
-    },
     "Test Function without logColours": {
         "content": [
             {
@@ -95,16 +75,6 @@
         },
         "timestamp": "2024-02-28T12:03:17.969323"
     },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:14.366181"
-    },
     "Test Function with logColours": {
         "content": [
             {
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 842dc43..8fb3016 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
@@ -94,7 +94,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap
index 41eb52f..4790f69 100644
--- a/tests/germline_small.nf.test.snap
+++ b/tests/germline_small.nf.test.snap
@@ -2,77 +2,10 @@
     "-stub": {
         "content": [
             62,
-            {
-                "BCFTOOLS_DEDUP": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_FILTER": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_MERGE": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_NORM": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_1": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_2": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_3": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_4": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "HAPPY_HAPPY": {
-                    "hap.py": "0.3.14"
-                },
-                "HAPPY_PREPY": {
-                    "pre.py": "0.3.14"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "REFORMAT_HEADER": {
-                    "tabix": 1.12
-                },
-                "RTGTOOLS_FORMAT": {
-                    "rtg-tools": "3.12.1"
-                },
-                "RTGTOOLS_VCFEVAL": {
-                    "rtg-tools": "3.12.1"
-                },
-                "VCF_TO_CSV": {
-                    "python": "3.12.4"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "references",
                 "references/rtgtools",
                 "references/rtgtools/genome.sdf",
@@ -244,82 +177,15 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-23T14:25:38.877918008"
+        "timestamp": "2025-01-29T12:14:19.21651889"
     },
     "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": {
         "content": [
             62,
-            {
-                "BCFTOOLS_DEDUP": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_FILTER": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_MERGE": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_NORM": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_1": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_2": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_3": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_4": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "HAPPY_HAPPY": {
-                    "hap.py": "0.3.14"
-                },
-                "HAPPY_PREPY": {
-                    "pre.py": "0.3.14"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "REFORMAT_HEADER": {
-                    "tabix": 1.12
-                },
-                "RTGTOOLS_FORMAT": {
-                    "rtg-tools": "3.12.1"
-                },
-                "RTGTOOLS_VCFEVAL": {
-                    "rtg-tools": "3.12.1"
-                },
-                "VCF_TO_CSV": {
-                    "python": "3.12.4"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "references",
                 "references/rtgtools",
                 "references/rtgtools/genome.sdf",
@@ -601,6 +467,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-23T14:23:40.862874525"
+        "timestamp": "2025-01-29T12:12:18.418200369"
     }
 }
\ No newline at end of file
diff --git a/tests/germline_sv.nf.test.snap b/tests/germline_sv.nf.test.snap
index c56fade..b854110 100644
--- a/tests/germline_sv.nf.test.snap
+++ b/tests/germline_sv.nf.test.snap
@@ -2,95 +2,10 @@
     "Params: --analysis 'germline' --variant_type 'structural' --method 'truvari,svbenchmark,wittyer'": {
         "content": [
             121,
-            {
-                "BCFTOOLS_DEDUP": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_FILTER": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_NORM": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_1": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_2": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_3": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_4": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "BCFTOOLS_VIEW_CONTIGS": {
-                    "bcftools": 1.2
-                },
-                "BGZIP_TABIX": {
-                    "tabix": 1.12
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "SURVIVOR_MERGE": {
-                    "survivor": "1.0.7"
-                },
-                "SURVIVOR_STATS": {
-                    "survivor": "1.0.7"
-                },
-                "SVANALYZER_SVBENCHMARK": {
-                    "svanalyzer": 0.36
-                },
-                "SVYNC": {
-                    "svync": "0.1.2"
-                },
-                "TABIX_BGZIP_QUERY": {
-                    "tabix": "1.19.1"
-                },
-                "TABIX_BGZIP_TRUTH": {
-                    "tabix": "1.19.1"
-                },
-                "TABIX_BGZIP_UNZIP": {
-                    "tabix": "1.19.1"
-                },
-                "TRUVARI_BENCH": {
-                    "truvari": "4.1.0)"
-                },
-                "VARIANT_EXTRACTOR": {
-                    "python": "3.12.4"
-                },
-                "VCF_TO_CSV": {
-                    "python": "3.12.4"
-                },
-                "WITTYER": {
-                    "wittyer": "0.5.2.0"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "structural",
                 "structural/HG002",
                 "structural/HG002/preprocess",
@@ -362,100 +277,15 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-23T14:44:34.135136556"
+        "timestamp": "2025-01-29T12:17:47.644313415"
     },
     "-stub": {
         "content": [
             121,
-            {
-                "BCFTOOLS_DEDUP": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_FILTER": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_NORM": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_1": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_2": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_3": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_4": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "BCFTOOLS_VIEW_CONTIGS": {
-                    "bcftools": 1.2
-                },
-                "BGZIP_TABIX": {
-                    "tabix": 1.12
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "SURVIVOR_MERGE": {
-                    "survivor": "1.0.7"
-                },
-                "SURVIVOR_STATS": {
-                    "survivor": "1.0.7"
-                },
-                "SVANALYZER_SVBENCHMARK": {
-                    "svanalyzer": 0.36
-                },
-                "SVYNC": {
-                    "svync": "0.1.2"
-                },
-                "TABIX_BGZIP_QUERY": {
-                    "tabix": "1.19.1"
-                },
-                "TABIX_BGZIP_TRUTH": {
-                    "tabix": "1.19.1"
-                },
-                "TABIX_BGZIP_UNZIP": {
-                    "tabix": "1.19.1"
-                },
-                "TRUVARI_BENCH": {
-                    "truvari": "4.1.0)"
-                },
-                "VARIANT_EXTRACTOR": {
-                    "python": "3.12.4"
-                },
-                "VCF_TO_CSV": {
-                    "python": "3.12.4"
-                },
-                "WITTYER": {
-                    "wittyer": "0.5.2.0"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "structural",
                 "structural/HG002",
                 "structural/HG002/preprocess",
@@ -666,6 +496,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-23T14:46:46.270536815"
+        "timestamp": "2025-01-29T12:20:02.006578062"
     }
 }
\ No newline at end of file
diff --git a/tests/liftover_test.nf.test.snap b/tests/liftover_test.nf.test.snap
index 7a2f9c5..ca7620b 100644
--- a/tests/liftover_test.nf.test.snap
+++ b/tests/liftover_test.nf.test.snap
@@ -2,71 +2,10 @@
     "Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover 'test'": {
         "content": [
             57,
-            {
-                "BCFTOOLS_REHEADER_1": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_2": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_3": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_4": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "BCFTOOLS_VIEW_CONTIGS": {
-                    "bcftools": 1.2
-                },
-                "BGZIP_TABIX": {
-                    "tabix": 1.12
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PICARD_CREATESEQUENCEDICTIONARY": {
-                    "picard": "3.2.0-1-g3948afb6b"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "SURVIVOR_MERGE": {
-                    "survivor": "1.0.7"
-                },
-                "SURVIVOR_STATS": {
-                    "survivor": "1.0.7"
-                },
-                "TABIX_BGZIP": {
-                    "tabix": "1.19.1"
-                },
-                "TABIX_BGZIP_UNZIP": {
-                    "tabix": "1.19.1"
-                },
-                "TRUVARI_BENCH": {
-                    "truvari": "4.1.0)"
-                },
-                "VCF_TO_CSV": {
-                    "python": "3.12.4"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "references",
                 "references/dictionary",
                 "references/dictionary/genome.dict",
@@ -220,6 +159,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-24T08:56:44.966454325"
+        "timestamp": "2025-01-29T12:23:50.918953841"
     }
 }
\ No newline at end of file
diff --git a/tests/liftover_truth.nf.test.snap b/tests/liftover_truth.nf.test.snap
index fce9df1..2e19c0f 100644
--- a/tests/liftover_truth.nf.test.snap
+++ b/tests/liftover_truth.nf.test.snap
@@ -2,80 +2,10 @@
     "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools' --liftover 'truth'": {
         "content": [
             68,
-            {
-                "BCFTOOLS_DEDUP": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_MERGE": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_NORM": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_1": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_2": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_3": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_4": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SPLIT_MULTI": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "BCFTOOLS_VIEW_CONTIGS": {
-                    "bcftools": 1.2
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "HAPPY_HAPPY": {
-                    "hap.py": "0.3.14"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "REFORMAT_HEADER": {
-                    "tabix": 1.12
-                },
-                "RTGTOOLS_FORMAT": {
-                    "rtg-tools": "3.12.1"
-                },
-                "RTGTOOLS_VCFEVAL": {
-                    "rtg-tools": "3.12.1"
-                },
-                "UCSC_LIFTOVER": {
-                    "ucsc": 377
-                },
-                "VCF_TO_CSV": {
-                    "python": "3.12.4"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "references",
                 "references/dictionary",
                 "references/dictionary/genome.dict",
@@ -363,6 +293,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-24T08:45:10.41490994"
+        "timestamp": "2025-01-29T12:28:06.56131727"
     }
 }
\ No newline at end of file
diff --git a/tests/somatic_indel.nf.test.snap b/tests/somatic_indel.nf.test.snap
index 2e11e13..408df18 100644
--- a/tests/somatic_indel.nf.test.snap
+++ b/tests/somatic_indel.nf.test.snap
@@ -2,44 +2,7 @@
     "Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy'": {
         "content": [
             21,
-            {
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "BCFTOOLS_VIEW_CONTIGS": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_VIEW_FILTERMISSING": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_VIEW_SUBSAMPLE": {
-                    "bcftools": 1.2
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "HAPPY_SOMPY": {
-                    "hap.py": "0.3.14"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "indel",
                 "indel/SEQC2",
@@ -169,7 +132,7 @@
                 "indel/test2/stats/bcftools",
                 "indel/test2/stats/bcftools/test2.strelka.bcftools_stats.txt",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml"
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml"
             ],
             [
                 "SEQC2.bcftools_stats.txt:md5,97beec3b6ce6471625018d91c75df08d",
@@ -181,6 +144,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-23T15:22:31.866027222"
+        "timestamp": "2025-01-29T12:30:05.839484004"
     }
 }
\ No newline at end of file
diff --git a/tests/somatic_snv.nf.test.snap b/tests/somatic_snv.nf.test.snap
index fafc685..1426953 100644
--- a/tests/somatic_snv.nf.test.snap
+++ b/tests/somatic_snv.nf.test.snap
@@ -2,47 +2,10 @@
     "-stub": {
         "content": [
             29,
-            {
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "BCFTOOLS_VIEW_CONTIGS": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_VIEW_FILTERMISSING": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_VIEW_SUBSAMPLE": {
-                    "bcftools": 1.2
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "HAPPY_SOMPY": {
-                    "hap.py": "0.3.14"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "snv",
                 "snv/SEQC2",
                 "snv/SEQC2/preprocess",
@@ -132,6 +95,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-23T15:15:47.829389807"
+        "timestamp": "2025-01-29T12:33:52.837161011"
     }
 }
\ No newline at end of file
diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap
index ffadf6b..f061062 100644
--- a/tests/somatic_sv.nf.test.snap
+++ b/tests/somatic_sv.nf.test.snap
@@ -2,74 +2,10 @@
     "Params: --analysis 'somatic' --variant_type 'structural' --method 'truvari,svbenchmark'": {
         "content": [
             53,
-            {
-                "BCFTOOLS_REHEADER_1": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_2": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_3": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_4": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_QUERY": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_REHEADER_TRUTH": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_SORT": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_STATS": {
-                    "bcftools": 1.18
-                },
-                "BCFTOOLS_VIEW_CONTIGS": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_VIEW_FILTERMISSING": {
-                    "bcftools": 1.2
-                },
-                "BCFTOOLS_VIEW_SUBSAMPLE": {
-                    "bcftools": 1.2
-                },
-                "BGZIP_TABIX": {
-                    "tabix": 1.12
-                },
-                "DATAVZRD": {
-                    "datavzrd": "2.36.12"
-                },
-                "MERGE_REPORTS": {
-                    "python": "3.13.0"
-                },
-                "PLOTS": {
-                    "r-base": "4.3.1"
-                },
-                "SURVIVOR_MERGE": {
-                    "survivor": "1.0.7"
-                },
-                "SURVIVOR_STATS": {
-                    "survivor": "1.0.7"
-                },
-                "TABIX_BGZIP_UNZIP": {
-                    "tabix": "1.19.1"
-                },
-                "TRUVARI_BENCH": {
-                    "truvari": "4.1.0)"
-                },
-                "VCF_TO_CSV": {
-                    "python": "3.12.4"
-                },
-                "Workflow": {
-                    "nf-core/variantbenchmarking": "v1.0dev"
-                }
-            },
+            null,
             [
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
                 "structural",
                 "structural/SEQC2",
                 "structural/SEQC2/preprocess",
@@ -218,6 +154,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-23T15:08:15.346103131"
+        "timestamp": "2025-01-29T12:35:54.329231974"
     }
 }
\ No newline at end of file
diff --git a/workflows/variantbenchmarking.nf b/workflows/variantbenchmarking.nf
index 5714c78..7bd1558 100644
--- a/workflows/variantbenchmarking.nf
+++ b/workflows/variantbenchmarking.nf
@@ -263,7 +263,7 @@ workflow VARIANTBENCHMARKING {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
+            name: 'nf_core_'  +  'variantbenchmarking_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
@@ -284,7 +284,6 @@ workflow VARIANTBENCHMARKING {
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml',sort: true))
     ch_multiqc_files                      = ch_multiqc_files.mix(REPORT_BENCHMARK_STATISTICS.out.ch_plots)
 
-
     MULTIQC (
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),