diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index ea27a58..b290e09 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {
@@ -9,15 +10,7 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.
diff --git a/.editorconfig b/.editorconfig
index b6b3190..dd9ffa5 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -18,7 +18,20 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py,md}]
+indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 4025bd8..e39603d 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,9 +1,9 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: Contributing Guidelines
+# nf-cmgg/wisecondorx: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx.
+Many thanks for taking an interest in improving nf-cmgg/wisecondorx.
 
-We try to manage the required tasks for CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-cmgg/wisecondorx using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
@@ -11,10 +11,10 @@ Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx, the standard workflow is as follows:
+If you'd like to write some code for nf-cmgg/wisecondorx, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx issues](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx repository](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-cmgg/wisecondorx issues](https://github.com/nf-cmgg/wisecondorx/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-cmgg/wisecondorx repository](https://github.com/nf-cmgg/wisecondorx) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -23,6 +23,12 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
@@ -52,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx 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-cmgg/wisecondorx 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
 
@@ -79,7 +85,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 
@@ -102,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/codespaces)
+- Open the repo in [Codespaces](https://github.com/nf-cmgg/wisecondorx/codespaces)
 - Tools installed
   - nf-core
   - Nextflow
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index fcc1aed..efe086d 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -38,7 +38,7 @@ body:
     id: system
     attributes:
       label: System information
-      description: "* Nextflow version _(eg. 22.10.1)_
+      description: "* Nextflow version _(eg. 23.04.0)_
 
         * Hardware _(eg. HPC, Desktop, Cloud)_
 
@@ -49,7 +49,6 @@ body:
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 
-        * Version of CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx _(eg. 1.1, 1.5,
-        1.8.2)_
+        * Version of nf-cmgg/wisecondorx _(eg. 1.1, 1.5, 1.8.2)_
 
         "
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 8655485..ed88af0 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pipeline
+description: Suggest an idea for the nf-cmgg/wisecondorx pipeline
 labels: enhancement
 body:
   - type: textarea
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 6002e91..c37a5c8 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,23 +1,24 @@
 <!--
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pull request
+# nf-cmgg/wisecondorx pull request
 
-Many thanks for contributing to CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx!
+Many thanks for contributing to nf-cmgg/wisecondorx!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/wisecondorx/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/wisecondorx/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 360dd1e..12c77c6 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -11,15 +11,15 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx'
+        if: github.repository == 'nf-cmgg/wisecondorx'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-cmgg/wisecondorx ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3ca5069..520a082 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,16 +19,16 @@ jobs:
   test:
     name: Run nf-test with Nextflow version ${{ matrix.NXF_VER }}
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/wisecondorx') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -39,6 +39,9 @@ jobs:
         run: |
           conda install -c bioconda nf-test
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run pipeline with test data
         run: |
           $CONDA/bin/nf-test test --junitxml=default.xml
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
new file mode 100644
index 0000000..0b6b1f2
--- /dev/null
+++ b/.github/workflows/clean-up.yml
@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
new file mode 100644
index 0000000..08622fd
--- /dev/null
+++ b/.github/workflows/download_pipeline.yml
@@ -0,0 +1,72 @@
+name: Test successful pipeline download with 'nf-core download'
+
+# Run the workflow when:
+#  - dispatched manually
+#  - when a PR is opened or reopened to 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:
+    inputs:
+      testbranch:
+        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        required: true
+        default: "dev"
+  pull_request:
+    types:
+      - opened
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  download:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install dependencies
+        run: |
+          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: Download the pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+        run: |
+          nf-core download ${{ env.REPO_LOWERCASE }} \
+          --revision ${{ env.REPO_BRANCH }} \
+          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          --compress "none" \
+          --container-system 'singularity' \
+          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-cache-utilisation 'amend' \
+          --download-configuration
+
+      - name: Inspect download
+        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+
+      - name: Run the downloaded pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 94758ce..8c70154 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -4,19 +4,26 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix-linting:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx'
+      github.repository == 'nf-cmgg/wisecondorx'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
@@ -24,32 +31,59 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
 
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: steps.pre-commit.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "+1"
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix code linting"
           git push
+
+      - name: react if linting errors were fixed
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/nf-cmgg/wisecondorx/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 888cb4b..073e187 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,74 +11,35 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - uses: actions/setup-node@v3
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-node@v3
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          python-version: 3.11
+          cache: "pip"
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies
@@ -99,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 0bbcd30..b706875 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
new file mode 100644
index 0000000..d468aea
--- /dev/null
+++ b/.github/workflows/release-announcements.yml
@@ -0,0 +1,75 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - name: get topics and convert to hashtags
+        id: get_topics
+        run: |
+          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # 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:
+      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #
diff --git a/.gitignore b/.gitignore
index fbf0ffc..68a02a1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 .nextflow*
+.nf-test*
 work/
 data/
 results/
diff --git a/.gitpod.yml b/.gitpod.yml
index 85d95ec..105a182 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -1,14 +1,20 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
     - 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
+    # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
index 23b513c..6214e91 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,20 +1,28 @@
-repository_type: pipeline
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md
-    - assets/nf-core-nf-cmgg-wisecondorx_logo_light.png
-    - docs/images/nf-core-nf-cmgg-wisecondorx_logo_light.png
-    - docs/images/nf-core-nf-cmgg-wisecondorx_logo_dark.png
+    - assets/nf-core-wisecondorx_logo_light.png
+    - docs/images/nf-core-wisecondorx_logo_light.png
+    - docs/images/nf-core-wisecondorx_logo_dark.png
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
-    - lib/WorkflowNf-cmgg-wisecondorx.groovy
+  files_unchanged:
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-wisecondorx_logo_light.png
+    - docs/images/nf-core-wisecondorx_logo_light.png
+    - docs/images/nf-core-wisecondorx_logo_dark.png
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - assets/sendmail_template.txt
+    - .gitignore
+  multiqc_config:
+    - report_comment
   nextflow_config:
     - manifest.name
     - manifest.homePage
-  multiqc_config:
-    - report_comment
-  files_unchanged:
-    - .github/ISSUE_TEMPLATE/bug_report.yml
-  schema_params: false
-  pipeline_name_conventions: false
+repository_type: pipeline
+template:
+  author: nvnieuwk
+  description: A nextflow pipeline for creating references for WisecondorX
+  name: wisecondorx
+  prefix: nf-cmgg
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0c31cdb..af57081 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6b891b0..0d37a2e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,23 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: Changelog
+# nf-cmgg/wisecondorx: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.2.0 - Intermediate worker - [24 Apr 2024]
+
+### New features
+
+1. The metrics are now in the multiqc report instead of in a separate file
+
+### Changes
+
+1. Updated the pipeline template to nf-core v2.13.1
+2. Migrate from nf-validation to nf-schema
+3. The `--bin_sizes` parameter now only takes kilobases as input (bases are no longer allowed)
+
 ## v1.1.0 - Naive Junior - [15 Sep 2023]
 
-## New features
+### New features
 
 1. Added a new parameter `--bin_sizes` that takes a comma-delimited list of bin sizes to create references for. This will make it possible to create references for multiple bin sizes at once.
 
@@ -22,4 +34,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.0.0 - Clumsy Apprentice - [22 May 2023]
 
-Initial release of CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx, created with the [nf-core](https://nf-co.re/) template.
+Initial release of nf-cmgg/wisecondorx, created with the [nf-core](https://nf-co.re/) template.
diff --git a/CITATIONS.md b/CITATIONS.md
index f33857f..d0fc75f 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -1,4 +1,4 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: Citations
+# nf-cmgg/wisecondorx: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
@@ -12,7 +12,10 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
@@ -31,5 +34,8 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
diff --git a/README.md b/README.md
index fbd06f5..5f221fe 100644
--- a/README.md
+++ b/README.md
@@ -1,27 +1,29 @@
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![GitHub Actions CI Status](https://github.com/nf-cmgg/wisecondorx/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-cmgg/wisecondorx/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-cmgg/wisecondorx/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/wisecondorx/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
+
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-cmgg/wisecondorx)
 
 ## Introduction
 
-**CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx** is a bioinformatics pipeline that creates a reference for WisecondorX
+**nf-cmgg/wisecondorx** is a bioinformatics pipeline that creates a reference for WisecondorX
 
 1. Convert the alignment files to NPZ format (`WisecondorX convert`)
 2. Create a reference from all NPZ files (`WisecondorX newref`)
 
 ## Usage
 
-> **Note**
-> 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.
+> [!NOTE]
+> 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.
 
 Now, you can run the pipeline using:
 
 ```bash
-nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx \
+nextflow run nf-cmgg/wisecondorx \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
@@ -29,14 +31,17 @@ nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx \
 
 See the [parameters](docs/parameters.md) documentation for more information on all the options.
 
-> **Warning:**
-> 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**_;
+> [!WARNING]
+> 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/usage/configuration#custom-configuration-files).
 
 ## Credits
 
-CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx was originally written by nvnieuwk.
+nf-cmgg/wisecondorx was originally written by nvnieuwk.
+
+We thank the following people for their extensive assistance in the development of this pipeline:
+
+<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
 
 ## Contributions and Support
 
@@ -44,6 +49,11 @@ If you would like to contribute to this pipeline, please see the [contributing g
 
 ## Citations
 
+<!-- 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. -->
+<!-- If you use nf-cmgg/wisecondorx for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
index f611ef6..9e21211 100644
--- a/assets/adaptivecard.json
+++ b/assets/adaptivecard.json
@@ -17,7 +17,7 @@
                         "size": "Large",
                         "weight": "Bolder",
                         "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
-                        "text": "CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx v${version} - ${runName}",
+                        "text": "nf-cmgg/wisecondorx v${version} - ${runName}",
                         "wrap": true
                     },
                     {
diff --git a/assets/email_template.html b/assets/email_template.html
index 58a0d2c..1fb6d50 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -4,21 +4,21 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: A nextflow pipeline for creating references for WisecondorX">
-  <title>CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx Pipeline Report</title>
+  <meta name="description" content="nf-cmgg/wisecondorx: A nextflow pipeline for creating references for WisecondorX">
+  <title>nf-cmgg/wisecondorx Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx v${version}</h1>
+<h1>nf-cmgg/wisecondorx ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">nf-cmgg/wisecondorx execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -27,7 +27,7 @@ <h4 style="margin-top:0; color: inherit;">CenterForMedicalGeneticsGhent/nf-cmgg-
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx execution completed successfully!
+        nf-cmgg/wisecondorx execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx</p>
-<p><a href="https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx">https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx</a></p>
+<p>nf-cmgg/wisecondorx</p>
+<p><a href="https://github.com/nf-cmgg/wisecondorx">https://github.com/nf-cmgg/wisecondorx</a></p>
 
 </div>
 
diff --git a/assets/email_template.txt b/assets/email_template.txt
index 48487b8..20432fc 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -1,10 +1,10 @@
 Run Name: $runName
 
 <% if (success){
-    out << "## CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx execution completed successfully! ##"
+    out << "## nf-cmgg/wisecondorx execution completed successfully! ##"
 } else {
     out << """####################################################
-## CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx execution completed unsuccessfully! ##
+## nf-cmgg/wisecondorx execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -27,5 +27,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx
-https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx
+nf-cmgg/wisecondorx
+https://github.com/nf-cmgg/wisecondorx
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 2dab501..1a5c3fe 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -1,17 +1,23 @@
-id: "CenterForMedicalGeneticsGhent-nf-cmgg-wisecondorx-methods-description"
+id: "nf-cmgg-wisecondorx-methods-description"
 description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx Methods Description"
-section_href: "https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx"
+section_name: "nf-cmgg/wisecondorx Methods Description"
+section_href: "https://github.com/nf-cmgg/wisecondorx"
 plot_type: "html"
+## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
+## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx v${workflow.manifest.version} ${doi_text}.
+  <p>Data was processed using nf-cmgg/wisecondorx v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
+  <p>${tool_citations}</p>
   <h4>References</h4>
   <ul>
-    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
-    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
+    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
+    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    ${tool_bibliography}
   </ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 3fdbe3b..d9a8c6f 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,12 +1,16 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx" target="_blank">CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx</a>
+
+  This report has been generated by the <a href="https://github.com/nf-cmgg/wisecondorx/releases/tag/1.2.0" target="_blank">nf-cmgg/wisecondorx</a>
   analysis pipeline.
+
 report_section_order:
-  "CenterForMedicalGeneticsGhent-nf-cmgg-wisecondorx-methods-description":
+  "nf-cmgg-wisecondorx-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "CenterForMedicalGeneticsGhent-nf-cmgg-wisecondorx-summary":
+  "nf-cmgg-wisecondorx-summary":
     order: -1002
 
 export_plots: true
+
+disable_version_detection: true
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index e1fbd31..e8069be 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
 cram,crai,gender
-https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,male
-https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,
+https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,male
+https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,
diff --git a/assets/schema_input.json b/assets/schema_input.json
index e689ff6..7787288 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,8 +1,8 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/master/assets/schema_input.json",
-    "title": "Samplesheet validation schema",
-    "description": "Schema for the samplesheet used in this pipeline",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-cmgg/wisecondorx/master/assets/schema_input.json",
+    "title": "nf-cmgg/wisecondorx pipeline - params.input schema",
+    "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {
         "type": "object",
@@ -10,16 +10,19 @@
             "cram": {
                 "type": "string",
                 "pattern": "^\\S+\\.(b|cr)am$",
-                "format": "file-path"
+                "format": "file-path",
+                "exists": true
             },
             "crai": {
                 "type": "string",
                 "pattern": "^\\S+\\.(b|cr)ai$",
-                "format": "file-path"
+                "format": "file-path",
+                "exists": true
             },
             "gender": {
                 "type": "string",
-                "pattern": "^(male|female)$",
+                "errorMessage": "The gender needs to be either 'male' or 'female'",
+                "enum": ["male", "female"],
                 "meta": ["gender"]
             }
         },
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
index ad79ea7..a8ecbd1 100644
--- a/assets/sendmail_template.txt
+++ b/assets/sendmail_template.txt
@@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="CenterForMedicalGeneticsGhent-nf-cmgg-wisecondorx_logo.png"
+Content-Type: image/png;name="wisecondorx_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
-Content-Disposition: inline; filename="CenterForMedicalGeneticsGhent-nf-cmgg-wisecondorx_logo_light.png"
+Content-Disposition: inline; filename="wisecondorx_logo_light.png"
 
-<% out << new File("$projectDir/assets/CenterForMedicalGeneticsGhent-nf-cmgg-wisecondorx_logo_light.png").
+<% out << new File("$projectDir/assets/wisecondorx_logo_light.png").
     bytes.
     encodeBase64().
     toString().
diff --git a/assets/slackreport.json b/assets/slackreport.json
index 043d02f..c55f465 100644
--- a/assets/slackreport.json
+++ b/assets/slackreport.json
@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+            "author_name": "nf-cmgg/wisecondorx ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
deleted file mode 100755
index 4a758fe..0000000
--- a/bin/check_samplesheet.py
+++ /dev/null
@@ -1,259 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide a command line tool to validate and transform tabular samplesheets."""
-
-
-import argparse
-import csv
-import logging
-import sys
-from collections import Counter
-from pathlib import Path
-
-logger = logging.getLogger()
-
-
-class RowChecker:
-    """
-    Define a service that can validate and transform each given row.
-
-    Attributes:
-        modified (list): A list of dicts, where each dict corresponds to a previously
-            validated and transformed row. The order of rows is maintained.
-
-    """
-
-    VALID_FORMATS = (
-        ".fq.gz",
-        ".fastq.gz",
-    )
-
-    def __init__(
-        self,
-        sample_col="sample",
-        first_col="fastq_1",
-        second_col="fastq_2",
-        single_col="single_end",
-        **kwargs,
-    ):
-        """
-        Initialize the row checker with the expected column names.
-
-        Args:
-            sample_col (str): The name of the column that contains the sample name
-                (default "sample").
-            first_col (str): The name of the column that contains the first (or only)
-                FASTQ file path (default "fastq_1").
-            second_col (str): The name of the column that contains the second (if any)
-                FASTQ file path (default "fastq_2").
-            single_col (str): The name of the new column that will be inserted and
-                records whether the sample contains single- or paired-end sequencing
-                reads (default "single_end").
-
-        """
-        super().__init__(**kwargs)
-        self._sample_col = sample_col
-        self._first_col = first_col
-        self._second_col = second_col
-        self._single_col = single_col
-        self._seen = set()
-        self.modified = []
-
-    def validate_and_transform(self, row):
-        """
-        Perform all validations on the given row and insert the read pairing status.
-
-        Args:
-            row (dict): A mapping from column headers (keys) to elements of that row
-                (values).
-
-        """
-        self._validate_sample(row)
-        self._validate_first(row)
-        self._validate_second(row)
-        self._validate_pair(row)
-        self._seen.add((row[self._sample_col], row[self._first_col]))
-        self.modified.append(row)
-
-    def _validate_sample(self, row):
-        """Assert that the sample name exists and convert spaces to underscores."""
-        if len(row[self._sample_col]) <= 0:
-            raise AssertionError("Sample input is required.")
-        # Sanitize samples slightly.
-        row[self._sample_col] = row[self._sample_col].replace(" ", "_")
-
-    def _validate_first(self, row):
-        """Assert that the first FASTQ entry is non-empty and has the right format."""
-        if len(row[self._first_col]) <= 0:
-            raise AssertionError("At least the first FASTQ file is required.")
-        self._validate_fastq_format(row[self._first_col])
-
-    def _validate_second(self, row):
-        """Assert that the second FASTQ entry has the right format if it exists."""
-        if len(row[self._second_col]) > 0:
-            self._validate_fastq_format(row[self._second_col])
-
-    def _validate_pair(self, row):
-        """Assert that read pairs have the same file extension. Report pair status."""
-        if row[self._first_col] and row[self._second_col]:
-            row[self._single_col] = False
-            first_col_suffix = Path(row[self._first_col]).suffixes[-2:]
-            second_col_suffix = Path(row[self._second_col]).suffixes[-2:]
-            if first_col_suffix != second_col_suffix:
-                raise AssertionError("FASTQ pairs must have the same file extensions.")
-        else:
-            row[self._single_col] = True
-
-    def _validate_fastq_format(self, filename):
-        """Assert that a given filename has one of the expected FASTQ extensions."""
-        if not any(filename.endswith(extension) for extension in self.VALID_FORMATS):
-            raise AssertionError(
-                f"The FASTQ file has an unrecognized extension: {filename}\n"
-                f"It should be one of: {', '.join(self.VALID_FORMATS)}"
-            )
-
-    def validate_unique_samples(self):
-        """
-        Assert that the combination of sample name and FASTQ filename is unique.
-
-        In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the
-        number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment.
-
-        """
-        if len(self._seen) != len(self.modified):
-            raise AssertionError("The pair of sample name and FASTQ must be unique.")
-        seen = Counter()
-        for row in self.modified:
-            sample = row[self._sample_col]
-            seen[sample] += 1
-            row[self._sample_col] = f"{sample}_T{seen[sample]}"
-
-
-def read_head(handle, num_lines=10):
-    """Read the specified number of lines from the current position in the file."""
-    lines = []
-    for idx, line in enumerate(handle):
-        if idx == num_lines:
-            break
-        lines.append(line)
-    return "".join(lines)
-
-
-def sniff_format(handle):
-    """
-    Detect the tabular format.
-
-    Args:
-        handle (text file): A handle to a `text file`_ object. The read position is
-        expected to be at the beginning (index 0).
-
-    Returns:
-        csv.Dialect: The detected tabular format.
-
-    .. _text file:
-        https://docs.python.org/3/glossary.html#term-text-file
-
-    """
-    peek = read_head(handle)
-    handle.seek(0)
-    sniffer = csv.Sniffer()
-    dialect = sniffer.sniff(peek)
-    return dialect
-
-
-def check_samplesheet(file_in, file_out):
-    """
-    Check that the tabular samplesheet has the structure expected by nf-core pipelines.
-
-    Validate the general shape of the table, expected columns, and each row. Also add
-    an additional column which records whether one or two FASTQ reads were found.
-
-    Args:
-        file_in (pathlib.Path): The given tabular samplesheet. The format can be either
-            CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``.
-        file_out (pathlib.Path): Where the validated and transformed samplesheet should
-            be created; always in CSV format.
-
-    Example:
-        This function checks that the samplesheet follows the following structure,
-        see also the `viral recon samplesheet`_::
-
-            sample,fastq_1,fastq_2
-            SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
-            SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
-            SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
-
-    .. _viral recon samplesheet:
-        https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
-
-    """
-    required_columns = {"sample", "fastq_1", "fastq_2"}
-    # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
-    with file_in.open(newline="") as in_handle:
-        reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
-        # Validate the existence of the expected header columns.
-        if not required_columns.issubset(reader.fieldnames):
-            req_cols = ", ".join(required_columns)
-            logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
-            sys.exit(1)
-        # Validate each row.
-        checker = RowChecker()
-        for i, row in enumerate(reader):
-            try:
-                checker.validate_and_transform(row)
-            except AssertionError as error:
-                logger.critical(f"{str(error)} On line {i + 2}.")
-                sys.exit(1)
-        checker.validate_unique_samples()
-    header = list(reader.fieldnames)
-    header.insert(1, "single_end")
-    # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
-    with file_out.open(mode="w", newline="") as out_handle:
-        writer = csv.DictWriter(out_handle, header, delimiter=",")
-        writer.writeheader()
-        for row in checker.modified:
-            writer.writerow(row)
-
-
-def parse_args(argv=None):
-    """Define and immediately parse command line arguments."""
-    parser = argparse.ArgumentParser(
-        description="Validate and transform a tabular samplesheet.",
-        epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv",
-    )
-    parser.add_argument(
-        "file_in",
-        metavar="FILE_IN",
-        type=Path,
-        help="Tabular input samplesheet in CSV or TSV format.",
-    )
-    parser.add_argument(
-        "file_out",
-        metavar="FILE_OUT",
-        type=Path,
-        help="Transformed output samplesheet in CSV format.",
-    )
-    parser.add_argument(
-        "-l",
-        "--log-level",
-        help="The desired log level (default WARNING).",
-        choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
-        default="WARNING",
-    )
-    return parser.parse_args(argv)
-
-
-def main(argv=None):
-    """Coordinate argument parsing and program execution."""
-    args = parse_args(argv)
-    logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s")
-    if not args.file_in.is_file():
-        logger.error(f"The given input file {args.file_in} was not found!")
-        sys.exit(2)
-    args.file_out.parent.mkdir(parents=True, exist_ok=True)
-    check_samplesheet(args.file_in, args.file_out)
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/conf/base.config b/conf/base.config
index b8a2d60..71d46e9 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx Nextflow base config file
+    nf-cmgg/wisecondorx Nextflow base config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on
@@ -51,7 +51,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index 9325b91..0d3da09 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -16,9 +16,16 @@ process {
         enabled: false
     ]
 
+    def Integer lowestBinSize = params.bin_sizes.tokenize(",").collect { it as Integer }.min()
+
+    withName: WISECONDORX_CONVERT {
+        ext.args = "--binsize ${lowestBinSize * 1000}"
+    }
+
     withName: WISECONDORX_NEWREF {
-        ext.prefix = {"${meta.id}_${meta.bin_size as Integer > 1000 ? meta.bin_size as Integer/1000 : meta.bin_size}${meta.bin_size as Integer > 1000 ? "k" : ""}bp"}
-        ext.args = { "--binsize ${meta.bin_size}" }
+        tag = {"${meta.id}_${meta.bin_size}kbp"}
+        ext.prefix = {"${meta.id}_${meta.bin_size}kbp"}
+        ext.args = { "--binsize ${meta.bin_size.toInteger() * 1000}" }
         publishDir = [
             enabled: true,
             path: { "${params.outdir}" },
@@ -27,24 +34,13 @@ process {
         ]
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            enabled: true,
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
-    withName: MULTIQC {
+    withName: 'MULTIQC' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
-            overwrite: true,
-            path: { "${params.outdir}/multiqc_reports" },
+            path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
-        errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
-        ext.args      = { params.multiqc_config ? "--config $multiqc_custom_config" : "" }
     }
 
 }
diff --git a/conf/nf_test.config b/conf/nf_test.config
deleted file mode 100644
index 51f6fe2..0000000
--- a/conf/nf_test.config
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx -profile test,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
-
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
-    genomes_ignore = true
-
-    fasta           = params.test_data["homo_sapiens"]["genome"]["genome_fasta"]
-    fai             = params.test_data["homo_sapiens"]["genome"]["genome_fasta_fai"]
-
-    // Input data
-    input  = "${projectDir}/tests/inputs/samplesheet.csv"
-    outdir = "${params.outputDir}"
-
-}
diff --git a/conf/test.config b/conf/test.config
index 2adb674..a4619d2 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-cmgg/wisecondorx -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -21,7 +21,7 @@ params {
 
     genomes_ignore = true
 
-    bin_sizes       = "10000,5"
+    bin_sizes       = "10,5"
 
     fasta           = params.test_data["homo_sapiens"]["genome"]["genome_fasta"]
     fai             = null //params.test_data["homo_sapiens"]["genome"]["genome_fasta_fai"]
diff --git a/conf/test_full.config b/conf/test_full.config
index 20967d5..613e151 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -5,13 +5,11 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-cmgg/wisecondorx -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
 
-cleanup = true
-
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
diff --git a/docs/README.md b/docs/README.md
index d338a42..2399c52 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,6 +1,6 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: Documentation
+# nf-cmgg/wisecondorx: Documentation
 
-The CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx documentation is split into the following pages:
+The nf-cmgg/wisecondorx documentation is split into the following pages:
 
 - [Usage](usage.md)
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
diff --git a/docs/output.md b/docs/output.md
index 2f6af0c..6bad85d 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,4 +1,4 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: Output
+# nf-cmgg/wisecondorx: Output
 
 ## Introduction
 
diff --git a/docs/parameters.md b/docs/parameters.md
index 841bc00..1631264 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -1,4 +1,4 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pipeline parameters
+# nf-cmgg/wisecondorx pipeline parameters
 
 A nextflow pipeline for creating references for WisecondorX
 
diff --git a/docs/usage.md b/docs/usage.md
index 2cb408e..5564253 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,4 +1,4 @@
-# CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx: Usage
+# nf-cmgg/wisecondorx: Usage
 
 > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
 
@@ -55,11 +55,14 @@ 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>`.
 
-> ⚠️ 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:
+:::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:
 
 ```bash
-nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx -profile docker -params-file params.yaml
+nextflow run nf-cmgg/wisecondorx -profile docker -params-file params.yaml
 ```
 
 with `params.yaml` containing:
@@ -68,7 +71,6 @@ with `params.yaml` containing:
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'
-input: 'data'
 <...>
 ```
 
@@ -79,24 +81,28 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
 ```bash
-nextflow pull CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx
+nextflow pull nf-cmgg/wisecondorx
 ```
 
 ### 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.
 
-First, go to the [CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx releases page](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/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.
+First, go to the [nf-cmgg/wisecondorx releases page](https://github.com/nf-cmgg/wisecondorx/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.
 
-> 💡 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
 
-> **NB:** 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`
 
@@ -104,7 +110,9 @@ 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.
 
-> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::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.
+:::
 
 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).
 
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
deleted file mode 100755
index 9b34804..0000000
--- a/lib/NfcoreSchema.groovy
+++ /dev/null
@@ -1,530 +0,0 @@
-//
-// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
-//
-
-import nextflow.Nextflow
-import org.everit.json.schema.Schema
-import org.everit.json.schema.loader.SchemaLoader
-import org.everit.json.schema.ValidationException
-import org.json.JSONObject
-import org.json.JSONTokener
-import org.json.JSONArray
-import groovy.json.JsonSlurper
-import groovy.json.JsonBuilder
-
-class NfcoreSchema {
-
-    //
-    // Resolve Schema path relative to main workflow directory
-    //
-    public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') {
-        return "${workflow.projectDir}/${schema_filename}"
-    }
-
-    //
-    // Function to loop over all parameters defined in schema and check
-    // whether the given parameters adhere to the specifications
-    //
-    /* groovylint-disable-next-line UnusedPrivateMethodParameter */
-    public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') {
-        def has_error = false
-        //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
-        // Check for nextflow core params and unexpected params
-        def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text
-        def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
-        def nf_params = [
-            // Options for base `nextflow` command
-            'bg',
-            'c',
-            'C',
-            'config',
-            'd',
-            'D',
-            'dockerize',
-            'h',
-            'log',
-            'q',
-            'quiet',
-            'syslog',
-            'v',
-
-            // Options for `nextflow run` command
-            'ansi',
-            'ansi-log',
-            'bg',
-            'bucket-dir',
-            'c',
-            'cache',
-            'config',
-            'dsl2',
-            'dump-channels',
-            'dump-hashes',
-            'E',
-            'entry',
-            'latest',
-            'lib',
-            'main-script',
-            'N',
-            'name',
-            'offline',
-            'params-file',
-            'pi',
-            'plugins',
-            'poll-interval',
-            'pool-size',
-            'profile',
-            'ps',
-            'qs',
-            'queue-size',
-            'r',
-            'resume',
-            'revision',
-            'stdin',
-            'stub',
-            'stub-run',
-            'test',
-            'w',
-            'with-apptainer',
-            'with-charliecloud',
-            'with-conda',
-            'with-dag',
-            'with-docker',
-            'with-mpi',
-            'with-notification',
-            'with-podman',
-            'with-report',
-            'with-singularity',
-            'with-timeline',
-            'with-tower',
-            'with-trace',
-            'with-weblog',
-            'without-docker',
-            'without-podman',
-            'work-dir'
-        ]
-        def unexpectedParams = []
-
-        // Collect expected parameters from the schema
-        def expectedParams = []
-        def enums = [:]
-        for (group in schemaParams) {
-            for (p in group.value['properties']) {
-                expectedParams.push(p.key)
-                if (group.value['properties'][p.key].containsKey('enum')) {
-                    enums[p.key] = group.value['properties'][p.key]['enum']
-                }
-            }
-        }
-
-        for (specifiedParam in params.keySet()) {
-            // nextflow params
-            if (nf_params.contains(specifiedParam)) {
-                log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
-                has_error = true
-            }
-            // unexpected params
-            def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
-            def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
-            def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
-            def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
-            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
-                // Temporarily remove camelCase/camel-case params #1035
-                def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
-                if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
-                    unexpectedParams.push(specifiedParam)
-                }
-            }
-        }
-
-        //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
-        // Validate parameters against the schema
-        InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream()
-        JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))
-
-        // Remove anything that's in params.schema_ignore_params
-        raw_schema = removeIgnoredParams(raw_schema, params)
-
-        Schema schema = SchemaLoader.load(raw_schema)
-
-        // Clean the parameters
-        def cleanedParams = cleanParameters(params)
-
-        // Convert to JSONObject
-        def jsonParams = new JsonBuilder(cleanedParams)
-        JSONObject params_json = new JSONObject(jsonParams.toString())
-
-        // Validate
-        try {
-            schema.validate(params_json)
-        } catch (ValidationException e) {
-            println ''
-            log.error 'ERROR: Validation of pipeline parameters failed!'
-            JSONObject exceptionJSON = e.toJSON()
-            printExceptions(exceptionJSON, params_json, log, enums)
-            println ''
-            has_error = true
-        }
-
-        // Check for unexpected parameters
-        if (unexpectedParams.size() > 0) {
-            Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
-            println ''
-            def warn_msg = 'Found unexpected parameters:'
-            for (unexpectedParam in unexpectedParams) {
-                warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}"
-            }
-            log.warn warn_msg
-            log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}"
-            println ''
-        }
-
-        if (has_error) {
-            Nextflow.error('Exiting!')
-        }
-    }
-
-    //
-    // Beautify parameters for --help
-    //
-    public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') {
-        Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
-        Integer num_hidden = 0
-        String output  = ''
-        output        += 'Typical pipeline command:\n\n'
-        output        += "  ${colors.cyan}${command}${colors.reset}\n\n"
-        Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
-        Integer max_chars  = paramsMaxChars(params_map) + 1
-        Integer desc_indent = max_chars + 14
-        Integer dec_linewidth = 160 - desc_indent
-        for (group in params_map.keySet()) {
-            Integer num_params = 0
-            String group_output = colors.underlined + colors.bold + group + colors.reset + '\n'
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                if (group_params.get(param).hidden && !params.show_hidden_params) {
-                    num_hidden += 1
-                    continue;
-                }
-                def type = '[' + group_params.get(param).type + ']'
-                def description = group_params.get(param).description
-                def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : ''
-                def description_default = description + colors.dim + defaultValue + colors.reset
-                // Wrap long description texts
-                // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap
-                if (description_default.length() > dec_linewidth){
-                    List olines = []
-                    String oline = "" // " " * indent
-                    description_default.split(" ").each() { wrd ->
-                        if ((oline.size() + wrd.size()) <= dec_linewidth) {
-                            oline += wrd + " "
-                        } else {
-                            olines += oline
-                            oline = wrd + " "
-                        }
-                    }
-                    olines += oline
-                    description_default = olines.join("\n" + " " * desc_indent)
-                }
-                group_output += "  --" +  param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n'
-                num_params += 1
-            }
-            group_output += '\n'
-            if (num_params > 0){
-                output += group_output
-            }
-        }
-        if (num_hidden > 0){
-            output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset
-        }
-        output += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return output
-    }
-
-    //
-    // Groovy Map summarising parameters/workflow options used by the pipeline
-    //
-    public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') {
-        // Get a selection of core Nextflow workflow options
-        def Map workflow_summary = [:]
-        if (workflow.revision) {
-            workflow_summary['revision'] = workflow.revision
-        }
-        workflow_summary['runName']      = workflow.runName
-        if (workflow.containerEngine) {
-            workflow_summary['containerEngine'] = workflow.containerEngine
-        }
-        if (workflow.container) {
-            workflow_summary['container'] = workflow.container
-        }
-        workflow_summary['launchDir']    = workflow.launchDir
-        workflow_summary['workDir']      = workflow.workDir
-        workflow_summary['projectDir']   = workflow.projectDir
-        workflow_summary['userName']     = workflow.userName
-        workflow_summary['profile']      = workflow.profile
-        workflow_summary['configFiles']  = workflow.configFiles.join(', ')
-
-        // Get pipeline parameters defined in JSON Schema
-        def Map params_summary = [:]
-        def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
-        for (group in params_map.keySet()) {
-            def sub_params = new LinkedHashMap()
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                if (params.containsKey(param)) {
-                    def params_value = params.get(param)
-                    def schema_value = group_params.get(param).default
-                    def param_type   = group_params.get(param).type
-                    if (schema_value != null) {
-                        if (param_type == 'string') {
-                            if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
-                                def sub_string = schema_value.replace('\$projectDir', '')
-                                sub_string     = sub_string.replace('\${projectDir}', '')
-                                if (params_value.contains(sub_string)) {
-                                    schema_value = params_value
-                                }
-                            }
-                            if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) {
-                                def sub_string = schema_value.replace('\$params.outdir', '')
-                                sub_string     = sub_string.replace('\${params.outdir}', '')
-                                if ("${params.outdir}${sub_string}" == params_value) {
-                                    schema_value = params_value
-                                }
-                            }
-                        }
-                    }
-
-                    // We have a default in the schema, and this isn't it
-                    if (schema_value != null && params_value != schema_value) {
-                        sub_params.put(param, params_value)
-                    }
-                    // No default in the schema, and this isn't empty
-                    else if (schema_value == null && params_value != "" && params_value != null && params_value != false) {
-                        sub_params.put(param, params_value)
-                    }
-                }
-            }
-            params_summary.put(group, sub_params)
-        }
-        return [ 'Core Nextflow options' : workflow_summary ] << params_summary
-    }
-
-    //
-    // Beautify parameters for summary and return as string
-    //
-    public static String paramsSummaryLog(workflow, params) {
-        Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
-        String output  = ''
-        def params_map = paramsSummaryMap(workflow, params)
-        def max_chars  = paramsMaxChars(params_map)
-        for (group in params_map.keySet()) {
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            if (group_params) {
-                output += colors.bold + group + colors.reset + '\n'
-                for (param in group_params.keySet()) {
-                    output += "  " + colors.blue + param.padRight(max_chars) + ": " + colors.green +  group_params.get(param) + colors.reset + '\n'
-                }
-                output += '\n'
-            }
-        }
-        output += "!! Only displaying parameters that differ from the pipeline defaults !!\n"
-        output += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return output
-    }
-
-    //
-    // Loop over nested exceptions and print the causingException
-    //
-    private static void printExceptions(ex_json, params_json, log, enums, limit=5) {
-        def causingExceptions = ex_json['causingExceptions']
-        if (causingExceptions.length() == 0) {
-            def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
-            // Missing required param
-            if (m.matches()) {
-                log.error "* Missing required parameter: --${m[0][1]}"
-            }
-            // Other base-level error
-            else if (ex_json['pointerToViolation'] == '#') {
-                log.error "* ${ex_json['message']}"
-            }
-            // Error with specific param
-            else {
-                def param = ex_json['pointerToViolation'] - ~/^#\//
-                def param_val = params_json[param].toString()
-                if (enums.containsKey(param)) {
-                    def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices"
-                    if (enums[param].size() > limit) {
-                        log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
-                    } else {
-                        log.error "${error_msg}: ${enums[param].join(', ')})"
-                    }
-                } else {
-                    log.error "* --${param}: ${ex_json['message']} (${param_val})"
-                }
-            }
-        }
-        for (ex in causingExceptions) {
-            printExceptions(ex, params_json, log, enums)
-        }
-    }
-
-    //
-    // Remove an element from a JSONArray
-    //
-    private static JSONArray removeElement(json_array, element) {
-        def list = []
-        int len = json_array.length()
-        for (int i=0;i<len;i++){
-            list.add(json_array.get(i).toString())
-        }
-        list.remove(element)
-        JSONArray jsArray = new JSONArray(list)
-        return jsArray
-    }
-
-    //
-    // Remove ignored parameters
-    //
-    private static JSONObject removeIgnoredParams(raw_schema, params) {
-        // Remove anything that's in params.schema_ignore_params
-        params.schema_ignore_params.split(',').each{ ignore_param ->
-            if(raw_schema.keySet().contains('definitions')){
-                raw_schema.definitions.each { definition ->
-                    for (key in definition.keySet()){
-                        if (definition[key].get("properties").keySet().contains(ignore_param)){
-                            // Remove the param to ignore
-                            definition[key].get("properties").remove(ignore_param)
-                            // If the param was required, change this
-                            if (definition[key].has("required")) {
-                                def cleaned_required = removeElement(definition[key].required, ignore_param)
-                                definition[key].put("required", cleaned_required)
-                            }
-                        }
-                    }
-                }
-            }
-            if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) {
-                raw_schema.get("properties").remove(ignore_param)
-            }
-            if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) {
-                def cleaned_required = removeElement(raw_schema.required, ignore_param)
-                raw_schema.put("required", cleaned_required)
-            }
-        }
-        return raw_schema
-    }
-
-    //
-    // Clean and check parameters relative to Nextflow native classes
-    //
-    private static Map cleanParameters(params) {
-        def new_params = params.getClass().newInstance(params)
-        for (p in params) {
-            // remove anything evaluating to false
-            if (!p['value']) {
-                new_params.remove(p.key)
-            }
-            // Cast MemoryUnit to String
-            if (p['value'].getClass() == nextflow.util.MemoryUnit) {
-                new_params.replace(p.key, p['value'].toString())
-            }
-            // Cast Duration to String
-            if (p['value'].getClass() == nextflow.util.Duration) {
-                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
-            }
-            // Cast LinkedHashMap to String
-            if (p['value'].getClass() == LinkedHashMap) {
-                new_params.replace(p.key, p['value'].toString())
-            }
-        }
-        return new_params
-    }
-
-    //
-    // This function tries to read a JSON params file
-    //
-    private static LinkedHashMap paramsLoad(String json_schema) {
-        def params_map = new LinkedHashMap()
-        try {
-            params_map = paramsRead(json_schema)
-        } catch (Exception e) {
-            println "Could not read parameters settings from JSON. $e"
-            params_map = new LinkedHashMap()
-        }
-        return params_map
-    }
-
-    //
-    // Method to actually read in JSON file using Groovy.
-    // Group (as Key), values are all parameters
-    //    - Parameter1 as Key, Description as Value
-    //    - Parameter2 as Key, Description as Value
-    //    ....
-    // Group
-    //    -
-    private static LinkedHashMap paramsRead(String json_schema) throws Exception {
-        def json = new File(json_schema).text
-        def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
-        def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
-        /* Tree looks like this in nf-core schema
-        * definitions <- this is what the first get('definitions') gets us
-                group 1
-                    title
-                    description
-                        properties
-                        parameter 1
-                            type
-                            description
-                        parameter 2
-                            type
-                            description
-                group 2
-                    title
-                    description
-                        properties
-                        parameter 1
-                            type
-                            description
-        * properties <- parameters can also be ungrouped, outside of definitions
-                parameter 1
-                    type
-                    description
-        */
-
-        // Grouped params
-        def params_map = new LinkedHashMap()
-        schema_definitions.each { key, val ->
-            def Map group = schema_definitions."$key".properties // Gets the property object of the group
-            def title = schema_definitions."$key".title
-            def sub_params = new LinkedHashMap()
-            group.each { innerkey, value ->
-                sub_params.put(innerkey, value)
-            }
-            params_map.put(title, sub_params)
-        }
-
-        // Ungrouped params
-        def ungrouped_params = new LinkedHashMap()
-        schema_properties.each { innerkey, value ->
-            ungrouped_params.put(innerkey, value)
-        }
-        params_map.put("Other parameters", ungrouped_params)
-
-        return params_map
-    }
-
-    //
-    // Get maximum number of characters across all parameter names
-    //
-    private static Integer paramsMaxChars(params_map) {
-        Integer max_chars = 0
-        for (group in params_map.keySet()) {
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                if (param.size() > max_chars) {
-                    max_chars = param.size()
-                }
-            }
-        }
-        return max_chars
-    }
-}
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
deleted file mode 100755
index 000bb92..0000000
--- a/lib/NfcoreTemplate.groovy
+++ /dev/null
@@ -1,331 +0,0 @@
-//
-// This file holds several functions used within the nf-core pipeline template.
-//
-
-import org.yaml.snakeyaml.Yaml
-
-class NfcoreTemplate {
-
-    //
-    // Check AWS Batch related parameters have been specified correctly
-    //
-    public static void awsBatch(workflow, params) {
-        if (workflow.profile.contains('awsbatch')) {
-            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
-            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-            // Check outdir paths to be S3 buckets if running on AWSBatch
-            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
-        }
-    }
-
-    //
-    //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
-    //
-    public static void checkConfigProvided(workflow, log) {
-        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-                    "Please refer to the quick start section and usage docs for the pipeline.\n "
-        }
-    }
-
-    //
-    // Generate version string
-    //
-    public static String version(workflow) {
-        String version_string = ""
-
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
-        }
-
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
-        }
-
-        return version_string
-    }
-
-    //
-    // Construct and send completion email
-    //
-    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
-
-        // Set up the e-mail variables
-        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
-        if (!workflow.success) {
-            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
-        }
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            summary << summary_params[group]
-        }
-
-        def misc_fields = [:]
-        misc_fields['Date Started']              = workflow.start
-        misc_fields['Date Completed']            = workflow.complete
-        misc_fields['Pipeline script file path'] = workflow.scriptFile
-        misc_fields['Pipeline script hash ID']   = workflow.scriptId
-        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-        misc_fields['Nextflow Version']           = workflow.nextflow.version
-        misc_fields['Nextflow Build']             = workflow.nextflow.build
-        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
-
-        def email_fields = [:]
-        email_fields['version']      = NfcoreTemplate.version(workflow)
-        email_fields['runName']      = workflow.runName
-        email_fields['success']      = workflow.success
-        email_fields['dateComplete'] = workflow.complete
-        email_fields['duration']     = workflow.duration
-        email_fields['exitStatus']   = workflow.exitStatus
-        email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-        email_fields['errorReport']  = (workflow.errorReport ?: 'None')
-        email_fields['commandLine']  = workflow.commandLine
-        email_fields['projectDir']   = workflow.projectDir
-        email_fields['summary']      = summary << misc_fields
-
-        // On success try attach the 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]
-                }
-            }
-        } catch (all) {
-            if (multiqc_report) {
-                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
-            }
-        }
-
-        // Check if we are only sending emails on failure
-        def email_address = params.email
-        if (!params.email && params.email_on_fail && !workflow.success) {
-            email_address = params.email_on_fail
-        }
-
-        // Render the TXT template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        def tf           = new File("$projectDir/assets/email_template.txt")
-        def txt_template = engine.createTemplate(tf).make(email_fields)
-        def email_txt    = txt_template.toString()
-
-        // Render the HTML template
-        def hf            = new File("$projectDir/assets/email_template.html")
-        def html_template = engine.createTemplate(hf).make(email_fields)
-        def email_html    = html_template.toString()
-
-        // Render the sendmail template
-        def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
-        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
-        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
-        def sendmail_html          = sendmail_template.toString()
-
-        // Send the HTML e-mail
-        Map colors = logColours(params.monochrome_logs)
-        if (email_address) {
-            try {
-                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
-                // Try to send HTML e-mail using sendmail
-                [ 'sendmail', '-t' ].execute() << sendmail_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-            } catch (all) {
-                // Catch failures and try with plaintext
-                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
-                    mail_cmd += [ '-A', mqc_report ]
-                }
-                mail_cmd.execute() << email_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
-            }
-        }
-
-        // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-        def output_hf = new File(output_d, "pipeline_report.html")
-        output_hf.withWriter { w -> w << email_html }
-        def output_tf = new File(output_d, "pipeline_report.txt")
-        output_tf.withWriter { w -> w << email_txt }
-    }
-
-    //
-    // Construct and send a notification to a web server as JSON
-    // e.g. Microsoft Teams and Slack
-    //
-    public static void IM_notification(workflow, params, summary_params, projectDir, log) {
-        def hook_url = params.hook_url
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            summary << summary_params[group]
-        }
-
-        def misc_fields = [:]
-        misc_fields['start']                                = workflow.start
-        misc_fields['complete']                             = workflow.complete
-        misc_fields['scriptfile']                           = workflow.scriptFile
-        misc_fields['scriptid']                             = workflow.scriptId
-        if (workflow.repository) misc_fields['repository']  = workflow.repository
-        if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-        if (workflow.revision)   misc_fields['revision']    = workflow.revision
-        misc_fields['nxf_version']                          = workflow.nextflow.version
-        misc_fields['nxf_build']                            = workflow.nextflow.build
-        misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
-
-        def msg_fields = [:]
-        msg_fields['version']      = NfcoreTemplate.version(workflow)
-        msg_fields['runName']      = workflow.runName
-        msg_fields['success']      = workflow.success
-        msg_fields['dateComplete'] = workflow.complete
-        msg_fields['duration']     = workflow.duration
-        msg_fields['exitStatus']   = workflow.exitStatus
-        msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-        msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-        msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-        msg_fields['projectDir']   = workflow.projectDir
-        msg_fields['summary']      = summary << misc_fields
-
-        // Render the JSON template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        // Different JSON depending on the service provider
-        // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-        def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-        def hf            = new File("$projectDir/assets/${json_path}")
-        def json_template = engine.createTemplate(hf).make(msg_fields)
-        def json_message  = json_template.toString()
-
-        // POST
-        def post = new URL(hook_url).openConnection();
-        post.setRequestMethod("POST")
-        post.setDoOutput(true)
-        post.setRequestProperty("Content-Type", "application/json")
-        post.getOutputStream().write(json_message.getBytes("UTF-8"));
-        def postRC = post.getResponseCode();
-        if (! postRC.equals(200)) {
-            log.warn(post.getErrorStream().getText());
-        }
-    }
-
-    //
-    // Print pipeline summary on completion
-    //
-    public static void summary(workflow, params, log) {
-        Map colors = logColours(params.monochrome_logs)
-        if (workflow.success) {
-            if (workflow.stats.ignoredCount == 0) {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-            } else {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
-            }
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
-        }
-    }
-
-    //
-    // ANSII Colours used for terminal logging
-    //
-    public static Map logColours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-
-        // Reset / Meta
-        colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
-        colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
-        colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
-        colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
-        colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
-        colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
-        colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
-
-        // Regular Colors
-        colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-        colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-        colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-        colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-        colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-        colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-        colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-        colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
-
-        // Bold
-        colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-        colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-        colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-        colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-        colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-        colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-        colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-        colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
-
-        // Underline
-        colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-        colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-        colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-        colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-        colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-        colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-        colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-        colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
-
-        // High Intensity
-        colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-        colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-        colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-        colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-        colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-        colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-        colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-        colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
-
-        // Bold High Intensity
-        colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-        colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-        colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-        colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-        colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-        colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-        colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-        colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
-
-        return colorcodes
-    }
-
-    //
-    // Does what is says on the tin
-    //
-    public static String dashedLine(monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    //
-    // nf-core logo
-    //
-    public static String logo(workflow, monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        String workflow_version = NfcoreTemplate.version(workflow)
-        String.format(
-            """\n
-            ${dashedLine(monochrome_logs)}
-            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
-            ${dashedLine(monochrome_logs)}
-            """.stripIndent()
-        )
-    }
-}
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
deleted file mode 100644
index 8d030f4..0000000
--- a/lib/Utils.groovy
+++ /dev/null
@@ -1,47 +0,0 @@
-//
-// This file holds several Groovy functions that could be useful for any Nextflow pipeline
-//
-
-import org.yaml.snakeyaml.Yaml
-
-class Utils {
-
-    //
-    // When running with -profile conda, warn if channels have not been set-up appropriately
-    //
-    public static void checkCondaChannels(log) {
-        Yaml parser = new Yaml()
-        def channels = []
-        try {
-            def config = parser.load("conda config --show channels".execute().text)
-            channels = config.channels
-        } catch(NullPointerException | IOException e) {
-            log.warn "Could not verify conda channel configuration."
-            return
-        }
-
-        // Check that all channels are present
-        // This channel list is ordered by required channel priority.
-        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
-        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
-        def n = required_channels_in_order.size()
-        for (int i = 0; i < n - 1; i++) {
-            channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
-        }
-
-        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" +
-                "  ${required_channels_in_order}\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        }
-    }
-}
diff --git a/lib/WorkflowCmggWisecondorx.groovy b/lib/WorkflowCmggWisecondorx.groovy
deleted file mode 100755
index 828b936..0000000
--- a/lib/WorkflowCmggWisecondorx.groovy
+++ /dev/null
@@ -1,79 +0,0 @@
-//
-// This file holds several functions specific to the workflow/nf-cmgg-wisecondorx.nf in the CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowCmggWisecondorx {
-
-    //
-    // Check and validate parameters
-    //
-    public static void initialise(params, log) {
-        genomeExistsError(params, log)
-
-
-        if (!params.fasta) {
-            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-        }
-    }
-
-    //
-    // Get workflow summary for MultiQC
-    //
-    public static String paramsSummaryMultiqc(workflow, summary) {
-        String summary_section = ''
-        for (group in summary.keySet()) {
-            def group_params = summary.get(group)  // This gets the parameters of that particular group
-            if (group_params) {
-                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-                summary_section += "    <dl class=\"dl-horizontal\">\n"
-                for (param in group_params.keySet()) {
-                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
-                }
-                summary_section += "    </dl>\n"
-            }
-        }
-
-        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
-        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-        yaml_file_text        += "plot_type: 'html'\n"
-        yaml_file_text        += "data: |\n"
-        yaml_file_text        += "${summary_section}"
-        return yaml_file_text
-    }
-
-    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
-        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
-        def meta = [:]
-        meta.workflow = run_workflow.toMap()
-        meta["manifest_map"] = run_workflow.manifest.toMap()
-
-        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
-
-        def methods_text = mqc_methods_yaml.text
-
-        def engine =  new SimpleTemplateEngine()
-        def description_html = engine.createTemplate(methods_text).make(meta)
-
-        return description_html
-    }
-
-    //
-    // Exit pipeline if incorrect --genome key provided
-    //
-    private static void genomeExistsError(params, log) {
-        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-                "  Currently, the available genome keys are:\n" +
-                "  ${params.genomes.keySet().join(", ")}\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-            Nextflow.error(error_string)
-        }
-    }
-}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
deleted file mode 100755
index 424aeaa..0000000
--- a/lib/WorkflowMain.groovy
+++ /dev/null
@@ -1,97 +0,0 @@
-//
-// This file holds several functions specific to the main.nf workflow in the CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowMain {
-
-    //
-    // Citation string for pipeline
-    //
-    public static String citation(workflow) {
-        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            "* The nf-core framework\n" +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-            "* Software dependencies\n" +
-            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-    }
-
-    //
-    // Generate help string
-    //
-    public static String help(workflow, params) {
-        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-        def help_string = ''
-        help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
-        help_string += NfcoreSchema.paramsHelp(workflow, params, command)
-        help_string += '\n' + citation(workflow) + '\n'
-        help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return help_string
-    }
-
-    //
-    // Generate parameter summary log string
-    //
-    public static String paramsSummaryLog(workflow, params) {
-        def summary_log = ''
-        summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
-        summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
-        summary_log += '\n' + citation(workflow) + '\n'
-        summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return summary_log
-    }
-
-    //
-    // Validate parameters and print summary to screen
-    //
-    public static void initialise(workflow, params, log) {
-        // Print help to screen if required
-        if (params.help) {
-            log.info help(workflow, params)
-            System.exit(0)
-        }
-
-        // Print workflow version and exit on --version
-        if (params.version) {
-            String workflow_version = NfcoreTemplate.version(workflow)
-            log.info "${workflow.manifest.name} ${workflow_version}"
-            System.exit(0)
-        }
-
-        // Print parameter summary log to screen
-        log.info paramsSummaryLog(workflow, params)
-
-        // Validate workflow parameters via the JSON schema
-        if (params.validate_params) {
-            NfcoreSchema.validateParameters(workflow, params, log)
-        }
-
-        // Check that a -profile or Nextflow config has been provided to run the pipeline
-        NfcoreTemplate.checkConfigProvided(workflow, log)
-
-        // Check that conda channels are set-up correctly
-        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-            Utils.checkCondaChannels(log)
-        }
-
-        // Check AWS batch settings
-        NfcoreTemplate.awsBatch(workflow, params)
-
-        // Check input has been provided
-        if (!params.input) {
-            Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
-        }
-    }
-    //
-    // Get attribute from genome config file e.g. fasta
-    //
-    public static Object getGenomeAttribute(params, attribute) {
-        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-            if (params.genomes[ params.genome ].containsKey(attribute)) {
-                return params.genomes[ params.genome ][ attribute ]
-            }
-        }
-        return null
-    }
-}
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
deleted file mode 100644
index 805c8bb..0000000
Binary files a/lib/nfcore_external_java_deps.jar and /dev/null differ
diff --git a/main.nf b/main.nf
index de73f66..10ba3d3 100644
--- a/main.nf
+++ b/main.nf
@@ -1,72 +1,135 @@
 #!/usr/bin/env nextflow
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx
+    nf-cmgg/wisecondorx
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Github : https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx----------------------------------------------------------------------------------------
+    Github : https://github.com/nf-cmgg/wisecondorx
+----------------------------------------------------------------------------------------
 */
 
 nextflow.enable.dsl = 2
 
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { paramsHelp         } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
-params.fai   = WorkflowMain.getGenomeAttribute(params, 'fai')
+include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_wisecondorx_pipeline'
+
+params.fasta = getGenomeAttribute('fasta')
+params.fai   = getGenomeAttribute('fai')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE & PRINT PARAMETER SUMMARY
+    ADDITIONAL INPUT VALIDATION
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// Print help message
-if (params.help) {
-    def String command = "nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx --input <input csv/tsv/yaml> --outdir <output folder>"
-    log.info paramsHelp(command)
-    exit 0
+def List val_bin_sizes = params.bin_sizes.split(",").collect { it as Integer }
+def Integer lowestBinSize = val_bin_sizes.min()
+val_bin_sizes.each { bin_size ->
+    if(bin_size % lowestBinSize != 0) {
+        error("""
+All bin sizes should be divisible by the lowest bin size!
+${bin_size} is not divisible by ${lowestBinSize}...
+""")
+    }
 }
 
-// Validate input parameters
-validateParameters()
-
-// Print parameter summary log to screen
-log.info paramsSummaryLog(workflow)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
+include { paramsSummaryLog        } from 'plugin/nf-schema'
+include { paramsHelp              } from 'plugin/nf-schema'
+include { validateParameters      } from 'plugin/nf-schema'
+include { WISECONDORX             } from './workflows/wisecondorx'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_wisecondorx_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_wisecondorx_pipeline'
+
+
 
-include { CMGGWISECONDORX } from './workflows/cmgg-wisecondorx'
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    NAMED WORKFLOWS FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
 
 //
-// WORKFLOW: Run main CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx analysis pipeline
+// WORKFLOW: Run main nf-cmgg/wisecondorx analysis pipeline
 //
-workflow CMGG_CMGGWISECONDORX {
-    CMGGWISECONDORX ()
+workflow NFCMGG_WISECONDORX {
+    take:
+    samplesheet // channel: samplesheet read in from --input
+
+    main:
+
+    //
+    // WORKFLOW: Run pipeline
+    //
+    WISECONDORX (
+        samplesheet,
+        params.fasta,
+        params.fai,
+        val_bin_sizes,
+        params.no_metrics,
+        params.prefix,
+        params.outdir,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    )
+
+    emit:
+    multiqc_report = WISECONDORX.out.multiqc_report // channel: /path/to/multiqc_report.html
+
 }
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN ALL WORKFLOWS
+    RUN MAIN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-//
-// WORKFLOW: Execute a single named workflow for the pipeline
-// See: https://github.com/nf-core/rnaseq/issues/619
-//
 workflow {
-    CMGG_CMGGWISECONDORX ()
+
+    main:
+
+    //
+    // SUBWORKFLOW: Run initialisation tasks
+    //
+    PIPELINE_INITIALISATION (
+        params.version,
+        params.help,
+        params.validate_params,
+        params.monochrome_logs,
+        args,
+        params.outdir,
+        params.input
+    )
+
+    //
+    // WORKFLOW: Run main workflow
+    //
+    NFCMGG_WISECONDORX (
+        PIPELINE_INITIALISATION.out.samplesheet
+    )
+
+    //
+    // SUBWORKFLOW: Run completion tasks
+    //
+    PIPELINE_COMPLETION (
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url,
+        NFCMGG_WISECONDORX.out.multiqc_report
+    )
 }
 
 /*
diff --git a/modules.json b/modules.json
index 308898e..f2e82b9 100644
--- a/modules.json
+++ b/modules.json
@@ -1,48 +1,62 @@
 {
-    "name": "CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx",
-    "homePage": "https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx",
+    "name": "nf-cmgg/wisecondorx",
+    "homePage": "https://github.com/nf-cmgg/wisecondorx",
     "repos": {
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": ["modules"]
-                    },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
+                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     },
                     "ngsbits/samplegender": {
                         "branch": "master",
-                        "git_sha": "e8d164fa8326069de538f74910d809da9f25826e",
+                        "git_sha": "023e119cfa102f319b6dcfd06abecf7f3c2b8df1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/ngsbits/samplegender/ngsbits-samplegender.diff"
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "git_sha": "f153f1f10e1083c49935565844cccb7453021682",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/index/samtools-index.diff"
                     },
                     "wisecondorx/convert": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "624e8cdc9f416fa7221edb1354374a7e69780e55",
                         "installed_by": ["modules"]
                     },
                     "wisecondorx/newref": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "624e8cdc9f416fa7221edb1354374a7e69780e55",
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "utils_nextflow_pipeline": {
+                        "branch": "master",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfcore_pipeline": {
+                        "branch": "master",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfvalidation_plugin": {
+                        "branch": "master",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
deleted file mode 100644
index 2af59ea..0000000
--- a/modules/local/samplesheet_check.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-process SAMPLESHEET_CHECK {
-    tag "$samplesheet"
-    label 'process_single'
-
-    conda "conda-forge::python=3.8.3"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'biocontainers/python:3.8.3' }"
-
-    input:
-    path samplesheet
-
-    output:
-    path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/bin/
-    """
-    check_samplesheet.py \\
-        $samplesheet \\
-        samplesheet.valid.csv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
deleted file mode 100644
index c9d014b..0000000
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_single'
-
-    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.15"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.yml"    , emit: yml
-    path "software_versions_mqc.yml", emit: mqc_yml
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    template 'dumpsoftwareversions.py'
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index c32657d..0000000
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - dump
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-      licence: ["MIT"]
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@drpatelh"
-  - "@grst"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
deleted file mode 100755
index da03340..0000000
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide functions to merge multiple versions.yml files."""
-
-
-import yaml
-import platform
-from textwrap import dedent
-
-
-def _make_versions_html(versions):
-    """Generate a tabular HTML output of all versions for MultiQC."""
-    html = [
-        dedent(
-            """\\
-            <style>
-            #nf-core-versions tbody:nth-child(even) {
-                background-color: #f2f2f2;
-            }
-            </style>
-            <table class="table" style="width:100%" id="nf-core-versions">
-                <thead>
-                    <tr>
-                        <th> Process Name </th>
-                        <th> Software </th>
-                        <th> Version  </th>
-                    </tr>
-                </thead>
-            """
-        )
-    ]
-    for process, tmp_versions in sorted(versions.items()):
-        html.append("<tbody>")
-        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
-            html.append(
-                dedent(
-                    f"""\\
-                    <tr>
-                        <td><samp>{process if (i == 0) else ''}</samp></td>
-                        <td><samp>{tool}</samp></td>
-                        <td><samp>{version}</samp></td>
-                    </tr>
-                    """
-                )
-            )
-        html.append("</tbody>")
-    html.append("</table>")
-    return "\\n".join(html)
-
-
-def main():
-    """Load all version files and generate merged output."""
-    versions_this_module = {}
-    versions_this_module["${task.process}"] = {
-        "python": platform.python_version(),
-        "yaml": yaml.__version__,
-    }
-
-    with open("$versions") as f:
-        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-    # aggregate versions by the module name (derived from fully-qualified process name)
-    versions_by_module = {}
-    for process, process_versions in versions_by_process.items():
-        module = process.split(":")[-1]
-        try:
-            if versions_by_module[module] != process_versions:
-                raise AssertionError(
-                    "We assume that software versions are the same between all modules. "
-                    "If you see this error-message it means you discovered an edge-case "
-                    "and should open an issue in nf-core/tools. "
-                )
-        except KeyError:
-            versions_by_module[module] = process_versions
-
-    versions_by_module["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
-        "$workflow.manifest.name": "$workflow.manifest.version",
-    }
-
-    versions_mqc = {
-        "id": "software_versions",
-        "section_name": "${workflow.manifest.name} Software Versions",
-        "section_href": "https://github.com/${workflow.manifest.name}",
-        "plot_type": "html",
-        "description": "are collected at run time from the software output.",
-        "data": _make_versions_html(versions_by_module),
-    }
-
-    with open("software_versions.yml", "w") as f:
-        yaml.dump(versions_by_module, f, default_flow_style=False)
-    with open("software_versions_mqc.yml", "w") as f:
-        yaml.dump(versions_mqc, f, default_flow_style=False)
-
-    with open("versions.yml", "w") as f:
-        yaml.dump(versions_this_module, f, default_flow_style=False)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
new file mode 100644
index 0000000..ca39fb6
--- /dev/null
+++ b/modules/nf-core/multiqc/environment.yml
@@ -0,0 +1,7 @@
+name: multiqc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::multiqc=1.21
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 65d7dd0..47ac352 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_single'
 
-    conda "bioconda::multiqc=1.15"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
@@ -25,12 +25,14 @@ process MULTIQC {
     def args = task.ext.args ?: ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
         $extra_config \\
+        $logo \\
         .
 
     cat <<-END_VERSIONS > versions.yml
@@ -41,7 +43,7 @@ process MULTIQC {
 
     stub:
     """
-    touch multiqc_data
+    mkdir multiqc_data
     touch multiqc_plots
     touch multiqc_report.html
 
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index f93b5ee..45a9bc3 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,4 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
-name: MultiQC
+name: multiqc
 description: Aggregate results from bioinformatics analyses across many samples into a single report
 keywords:
   - QC
@@ -13,7 +12,6 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
-
 input:
   - multiqc_files:
       type: file
@@ -31,7 +29,6 @@ input:
       type: file
       description: Optional logo file for MultiQC
       pattern: "*.{png}"
-
 output:
   - report:
       type: file
@@ -54,3 +51,8 @@ authors:
   - "@bunop"
   - "@drpatelh"
   - "@jfy133"
+maintainers:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
new file mode 100644
index 0000000..f1c4242
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -0,0 +1,84 @@
+nextflow_process {
+
+    name "Test Process MULTIQC"
+    script "../main.nf"
+    process "MULTIQC"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "multiqc"
+
+    test("sarscov2 single-end [fastqc]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
+            )
+        }
+
+    }
+
+    test("sarscov2 single-end [fastqc] [config]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.report.collect { file(it).getName() } +
+                                process.out.data.collect { file(it).getName() } +
+                                process.out.plots.collect { file(it).getName() } +
+                                process.out.versions ).match("multiqc_stub") }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
new file mode 100644
index 0000000..bfebd80
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -0,0 +1,41 @@
+{
+    "multiqc_versions_single": {
+        "content": [
+            [
+                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-29T08:48:55.657331"
+    },
+    "multiqc_stub": {
+        "content": [
+            [
+                "multiqc_report.html",
+                "multiqc_data",
+                "multiqc_plots",
+                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-29T08:49:49.071937"
+    },
+    "multiqc_versions_config": {
+        "content": [
+            [
+                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-29T08:49:25.457567"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
new file mode 100644
index 0000000..bea6c0d
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/tags.yml
@@ -0,0 +1,2 @@
+multiqc:
+  - modules/nf-core/multiqc/**
diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml
new file mode 100644
index 0000000..486c233
--- /dev/null
+++ b/modules/nf-core/ngsbits/samplegender/environment.yml
@@ -0,0 +1,7 @@
+name: ngsbits_samplegender
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ngs-bits=2023_02
diff --git a/modules/nf-core/ngsbits/samplegender/main.nf b/modules/nf-core/ngsbits/samplegender/main.nf
index b15f9d4..2e9d3f1 100644
--- a/modules/nf-core/ngsbits/samplegender/main.nf
+++ b/modules/nf-core/ngsbits/samplegender/main.nf
@@ -2,7 +2,7 @@ process NGSBITS_SAMPLEGENDER {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::ngs-bits=2023_02"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ngs-bits:2023_02--py311ha0b7adc_2':
         'biocontainers/ngs-bits:2023_02--py311ha0b7adc_2' }"
diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml
index ecb6a18..961462b 100644
--- a/modules/nf-core/ngsbits/samplegender/meta.yml
+++ b/modules/nf-core/ngsbits/samplegender/meta.yml
@@ -12,8 +12,7 @@ tools:
       homepage: "https://github.com/imgag/ngs-bits"
       documentation: "https://github.com/imgag/ngs-bits"
       tool_dev_url: "https://github.com/imgag/ngs-bits"
-      licence: "['MIT license']"
-
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -50,7 +49,6 @@ input:
       type: string
       description: The method to use to define the gender (posibilities are 'xy', 'hetx' and 'sry')
       pattern: "(xy|hetx|sry)"
-
 output:
   - meta:
       type: map
@@ -65,6 +63,7 @@ output:
       type: file
       description: An output TSV file containing the results of the gender prediction
       pattern: "*.tsv"
-
 authors:
   - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test
new file mode 100644
index 0000000..2cf4757
--- /dev/null
+++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test
@@ -0,0 +1,47 @@
+nextflow_process {
+
+    name "Test Process NGSBITS_SAMPLEGENDER"
+    script "../main.nf"
+    process "NGSBITS_SAMPLEGENDER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ngsbits"
+    tag "ngsbits/samplegender"
+
+    // Only a stub test here because the modules needs the full chrX and chrY
+    test("homo_sapiens - bam, bai, [], [], sry - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'reference'], // meta map
+                    []
+                ]
+                input[2] = [
+                    [ id:'reference'], // meta map
+                    []
+                ]
+                input[3] = "sry"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap
new file mode 100644
index 0000000..48fd8af
--- /dev/null
+++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "homo_sapiens - bam, bai, [], [], sry - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,72f3e70be3e6a734bf39d1a6bf6d604b"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,72f3e70be3e6a734bf39d1a6bf6d604b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-03-18T15:36:37.639882564"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ngsbits/samplegender/tests/tags.yml b/modules/nf-core/ngsbits/samplegender/tests/tags.yml
new file mode 100644
index 0000000..8b7a0da
--- /dev/null
+++ b/modules/nf-core/ngsbits/samplegender/tests/tags.yml
@@ -0,0 +1,2 @@
+ngsbits/samplegender:
+  - "modules/nf-core/ngsbits/samplegender/**"
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
new file mode 100644
index 0000000..9c24eb0
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -0,0 +1,10 @@
+name: samtools_faidx
+
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.19.2
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index 59ed308..cfe7ad9 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX {
     tag "$fasta"
     label 'process_single'
 
-    conda "bioconda::samtools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
+        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index 957b25e..f3c25de 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -39,6 +39,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - fa:
+      type: file
+      description: FASTA file
+      pattern: "*.{fa}"
   - fai:
       type: file
       description: FASTA index file
@@ -55,3 +59,7 @@ authors:
   - "@drpatelh"
   - "@ewels"
   - "@phue"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
+  - "@phue"
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test
new file mode 100644
index 0000000..17244ef
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test
@@ -0,0 +1,122 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_FAIDX"
+    script "../main.nf"
+    process "SAMTOOLS_FAIDX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/faidx"
+
+    test("test_samtools_faidx") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_bgzip") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_fasta") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_stub_fasta") {
+
+        config "./nextflow2.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_stub_fai") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
new file mode 100644
index 0000000..3e651ef
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
@@ -0,0 +1,249 @@
+{
+    "test_samtools_faidx": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:22:39.412601"
+    },
+    "test_samtools_faidx_bgzip": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:23:22.427966"
+    },
+    "test_samtools_faidx_fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
+                    ]
+                ],
+                "fai": [
+                    
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:24:04.107537"
+    },
+    "test_samtools_faidx_stub_fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "fai": [
+                    
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:24:45.868463"
+    },
+    "test_samtools_faidx_stub_fai": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:25:27.550554"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config
new file mode 100644
index 0000000..f76a3ba
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_FAIDX {
+        ext.args = 'MT192765.1 -o extract.fa'
+    }
+
+}
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config
new file mode 100644
index 0000000..33ebbd5
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config
@@ -0,0 +1,6 @@
+process {
+
+    withName: SAMTOOLS_FAIDX {
+        ext.args = '-o extract.fa'
+    }
+}
diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml
new file mode 100644
index 0000000..e4a8394
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/tags.yml
@@ -0,0 +1,2 @@
+samtools/faidx:
+  - modules/nf-core/samtools/faidx/**
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
new file mode 100644
index 0000000..a5e5064
--- /dev/null
+++ b/modules/nf-core/samtools/index/environment.yml
@@ -0,0 +1,8 @@
+name: samtools_index
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.19.2
+  - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index a770851..b5f7e61 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::samtools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
+        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
index 8bd2fa6..01a4ee0 100644
--- a/modules/nf-core/samtools/index/meta.yml
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -51,3 +51,7 @@ authors:
   - "@drpatelh"
   - "@ewels"
   - "@maxulysse"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
+  - "@maxulysse"
diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config
new file mode 100644
index 0000000..0ed260e
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_INDEX {
+        ext.args = '-c'
+    }
+
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test
new file mode 100644
index 0000000..bb7756d
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_INDEX"
+    script "../main.nf"
+    process "SAMTOOLS_INDEX"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/index"
+
+    test("bai") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.bai).match("bai") },
+                { assert snapshot(process.out.versions).match("bai_versions") }
+            )
+        }
+    }
+
+    test("crai") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.crai).match("crai") },
+                { assert snapshot(process.out.versions).match("crai_versions") }
+            )
+        }
+    }
+
+    test("csi") {
+
+        config "./csi.nextflow.config"
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.csi.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match("csi_versions") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
new file mode 100644
index 0000000..3dc8e7d
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap
@@ -0,0 +1,74 @@
+{
+    "crai_versions": {
+        "content": [
+            [
+                "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:12:00.324667957"
+    },
+    "csi_versions": {
+        "content": [
+            [
+                "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:12:07.885103162"
+    },
+    "crai": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T18:41:38.446424"
+    },
+    "bai": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T18:40:46.579747"
+    },
+    "bai_versions": {
+        "content": [
+            [
+                "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:11:51.641425452"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml
new file mode 100644
index 0000000..e0f58a7
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/tags.yml
@@ -0,0 +1,2 @@
+samtools/index:
+  - modules/nf-core/samtools/index/**
diff --git a/modules/nf-core/wisecondorx/convert/environment.yml b/modules/nf-core/wisecondorx/convert/environment.yml
new file mode 100644
index 0000000..6b26f79
--- /dev/null
+++ b/modules/nf-core/wisecondorx/convert/environment.yml
@@ -0,0 +1,7 @@
+name: wisecondorx_convert
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::wisecondorx=1.2.5
diff --git a/modules/nf-core/wisecondorx/convert/main.nf b/modules/nf-core/wisecondorx/convert/main.nf
index 68e1554..3602b1e 100644
--- a/modules/nf-core/wisecondorx/convert/main.nf
+++ b/modules/nf-core/wisecondorx/convert/main.nf
@@ -3,7 +3,7 @@ process WISECONDORX_CONVERT {
     label 'process_low'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::wisecondorx=1.2.5"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/wisecondorx:1.2.5--pyh5e36f6f_0':
         'biocontainers/wisecondorx:1.2.5--pyh5e36f6f_0' }"
diff --git a/modules/nf-core/wisecondorx/convert/meta.yml b/modules/nf-core/wisecondorx/convert/meta.yml
index 06c1069..d70d9d6 100644
--- a/modules/nf-core/wisecondorx/convert/meta.yml
+++ b/modules/nf-core/wisecondorx/convert/meta.yml
@@ -11,8 +11,7 @@ tools:
       documentation: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
-      licence: "['Attribution-NonCommercial-ShareAlike CC BY-NC-SA']"
-
+      licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
 input:
   - meta:
       type: map
@@ -45,7 +44,6 @@ input:
       type: file
       description: The index of the reference FASTA file (mandatory when using CRAM files)
       pattern: "*.fai"
-
 output:
   - meta:
       type: map
@@ -60,6 +58,7 @@ output:
       type: file
       description: The output NPZ file
       pattern: "*.npz"
-
 authors:
   - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/wisecondorx/convert/tests/main.nf.test b/modules/nf-core/wisecondorx/convert/tests/main.nf.test
new file mode 100644
index 0000000..1e093e9
--- /dev/null
+++ b/modules/nf-core/wisecondorx/convert/tests/main.nf.test
@@ -0,0 +1,97 @@
+nextflow_process {
+
+    name "Test Process WISECONDORX_CONVERT"
+    script "../main.nf"
+    process "WISECONDORX_CONVERT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "wisecondorx"
+    tag "wisecondorx/convert"
+
+    test("sarscov2 - bam, bai, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+                ]
+                input[1] = [[], []]
+                input[2] = [[], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - cram, crai, fasta, fai") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+                ]
+
+                input[1] = [
+                    [ id:'test' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+
+                input[2] = [
+                    [ id:'test' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam, bai - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+                ]
+                input[1] = [[], []]
+                input[2] = [[], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap b/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap
new file mode 100644
index 0000000..ac252a1
--- /dev/null
+++ b/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap
@@ -0,0 +1,107 @@
+{
+    "sarscov2 - cram, crai, fasta, fai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.npz:md5,154337aa93ceddf15ea7382969588524"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,917a47772d6f722fe520f900827fae01"
+                ],
+                "npz": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.npz:md5,154337aa93ceddf15ea7382969588524"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,917a47772d6f722fe520f900827fae01"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-03-18T16:57:23.88568683"
+    },
+    "sarscov2 - bam, bai, [], []": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.npz:md5,00c8acf1727e9eb78e56bce28b09ee3b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,917a47772d6f722fe520f900827fae01"
+                ],
+                "npz": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.npz:md5,00c8acf1727e9eb78e56bce28b09ee3b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,917a47772d6f722fe520f900827fae01"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-03-18T16:58:57.092145603"
+    },
+    "sarscov2 - bam, bai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.npz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,917a47772d6f722fe520f900827fae01"
+                ],
+                "npz": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.npz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,917a47772d6f722fe520f900827fae01"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-03-18T16:59:20.717480551"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/wisecondorx/convert/tests/tags.yml b/modules/nf-core/wisecondorx/convert/tests/tags.yml
new file mode 100644
index 0000000..0c3526e
--- /dev/null
+++ b/modules/nf-core/wisecondorx/convert/tests/tags.yml
@@ -0,0 +1,2 @@
+wisecondorx/convert:
+  - "modules/nf-core/wisecondorx/convert/**"
diff --git a/modules/nf-core/wisecondorx/newref/environment.yml b/modules/nf-core/wisecondorx/newref/environment.yml
new file mode 100644
index 0000000..bbda811
--- /dev/null
+++ b/modules/nf-core/wisecondorx/newref/environment.yml
@@ -0,0 +1,7 @@
+name: wisecondorx_newref
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::wisecondorx=1.2.5
diff --git a/modules/nf-core/wisecondorx/newref/main.nf b/modules/nf-core/wisecondorx/newref/main.nf
index fddd383..c029764 100644
--- a/modules/nf-core/wisecondorx/newref/main.nf
+++ b/modules/nf-core/wisecondorx/newref/main.nf
@@ -3,7 +3,7 @@ process WISECONDORX_NEWREF {
     label 'process_medium'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::wisecondorx=1.2.5"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/wisecondorx:1.2.5--pyh5e36f6f_0':
         'biocontainers/wisecondorx:1.2.5--pyh5e36f6f_0' }"
diff --git a/modules/nf-core/wisecondorx/newref/meta.yml b/modules/nf-core/wisecondorx/newref/meta.yml
index 9e862a8..d5efefe 100644
--- a/modules/nf-core/wisecondorx/newref/meta.yml
+++ b/modules/nf-core/wisecondorx/newref/meta.yml
@@ -11,8 +11,7 @@ tools:
       documentation: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
-      licence: "['Attribution-NonCommercial-ShareAlike CC BY-NC-SA']"
-
+      licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
 input:
   - meta:
       type: map
@@ -23,7 +22,6 @@ input:
       type: file
       description: Multiple NPZ files from healthy patients
       pattern: "*.{npz}"
-
 output:
   - meta:
       type: map
@@ -38,6 +36,7 @@ output:
       type: file
       description: The reference NPZ file
       pattern: "*.{npz}"
-
 authors:
   - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/wisecondorx/newref/tests/main.nf.test b/modules/nf-core/wisecondorx/newref/tests/main.nf.test
new file mode 100644
index 0000000..4ce9370
--- /dev/null
+++ b/modules/nf-core/wisecondorx/newref/tests/main.nf.test
@@ -0,0 +1,65 @@
+nextflow_process {
+
+    name "Test Process WISECONDORX_NEWREF"
+    script "../main.nf"
+    process "WISECONDORX_NEWREF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "wisecondorx"
+    tag "wisecondorx/newref"
+    tag "wisecondorx/convert"
+
+    test("homo_sapiens - [npz]") {
+
+        // Stub run because this process needs at least 30 samples to succesfully run
+        options "-stub"
+
+        setup {
+            run("WISECONDORX_CONVERT") {
+                script "../../convert/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test' ], // meta map
+                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                    ],
+                    [
+                        [ id: 'test2' ],
+                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+                    ])
+                    input[1] = [[],[]]
+                    input[2] = [[],[]]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = WISECONDORX_CONVERT.out.npz
+                    .map { meta, npz ->
+                        new_meta = meta + [id:"combined"]
+                        [new_meta, npz]
+                    }
+                    .groupTuple()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.npz.collect { it.collect { it instanceof Map ? it : file(it).name }}
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/wisecondorx/newref/tests/main.nf.test.snap b/modules/nf-core/wisecondorx/newref/tests/main.nf.test.snap
new file mode 100644
index 0000000..911cf7a
--- /dev/null
+++ b/modules/nf-core/wisecondorx/newref/tests/main.nf.test.snap
@@ -0,0 +1,22 @@
+{
+    "homo_sapiens - [npz]": {
+        "content": [
+            [
+                "versions.yml:md5,76cc7a445641380597ca00dfb5722c92"
+            ],
+            [
+                [
+                    {
+                        "id": "combined"
+                    },
+                    "combined.npz"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-03-19T10:39:17.199036914"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/wisecondorx/newref/tests/nextflow.config b/modules/nf-core/wisecondorx/newref/tests/nextflow.config
new file mode 100644
index 0000000..ddbf6b7
--- /dev/null
+++ b/modules/nf-core/wisecondorx/newref/tests/nextflow.config
@@ -0,0 +1,4 @@
+process {
+    withName: WISECONDORX_CONVERT {
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/wisecondorx/newref/tests/tags.yml b/modules/nf-core/wisecondorx/newref/tests/tags.yml
new file mode 100644
index 0000000..cbe8192
--- /dev/null
+++ b/modules/nf-core/wisecondorx/newref/tests/tags.yml
@@ -0,0 +1,2 @@
+wisecondorx/newref:
+  - "modules/nf-core/wisecondorx/newref/**"
diff --git a/nextflow.config b/nextflow.config
index 4d25b17..f5590af 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx Nextflow config file
+    nf-cmgg/wisecondorx Nextflow config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Default config options for all compute environments
 ----------------------------------------------------------------------------------------
@@ -15,7 +15,7 @@ params {
 
     // Other options
     no_metrics                 = false
-    bin_sizes                  = "1000000,500000,50000,30000,15000,10000,5000,1000"
+    bin_sizes                  = "1000,500,50,30,15,10,5,1"
 
     // References
     genome                     = "GRCh38"
@@ -33,7 +33,6 @@ params {
 
     // Boilerplate options
     outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
@@ -42,19 +41,14 @@ params {
     hook_url                   = null
     help                       = false
     version                    = false
-    validate_params            = true
-    validationSchemaIgnoreParams     = 'genomes,test_data,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
 
     // Config options
+    config_profile_name        = null
+    config_profile_description = null
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_description = null
     config_profile_contact     = null
     config_profile_url         = null
-    config_profile_name        = null
-
 
     // Max resource options
     // Defaults only, expecting to be overwritten
@@ -62,6 +56,9 @@ params {
     max_cpus                   = 16
     max_time                   = '240.h'
 
+    // Schema validation default options
+    validate_params                  = true
+
 }
 
 // Load base.config by default for all pipelines
@@ -74,26 +71,23 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-// Load CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
+// Load nf-cmgg/wisecondorx custom profiles from different institutions.
+// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
 // try {
-//   includeConfig "${params.custom_config_base}/pipeline/nf-cmgg-wisecondorx.config"
+//   includeConfig "${params.custom_config_base}/pipeline/wisecondorx.config"
 // } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/nf-cmgg-wisecondorx profiles: ${params.custom_config_base}/pipeline/nf-cmgg-wisecondorx.config")
+//   System.err.println("WARNING: Could not load nf-core/config/wisecondorx profiles: ${params.custom_config_base}/pipeline/wisecondorx.config")
 // }
 
 // Include test data config
 includeConfig 'https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/nf-cmgg-testdata.config'
 
-plugins {
-    id 'nf-validation@0.2.1'
-}
-
 profiles {
     debug {
         dumpHashes             = true
         process.beforeScript   = 'echo $HOSTNAME'
-        cleanup = false
+        cleanup                = false
+        nextflow.enable.configProcessNamesValidation = true
     }
     conda {
         conda.enabled          = true
@@ -102,6 +96,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        channels               = ['conda-forge', 'bioconda', 'defaults']
         apptainer.enabled      = false
     }
     mamba {
@@ -116,17 +111,16 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        docker.registry        = 'quay.io'
-        docker.userEmulation   = true
         conda.enabled          = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
+        docker.runOptions      = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled    = true
@@ -140,7 +134,6 @@ profiles {
     }
     podman {
         podman.enabled         = true
-        podman.registry        = 'quay.io'
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -168,6 +161,7 @@ profiles {
     }
     apptainer {
         apptainer.enabled      = true
+        apptainer.autoMounts   = true
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -177,14 +171,32 @@ profiles {
     }
     gitpod {
         executor.name          = 'local'
-        executor.cpus          = 16
-        executor.memory        = 60.GB
+        executor.cpus          = 4
+        executor.memory        = 8.GB
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
-    nf_test   { includeConfig 'conf/nf_test.config'   }
 }
 
+// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry   = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
+
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.0.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+validation {
+    failUnrecognisedParams = false
+    lenientMode            = false
+    defaultIgnoreParams    = ['genomes','igenomes_base','test_data']
+    showHiddenParams       = false
+}
 
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
@@ -209,32 +221,35 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
+// 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    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {
-    name            = 'CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx'
+    name            = 'nf-cmgg/wisecondorx'
     author          = """nvnieuwk"""
-    homePage        = 'https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx'
+    homePage        = 'https://github.com/nf-cmgg/wisecondorx'
     description     = """A nextflow pipeline for creating references for WisecondorX"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.10.1'
-    version = '1.1.0'
+    nextflowVersion = '!>=23.10.0'
+    version         = '1.2.0'
     doi             = ''
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f61d761..f60e7ea 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/master/nextflow_schema.json",
-    "title": "CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx pipeline parameters",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-cmgg/wisecondorx/master/nextflow_schema.json",
+    "title": "nf-cmgg/wisecondorx pipeline parameters",
     "description": "A nextflow pipeline for creating references for WisecondorX",
     "type": "object",
-    "definitions": {
+    "defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -15,9 +15,10 @@
                 "input": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
+                    "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
-                    "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
                     "fa_icon": "fas fa-file-csv"
@@ -30,7 +31,6 @@
                 },
                 "prefix": {
                     "type": "string",
-                    "default": "None",
                     "description": "The prefix to be used for the output file. If this parameter isn't given, the following format will be used: WisecondorX_DDMMYYYY"
                 },
                 "email": {
@@ -59,8 +59,8 @@
                 },
                 "bin_sizes": {
                     "type": "string",
-                    "description": "A comma-delimited list of bin sizes to use for the analysis",
-                    "default": "1000000,500000,50000,30000,15000,10000,5000,1000"
+                    "description": "A comma-delimited list of bin sizes in kilobases to use for the analysis",
+                    "default": "1000,500,50,30,15,10,5,1"
                 }
             }
         },
@@ -79,6 +79,7 @@
                 "fasta": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
                     "mimetype": "text/plain",
                     "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                     "description": "Path to FASTA genome file.",
@@ -95,7 +96,6 @@
                 },
                 "genomes_base": {
                     "type": "string",
-                    "default": "None",
                     "description": "The path to the directory containing the files specified by the CMGG references config."
                 },
                 "genomes_ignore": {
@@ -111,7 +111,6 @@
                     "type": "string",
                     "format": "directory-path",
                     "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes",
                     "fa_icon": "fas fa-cloud-download-alt",
                     "hidden": true
                 },
@@ -201,7 +200,7 @@
                     "description": "Maximum amount of time that can be requested for any single job.",
                     "default": "240.h",
                     "fa_icon": "far fa-clock",
-                    "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
+                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
                     "hidden": true,
                     "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
                 }
@@ -272,6 +271,7 @@
                 },
                 "multiqc_config": {
                     "type": "string",
+                    "format": "file-path",
                     "description": "Custom config file to supply to MultiQC.",
                     "fa_icon": "fas fa-cog",
                     "hidden": true
@@ -287,13 +287,6 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
-                "tracedir": {
-                    "type": "string",
-                    "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/pipeline_info",
-                    "fa_icon": "fas fa-cogs",
-                    "hidden": true
-                },
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",
@@ -303,7 +296,7 @@
                 },
                 "validationSchemaIgnoreParams": {
                     "type": "string",
-                    "default": "genomes,test_data",
+                    "default": "genomes,igenomes_base,test_data",
                     "hidden": true
                 },
                 "validationShowHiddenParams": {
@@ -332,22 +325,22 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/other_options"
+            "$ref": "#/defs/other_options"
         },
         {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/defs/max_job_request_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/defs/generic_options"
         }
     ]
 }
diff --git a/nf-test.config b/nf-test.config
index 75570e9..2fa82ad 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,6 +3,6 @@ config {
     testsDir "tests"
     workDir ".nf-test"
     configFile "tests/nextflow.config"
-    profile "nf_test,docker"
+    profile "docker"
 
 }
diff --git a/pipeline_template.yml b/pipeline_template.yml
deleted file mode 100644
index 990055a..0000000
--- a/pipeline_template.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-author: nvnieuwk
-description: A nextflow pipeline for creating references for WisecondorX
-name: nf-cmgg-wisecondorx
-prefix: CenterForMedicalGeneticsGhent
diff --git a/pyproject.toml b/pyproject.toml
index 0d62beb..5611062 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,10 +1,15 @@
-# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
 # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.black]
+[tool.ruff]
 line-length = 120
-target_version = ["py37", "py38", "py39", "py310"]
+target-version = "py38"
+cache-dir = "~/.cache/ruff"
 
-[tool.isort]
-profile = "black"
-known_first_party = ["nf_core"]
-multi_line_output = 3
+[tool.ruff.lint]
+select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["nf_core"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
deleted file mode 100644
index 0aecf87..0000000
--- a/subworkflows/local/input_check.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-//
-// Check input samplesheet and get read channels
-//
-
-include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
-
-workflow INPUT_CHECK {
-    take:
-    samplesheet // file: /path/to/samplesheet.csv
-
-    main:
-    SAMPLESHEET_CHECK ( samplesheet )
-        .csv
-        .splitCsv ( header:true, sep:',' )
-        .map { create_fastq_channel(it) }
-        .set { reads }
-
-    emit:
-    reads                                     // channel: [ val(meta), [ reads ] ]
-    versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
-}
-
-// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
-def create_fastq_channel(LinkedHashMap row) {
-    // create meta map
-    def meta = [:]
-    meta.id         = row.sample
-    meta.single_end = row.single_end.toBoolean()
-
-    // add path(s) of the fastq file(s) to the meta map
-    def fastq_meta = []
-    if (!file(row.fastq_1).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
-    }
-    if (meta.single_end) {
-        fastq_meta = [ meta, [ file(row.fastq_1) ] ]
-    } else {
-        if (!file(row.fastq_2).exists()) {
-            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
-        }
-        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
-    }
-    return fastq_meta
-}
diff --git a/subworkflows/local/utils_nfcore_wisecondorx_pipeline/main.nf b/subworkflows/local/utils_nfcore_wisecondorx_pipeline/main.nf
new file mode 100644
index 0000000..3758924
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_wisecondorx_pipeline/main.nf
@@ -0,0 +1,235 @@
+//
+// Subworkflow with functionality specific to the nf-cmgg/wisecondorx pipeline
+//
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
+include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
+include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+
+/*
+========================================================================================
+    SUBWORKFLOW TO INITIALISE PIPELINE
+========================================================================================
+*/
+
+workflow PIPELINE_INITIALISATION {
+
+    take:
+    version           // boolean: Display version and exit
+    help              // boolean: Display help text
+    validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
+    monochrome_logs   // boolean: Do not use coloured log outputs
+    nextflow_cli_args //   array: List of positional nextflow CLI args
+    outdir            //  string: The output directory where the results will be saved
+    input             //  string: Path to input samplesheet
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // Print version and exit if required and dump pipeline parameters to JSON file
+    //
+    UTILS_NEXTFLOW_PIPELINE (
+        version,
+        true,
+        outdir,
+        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
+    )
+
+    //
+    // Validate parameters and generate parameter summary to stdout
+    //
+    pre_help_text = nfCoreLogo(monochrome_logs)
+    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
+    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+    UTILS_NFVALIDATION_PLUGIN (
+        help,
+        workflow_command,
+        pre_help_text,
+        post_help_text,
+        validate_params,
+        "nextflow_schema.json"
+    )
+
+    //
+    // Check config provided to the pipeline
+    //
+    UTILS_NFCORE_PIPELINE (
+        nextflow_cli_args
+    )
+    //
+    // Custom validation for pipeline parameters
+    //
+    validateInputParameters()
+
+    //
+    // Create channel from input file provided through params.input
+    //
+
+    Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
+        .set { ch_samplesheet }
+
+    emit:
+    samplesheet = ch_samplesheet
+    versions    = ch_versions
+}
+
+/*
+========================================================================================
+    SUBWORKFLOW FOR PIPELINE COMPLETION
+========================================================================================
+*/
+
+workflow PIPELINE_COMPLETION {
+
+    take:
+    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
+    multiqc_report  //  string: Path to MultiQC report
+
+    main:
+
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+
+    //
+    // Completion email and summary
+    //
+    workflow.onComplete {
+        if (email || email_on_fail) {
+            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+        }
+
+        completionSummary(monochrome_logs)
+
+        if (hook_url) {
+            imNotification(summary_params, hook_url)
+        }
+    }
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+//
+// Check and validate pipeline parameters
+//
+def validateInputParameters() {
+    genomeExistsError()
+}
+
+//
+// Validate channels from input samplesheet
+//
+def validateInputSamplesheet(input) {
+    def (metas, fastqs) = input[1..2]
+
+    // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
+    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    if (!endedness_ok) {
+        error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
+    }
+
+    return [ metas[0], fastqs ]
+}
+//
+// Get attribute from genome config file e.g. fasta
+//
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[ params.genome ].containsKey(attribute)) {
+            return params.genomes[ params.genome ][ attribute ]
+        }
+    }
+    return null
+}
+
+//
+// Exit pipeline if incorrect --genome key provided
+//
+def genomeExistsError() {
+    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+            "  Currently, the available genome keys are:\n" +
+            "  ${params.genomes.keySet().join(", ")}\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        error(error_string)
+    }
+}
+
+//
+// Generate methods description for MultiQC
+//
+def toolCitationText() {
+    // TODO nf-core: Optionally add in-text citation tools to this list.
+    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
+    // Uncomment function in methodsDescriptionText to render in MultiQC report
+    def citation_text = [
+            "Tools used in the workflow included:",
+            "FastQC (Andrews 2010),",
+            "MultiQC (Ewels et al. 2016)",
+            "."
+        ].join(' ').trim()
+
+    return citation_text
+}
+
+def toolBibliographyText() {
+    // TODO nf-core: Optionally add bibliographic entries to this list.
+    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
+    // Uncomment function in methodsDescriptionText to render in MultiQC report
+    def reference_text = [
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+        ].join(' ').trim()
+
+    return reference_text
+}
+
+def methodsDescriptionText(mqc_methods_yaml) {
+    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    def meta = [:]
+    meta.workflow = workflow.toMap()
+    meta["manifest_map"] = workflow.manifest.toMap()
+
+    // Pipeline DOI
+    meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
+    meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+    // Tool references
+    meta["tool_citations"] = ""
+    meta["tool_bibliography"] = ""
+
+    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+    // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    // meta["tool_bibliography"] = toolBibliographyText()
+
+
+    def methods_text = mqc_methods_yaml.text
+
+    def engine =  new groovy.text.SimpleTemplateEngine()
+    def description_html = engine.createTemplate(methods_text).make(meta)
+
+    return description_html.toString()
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
new file mode 100644
index 0000000..ac31f28
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -0,0 +1,126 @@
+//
+// Subworkflow with functionality that may be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NEXTFLOW_PIPELINE {
+
+    take:
+    print_version        // boolean: print version
+    dump_parameters      // boolean: dump parameters
+    outdir               //    path: base directory used to publish pipeline results
+    check_conda_channels // boolean: check conda channels
+
+    main:
+
+    //
+    // Print workflow version and exit on --version
+    //
+    if (print_version) {
+        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        System.exit(0)
+    }
+
+    //
+    // Dump pipeline parameters to a JSON file
+    //
+    if (dump_parameters && outdir) {
+        dumpParametersToJSON(outdir)
+    }
+
+    //
+    // When running with Conda, warn if channels have not been set-up appropriately
+    //
+    if (check_conda_channels) {
+        checkCondaChannels()
+    }
+
+    emit:
+    dummy_emit = true
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Generate version string
+//
+def getWorkflowVersion() {
+    String version_string = ""
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
+//
+// Dump pipeline parameters to a JSON file
+//
+def dumpParametersToJSON(outdir) {
+    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    def filename   = "params_${timestamp}.json"
+    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
+    def jsonStr    = JsonOutput.toJson(params)
+    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+
+    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    temp_pf.delete()
+}
+
+//
+// When running with -profile conda, warn if channels have not been set-up appropriately
+//
+def checkCondaChannels() {
+    Yaml parser = new Yaml()
+    def channels = []
+    try {
+        def config = parser.load("conda config --show channels".execute().text)
+        channels = config.channels
+    } catch(NullPointerException | IOException e) {
+        log.warn "Could not verify conda channel configuration."
+        return
+    }
+
+    // Check that all channels are present
+    // This channel list is ordered by required channel priority.
+    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    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
+    def n = required_channels_in_order.size()
+    for (int i = 0; i < n - 1; i++) {
+        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+    }
+
+    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" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
new file mode 100644
index 0000000..e5c3a0a
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
@@ -0,0 +1,38 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NEXTFLOW_PIPELINE"
+description: Subworkflow with functionality that may be useful for any Nextflow pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input:
+  - print_version:
+      type: boolean
+      description: |
+        Print the version of the pipeline and exit
+  - dump_parameters:
+      type: boolean
+      description: |
+        Dump the parameters of the pipeline to a JSON file
+  - output_directory:
+      type: directory
+      description: Path to output dir to write JSON file to.
+      pattern: "results/"
+  - check_conda_channel:
+      type: boolean
+      description: |
+        Check if the conda channel priority is correct.
+output:
+  - dummy_emit:
+      type: boolean
+      description: |
+        Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@adamrtalbot"
+  - "@drpatelh"
+maintainers:
+  - "@adamrtalbot"
+  - "@drpatelh"
+  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
new file mode 100644
index 0000000..68718e4
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -0,0 +1,54 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
+    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+    tag 'subworkflows'
+    tag 'utils_nextflow_pipeline'
+    tag 'subworkflows/utils_nextflow_pipeline'
+
+    test("Test Function getWorkflowVersion") {
+
+        function "getWorkflowVersion"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function dumpParametersToJSON") {
+
+        function "dumpParametersToJSON"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                input[0] = "$outputDir"
+                """.stripIndent()
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success }
+            )
+        }
+    }
+
+    test("Test Function checkCondaChannels") {
+
+        function "checkCondaChannels"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 0000000..e3f0baf
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,20 @@
+{
+    "Test Function getWorkflowVersion": {
+        "content": [
+            "v9.9.9"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:05.308243"
+    },
+    "Test Function checkCondaChannels": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:12.425833"
+    }
+}
\ No newline at end of file
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
new file mode 100644
index 0000000..ca964ce
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,111 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NEXTFLOW_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+    workflow "UTILS_NEXTFLOW_PIPELINE"
+    tag 'subworkflows'
+    tag 'utils_nextflow_pipeline'
+    tag 'subworkflows/utils_nextflow_pipeline'
+
+    test("Should run no inputs") {
+
+        when {
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = false
+                outdir               = null
+                check_conda_channels = false
+
+                input[0] = print_version
+                input[1] = dump_parameters
+                input[2] = outdir
+                input[3] = check_conda_channels
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should print version") {
+
+        when {
+            workflow {
+                """
+                print_version        = true
+                dump_parameters      = false
+                outdir               = null
+                check_conda_channels = false
+
+                input[0] = print_version
+                input[1] = dump_parameters
+                input[2] = outdir
+                input[3] = check_conda_channels
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
+            )
+        }
+    }
+
+    test("Should dump params") {
+
+        when {
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = true
+                outdir               = 'results'
+                check_conda_channels = false
+
+                input[0] = false
+                input[1] = true
+                input[2] = outdir
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should not create params JSON if no output directory") {
+
+        when {
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = true
+                outdir               = null
+                check_conda_channels = false
+
+                input[0] = false
+                input[1] = true
+                input[2] = outdir
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
new file mode 100644
index 0000000..d0a926b
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
new file mode 100644
index 0000000..f847611
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nextflow_pipeline:
+  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
new file mode 100644
index 0000000..a8b55d6
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -0,0 +1,440 @@
+//
+// Subworkflow with utility functions specific to the nf-core pipeline template
+//
+
+import org.yaml.snakeyaml.Yaml
+import nextflow.extension.FilesEx
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFCORE_PIPELINE {
+
+    take:
+    nextflow_cli_args
+
+    main:
+    valid_config = checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args)
+
+    emit:
+    valid_config
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
+//
+def checkConfigProvided() {
+    valid_config = true
+    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        valid_config = false
+    }
+    return valid_config
+}
+
+//
+// Exit pipeline if --profile contains spaces
+//
+def checkProfileProvided(nextflow_cli_args) {
+    if (workflow.profile.endsWith(',')) {
+        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+    if (nextflow_cli_args[0]) {
+        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+}
+
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The pipeline\n" +
+        "  ${workflow.manifest.doi}\n\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
+//
+// Generate workflow version string
+//
+def getWorkflowVersion() {
+    String version_string = ""
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
+//
+// Get software versions for pipeline
+//
+def processVersionsFromYAML(yaml_file) {
+    Yaml yaml = new Yaml()
+    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    return yaml.dumpAsMap(versions).trim()
+}
+
+//
+// Get workflow version for pipeline
+//
+def workflowVersionToYAML() {
+    return """
+    Workflow:
+        $workflow.manifest.name: ${getWorkflowVersion()}
+        Nextflow: $workflow.nextflow.version
+    """.stripIndent().trim()
+}
+
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions) {
+    return ch_versions
+                .unique()
+                .map { processVersionsFromYAML(it) }
+                .unique()
+                .mix(Channel.of(workflowVersionToYAML()))
+}
+
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+    def summary_section = ''
+    for (group in summary_params.keySet()) {
+        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
+        if (group_params) {
+            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+            summary_section += "    <dl class=\"dl-horizontal\">\n"
+            for (param in group_params.keySet()) {
+                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+            }
+            summary_section += "    </dl>\n"
+        }
+    }
+
+    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text        += "plot_type: 'html'\n"
+    yaml_file_text        += "data: |\n"
+    yaml_file_text        += "${summary_section}"
+
+    return yaml_file_text
+}
+
+//
+// nf-core logo
+//
+def nfCoreLogo(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    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}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
+
+//
+// Return dashed line
+//
+def dashedLine(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
+//
+// ANSII colours used for terminal logging
+//
+def logColours(monochrome_logs=true) {
+    Map colorcodes = [:]
+
+    // Reset / Meta
+    colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+    colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+    colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+    colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+    colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+    colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+    colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+    // Regular Colors
+    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+
+    // Bold
+    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+
+    // Underline
+    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+
+    // High Intensity
+    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+
+    // Bold High Intensity
+    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+
+    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]
+            }
+        }
+    } catch (all) {
+        if (multiqc_report) {
+            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+        }
+    }
+    return mqc_report
+}
+
+//
+// Construct and send completion email
+//
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
+
+    // Set up the e-mail variables
+    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    if (!workflow.success) {
+        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+    }
+
+    def summary = [:]
+    for (group in summary_params.keySet()) {
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['Date Started']              = workflow.start
+    misc_fields['Date Completed']            = workflow.complete
+    misc_fields['Pipeline script file path'] = workflow.scriptFile
+    misc_fields['Pipeline script hash ID']   = workflow.scriptId
+    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    misc_fields['Nextflow Version']           = workflow.nextflow.version
+    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    def email_fields = [:]
+    email_fields['version']      = getWorkflowVersion()
+    email_fields['runName']      = workflow.runName
+    email_fields['success']      = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration']     = workflow.duration
+    email_fields['exitStatus']   = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    email_fields['commandLine']  = workflow.commandLine
+    email_fields['projectDir']   = workflow.projectDir
+    email_fields['summary']      = summary << misc_fields
+
+    // On success try attach the multiqc report
+    def mqc_report = attachMultiqcReport(multiqc_report)
+
+    // Check if we are only sending emails on failure
+    def email_address = email
+    if (!email && email_on_fail && !workflow.success) {
+        email_address = email_on_fail
+    }
+
+    // Render the TXT template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    def tf           = new File("${workflow.projectDir}/assets/email_template.txt")
+    def txt_template = engine.createTemplate(tf).make(email_fields)
+    def email_txt    = txt_template.toString()
+
+    // Render the HTML template
+    def hf            = new File("${workflow.projectDir}/assets/email_template.html")
+    def html_template = engine.createTemplate(hf).make(email_fields)
+    def email_html    = html_template.toString()
+
+    // Render the sendmail template
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
+    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+    def sendmail_html          = sendmail_template.toString()
+
+    // Send the HTML e-mail
+    Map colors = logColours(monochrome_logs)
+    if (email_address) {
+        try {
+            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            // Try to send HTML e-mail using sendmail
+            def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+            sendmail_tf.withWriter { w -> w << sendmail_html }
+            [ 'sendmail', '-t' ].execute() << sendmail_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+        } catch (all) {
+            // Catch failures and try with plaintext
+            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            mail_cmd.execute() << email_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+        }
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
+    output_hf.withWriter { w -> w << email_html }
+    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    output_hf.delete()
+
+    // Write summary e-mail TXT to a file
+    def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
+    output_tf.withWriter { w -> w << email_txt }
+    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    output_tf.delete()
+}
+
+//
+// Print pipeline summary on completion
+//
+def completionSummary(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    if (workflow.success) {
+        if (workflow.stats.ignoredCount == 0) {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+        } else {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+        }
+    } else {
+        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+}
+
+//
+// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
+//
+def imNotification(summary_params, hook_url) {
+    def summary = [:]
+    for (group in summary_params.keySet()) {
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['start']                                = workflow.start
+    misc_fields['complete']                             = workflow.complete
+    misc_fields['scriptfile']                           = workflow.scriptFile
+    misc_fields['scriptid']                             = workflow.scriptId
+    if (workflow.repository) misc_fields['repository']  = workflow.repository
+    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+    if (workflow.revision)   misc_fields['revision']    = workflow.revision
+    misc_fields['nxf_version']                          = workflow.nextflow.version
+    misc_fields['nxf_build']                            = workflow.nextflow.build
+    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+    def msg_fields = [:]
+    msg_fields['version']      = getWorkflowVersion()
+    msg_fields['runName']      = workflow.runName
+    msg_fields['success']      = workflow.success
+    msg_fields['dateComplete'] = workflow.complete
+    msg_fields['duration']     = workflow.duration
+    msg_fields['exitStatus']   = workflow.exitStatus
+    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+    msg_fields['projectDir']   = workflow.projectDir
+    msg_fields['summary']      = summary << misc_fields
+
+    // Render the JSON template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    // Different JSON depending on the service provider
+    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
+    def json_template = engine.createTemplate(hf).make(msg_fields)
+    def json_message  = json_template.toString()
+
+    // POST
+    def post = new URL(hook_url).openConnection();
+    post.setRequestMethod("POST")
+    post.setDoOutput(true)
+    post.setRequestProperty("Content-Type", "application/json")
+    post.getOutputStream().write(json_message.getBytes("UTF-8"));
+    def postRC = post.getResponseCode();
+    if (! postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText());
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
new file mode 100644
index 0000000..d08d243
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
@@ -0,0 +1,24 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFCORE_PIPELINE"
+description: Subworkflow with utility functions specific to the nf-core pipeline template
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input:
+  - nextflow_cli_args:
+      type: list
+      description: |
+        Nextflow CLI positional arguments
+output:
+  - success:
+      type: boolean
+      description: |
+        Dummy output to indicate success
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
+  - "@maxulysse"
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
new file mode 100644
index 0000000..1dc317f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -0,0 +1,134 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Test Function checkConfigProvided") {
+
+        function "checkConfigProvided"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function checkProfileProvided") {
+
+        function "checkProfileProvided"
+
+        when {
+            function {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function workflowCitation") {
+
+        function "workflowCitation"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function nfCoreLogo") {
+
+        function "nfCoreLogo"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function dashedLine") {
+
+        function "dashedLine"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function without logColours") {
+
+        function "logColours"
+
+        when {
+            function {
+                """
+                input[0] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function with logColours") {
+        function "logColours"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+}
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
new file mode 100644
index 0000000..1037232
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,166 @@
+{
+    "Test Function checkProfileProvided": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:03.360873"
+    },
+    "Test Function checkConfigProvided": {
+        "content": [
+            true
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "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": [
+            {
+                "reset": "",
+                "bold": "",
+                "dim": "",
+                "underlined": "",
+                "blink": "",
+                "reverse": "",
+                "hidden": "",
+                "black": "",
+                "red": "",
+                "green": "",
+                "yellow": "",
+                "blue": "",
+                "purple": "",
+                "cyan": "",
+                "white": "",
+                "bblack": "",
+                "bred": "",
+                "bgreen": "",
+                "byellow": "",
+                "bblue": "",
+                "bpurple": "",
+                "bcyan": "",
+                "bwhite": "",
+                "ublack": "",
+                "ured": "",
+                "ugreen": "",
+                "uyellow": "",
+                "ublue": "",
+                "upurple": "",
+                "ucyan": "",
+                "uwhite": "",
+                "iblack": "",
+                "ired": "",
+                "igreen": "",
+                "iyellow": "",
+                "iblue": "",
+                "ipurple": "",
+                "icyan": "",
+                "iwhite": "",
+                "biblack": "",
+                "bired": "",
+                "bigreen": "",
+                "biyellow": "",
+                "biblue": "",
+                "bipurple": "",
+                "bicyan": "",
+                "biwhite": ""
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "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": [
+            {
+                "reset": "\u001b[0m",
+                "bold": "\u001b[1m",
+                "dim": "\u001b[2m",
+                "underlined": "\u001b[4m",
+                "blink": "\u001b[5m",
+                "reverse": "\u001b[7m",
+                "hidden": "\u001b[8m",
+                "black": "\u001b[0;30m",
+                "red": "\u001b[0;31m",
+                "green": "\u001b[0;32m",
+                "yellow": "\u001b[0;33m",
+                "blue": "\u001b[0;34m",
+                "purple": "\u001b[0;35m",
+                "cyan": "\u001b[0;36m",
+                "white": "\u001b[0;37m",
+                "bblack": "\u001b[1;30m",
+                "bred": "\u001b[1;31m",
+                "bgreen": "\u001b[1;32m",
+                "byellow": "\u001b[1;33m",
+                "bblue": "\u001b[1;34m",
+                "bpurple": "\u001b[1;35m",
+                "bcyan": "\u001b[1;36m",
+                "bwhite": "\u001b[1;37m",
+                "ublack": "\u001b[4;30m",
+                "ured": "\u001b[4;31m",
+                "ugreen": "\u001b[4;32m",
+                "uyellow": "\u001b[4;33m",
+                "ublue": "\u001b[4;34m",
+                "upurple": "\u001b[4;35m",
+                "ucyan": "\u001b[4;36m",
+                "uwhite": "\u001b[4;37m",
+                "iblack": "\u001b[0;90m",
+                "ired": "\u001b[0;91m",
+                "igreen": "\u001b[0;92m",
+                "iyellow": "\u001b[0;93m",
+                "iblue": "\u001b[0;94m",
+                "ipurple": "\u001b[0;95m",
+                "icyan": "\u001b[0;96m",
+                "iwhite": "\u001b[0;97m",
+                "biblack": "\u001b[1;90m",
+                "bired": "\u001b[1;91m",
+                "bigreen": "\u001b[1;92m",
+                "biyellow": "\u001b[1;93m",
+                "biblue": "\u001b[1;94m",
+                "bipurple": "\u001b[1;95m",
+                "bicyan": "\u001b[1;96m",
+                "biwhite": "\u001b[1;97m"
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:21.714424"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 0000000..8940d32
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,29 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFCORE_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    workflow "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Should run without failures") {
+
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
new file mode 100644
index 0000000..859d103
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "valid_config": [
+                    true
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
new file mode 100644
index 0000000..d0a926b
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
new file mode 100644
index 0000000..ac8523c
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfcore_pipeline:
+  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
new file mode 100644
index 0000000..50155c0
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -0,0 +1,62 @@
+//
+// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
+//
+
+/*
+========================================================================================
+    IMPORT NF-VALIDATION PLUGIN
+========================================================================================
+*/
+
+include { paramsHelp         } from 'plugin/nf-schema'
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFVALIDATION_PLUGIN {
+
+    take:
+    print_help       // boolean: print help
+    workflow_command //  string: default commmand used to run pipeline
+    pre_help_text    //  string: string to be printed before help text and summary log
+    post_help_text   //  string: string to be printed after help text and summary log
+    validate_params  // boolean: validate parameters
+    schema_filename  //    path: JSON schema file, null to use default value
+
+    main:
+
+    log.debug "Using schema file: ${schema_filename}"
+
+    // Default values for strings
+    pre_help_text    = pre_help_text    ?: ''
+    post_help_text   = post_help_text   ?: ''
+    workflow_command = workflow_command ?: ''
+
+    //
+    // Print help message if needed
+    //
+    if (print_help) {
+        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
+        System.exit(0)
+    }
+
+    //
+    // Print parameter summary to stdout
+    //
+    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
+
+    //
+    // Validate parameters relative to the parameter JSON schema
+    //
+    if (validate_params){
+        validateParameters(parameters_schema: schema_filename)
+    }
+
+    emit:
+    dummy_emit = true
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
new file mode 100644
index 0000000..3d4a6b0
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
@@ -0,0 +1,44 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFVALIDATION_PLUGIN"
+description: Use nf-validation to initiate and validate a pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - validation
+components: []
+input:
+  - print_help:
+      type: boolean
+      description: |
+        Print help message and exit
+  - workflow_command:
+      type: string
+      description: |
+        The command to run the workflow e.g. "nextflow run main.nf"
+  - pre_help_text:
+      type: string
+      description: |
+        Text to print before the help message
+  - post_help_text:
+      type: string
+      description: |
+        Text to print after the help message
+  - validate_params:
+      type: boolean
+      description: |
+        Validate the parameters and error if invalid.
+  - schema_filename:
+      type: string
+      description: |
+        The filename of the schema to validate against.
+output:
+  - dummy_emit:
+      type: boolean
+      description: |
+        Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
+  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
new file mode 100644
index 0000000..5784a33
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -0,0 +1,200 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFVALIDATION_PLUGIN"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "plugin/nf-validation"
+    tag "'plugin/nf-validation'"
+    tag "utils_nfvalidation_plugin"
+    tag "subworkflows/utils_nfvalidation_plugin"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+
+            workflow {
+                """
+                help             = false
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should run help") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } }
+            )
+        }
+    }
+
+    test("Should run help with command") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = "nextflow run noorg/doesntexist"
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } }
+            )
+        }
+    }
+
+    test("Should run help with extra text") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = "nextflow run noorg/doesntexist"
+                pre_help_text    = "pre-help-text"
+                post_help_text   = "post-help-text"
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('pre-help-text') } },
+                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } },
+                { assert workflow.stdout.any { it.contains('post-help-text') } }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+                outdir          = 1
+            }
+            workflow {
+                """
+                help             = false
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = true
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
new file mode 100644
index 0000000..7626c1c
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
@@ -0,0 +1,96 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "type": "object",
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+            "required": ["outdir"],
+            "properties": {
+                "validate_params": {
+                    "type": "boolean",
+                    "description": "Validate parameters?",
+                    "default": true,
+                    "hidden": true
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                },
+                "test_data_base": {
+                    "type": "string",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
+                    "description": "Base for test data directory",
+                    "hidden": true
+                },
+                "test_data": {
+                    "type": "string",
+                    "description": "Fake test data param",
+                    "hidden": true
+                }
+            }
+        },
+        "generic_options": {
+            "title": "Generic options",
+            "type": "object",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "properties": {
+                "help": {
+                    "type": "boolean",
+                    "description": "Display help text.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "logo": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Display nf-core logo in console output.",
+                    "fa_icon": "fas fa-image",
+                    "hidden": true
+                },
+                "singularity_pull_docker_container": {
+                    "type": "boolean",
+                    "description": "Pull Singularity container from Docker?",
+                    "hidden": true
+                },
+                "publish_dir_mode": {
+                    "type": "string",
+                    "default": "copy",
+                    "description": "Method used to save pipeline results to output directory.",
+                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+                    "fa_icon": "fas fa-copy",
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "hidden": true
+                },
+                "monochrome_logs": {
+                    "type": "boolean",
+                    "description": "Use monochrome_logs",
+                    "hidden": true
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
+        }
+    ]
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
new file mode 100644
index 0000000..60b1cff
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfvalidation_plugin:
+  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/tests/inputs/samplesheet.csv b/tests/inputs/samplesheet.csv
index e1fbd31..e8069be 100644
--- a/tests/inputs/samplesheet.csv
+++ b/tests/inputs/samplesheet.csv
@@ -1,3 +1,3 @@
 cram,crai,gender
-https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,male
-https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,
+https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,male
+https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 02eba75..f76cb77 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -4,21 +4,34 @@ nextflow_pipeline {
     script "main.nf"
     options "-stub"
 
+    tag "pipeline"
+
     test("Success") {
 
         when {
             params {
+                input  = "${projectDir}/tests/inputs/samplesheet.csv"
+                outdir = "${outputDir}"
                 prefix = "test_reference"
-                bin_sizes = "10000,5"
+                bin_sizes = "10,5"
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
             }
         }
 
         then {
-            assert workflow.success
-            assert file("${outputDir}/test_reference_10kbp.npz").exists()
-            assert file("${outputDir}/test_reference_5bp.npz").exists()
-            assert file("${outputDir}/metrics.txt").exists()
-            assert file("${outputDir}/multiqc_reports/multiqc_report.html").exists()
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.stdout,
+                    path("$outputDir")
+                        .list()
+                        .findAll {
+                            !it.toString().endsWith("pipeline_info")
+                        }
+                ).match() }
+            )
         }
     }
 }
diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
new file mode 100644
index 0000000..523cad8
--- /dev/null
+++ b/tests/main.nf.test.snap
@@ -0,0 +1,25 @@
+{
+    "Success": {
+        "content": [
+            [
+                
+            ],
+            [
+                [
+                    [
+                        
+                    ],
+                    "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "test_reference_10kbp.npz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_reference_5kbp.npz:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-04-10T13:09:17.340598729"
+    }
+}
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index c19b1ad..050b29b 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -3,3 +3,11 @@
     Nextflow config file for running tests
 ========================================================================================
 */
+
+params {
+    fasta = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna"
+    fai   = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai"
+
+    genomes_ignore  = true
+    igenomes_ignore = true
+}
diff --git a/workflows/cmgg-wisecondorx.nf b/workflows/wisecondorx.nf
similarity index 51%
rename from workflows/cmgg-wisecondorx.nf
rename to workflows/wisecondorx.nf
index 38d506a..1bc5f7f 100644
--- a/workflows/cmgg-wisecondorx.nf
+++ b/workflows/wisecondorx.nf
@@ -1,58 +1,19 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT PLUGINS
+    IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { fromSamplesheet; paramsSummaryMap } from 'plugin/nf-validation'
-
-def summary_params = paramsSummaryMap(workflow)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE INPUTS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-def checkPathParamList = [
-    params.input,
-    params.multiqc_config,
-    params.fasta,
-    params.fai
-]
-for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
-
-// Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// MODULE: Installed directly from nf-core/modules
-//
-
 include { SAMTOOLS_FAIDX              } from '../modules/nf-core/samtools/faidx/main'
 include { SAMTOOLS_INDEX              } from '../modules/nf-core/samtools/index/main'
 include { NGSBITS_SAMPLEGENDER        } from '../modules/nf-core/ngsbits/samplegender/main'
 include { WISECONDORX_CONVERT         } from '../modules/nf-core/wisecondorx/convert/main'
 include { WISECONDORX_NEWREF          } from '../modules/nf-core/wisecondorx/newref/main'
 include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { paramsSummaryMap            } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML      } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText      } from '../subworkflows/local/utils_nfcore_wisecondorx_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -60,22 +21,34 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// Info required for completion email and summary
-def multiqc_report = []
+workflow WISECONDORX {
+
+    take:
+    ch_samplesheet              // queue channel:   samplesheet read in from --input
+    fasta                       // string:          the reference fasta file
+    fai                         // string:          the index of the reference fasta file
+    val_bin_sizes               // list:            a list of bin sizes to use
+    no_metrics                  // boolean:         deactivate the generation of metrics
+    prefix                      // string:          the prefix to be used by the output file
+    outdir                      // string:          the path of the output directory
+    multiqc_config              // string:          the path to the multiqc config
+    multiqc_logo                // string:          the path to the multiqc logo
+    multiqc_methods_description // file:            the file containing the multiqc custom method descriptions
 
-workflow CMGGWISECONDORX {
+    main:
 
     ch_versions = Channel.empty()
+    ch_multiqc_files = Channel.empty()
 
     //
     // Create optional input files
     //
 
-    ch_fasta = Channel.fromPath(params.fasta, checkIfExists:true)
-        .map { [[id:params.genome ?: "fasta"], it] }
+    ch_fasta = Channel.fromPath(fasta, checkIfExists:true)
+        .map { [[id:"fasta"], it] }
         .collect()
 
-    if(!params.fai) {
+    if(!fai) {
         SAMTOOLS_FAIDX(
             ch_fasta,
             [[],[]]
@@ -85,16 +58,12 @@ workflow CMGGWISECONDORX {
         SAMTOOLS_FAIDX.out.fai
             .set { ch_fai }
     } else {
-        ch_fai = Channel.fromPath(params.fai, checkIfExists:true)
-            .map { [[id:params.genome ?: "fasta"], it] }
+        ch_fai = Channel.fromPath(fai, checkIfExists:true)
+            .map { [[id:"fasta"], it] }
             .collect()
     }
 
-    //
-    // Validate and convert the samplesheet
-    //
-
-    Channel.fromSamplesheet("input", immutable_meta: false)
+    ch_samplesheet
         .branch { meta, cram, crai ->
             new_meta = meta + [id:cram.baseName]
             indexed: crai
@@ -116,7 +85,7 @@ workflow CMGGWISECONDORX {
         .mix(ch_input.indexed)
         .set { ch_indexed }
 
-    if(!params.no_metrics){
+    if(!no_metrics){
 
         //
         // Define the gender if it's not given
@@ -159,6 +128,10 @@ workflow CMGGWISECONDORX {
                 counts
             }
             .map { genders -> create_metrics(genders)}
+            .collectFile(name: "metrics_mqc.tsv")
+            .set { ch_metrics }
+
+        ch_multiqc_files = ch_multiqc_files.mix(ch_metrics)
 
     }
 
@@ -183,11 +156,11 @@ workflow CMGGWISECONDORX {
 
     WISECONDORX_CONVERT.out.npz
         .map { meta, npz ->
-            new_meta = [id:params.prefix ?: dateFormat]
+            new_meta = [id:prefix ?: dateFormat]
             [ new_meta, npz ]
         }
         .groupTuple() // All files should be present here, so no size is needed
-        .combine(params.bin_sizes.split(","))
+        .combine(val_bin_sizes)
         .map { meta, npz, bin_size ->
             new_meta = meta + [bin_size:bin_size]
             [ new_meta, npz ]
@@ -198,26 +171,25 @@ workflow CMGGWISECONDORX {
     ch_versions = ch_versions.mix(WISECONDORX_NEWREF.out.versions.first())
 
     //
-    // Dump software versions
+    // Collate and save software versions
     //
-
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(storeDir: "${outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
+        .set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    workflow_summary    = WorkflowCmggWisecondorx.paramsSummaryMultiqc(workflow, summary_params)
-    ch_workflow_summary = Channel.value(workflow_summary)
-
-    methods_description    = WorkflowCmggWisecondorx.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
-    ch_methods_description = Channel.value(methods_description)
-
-    ch_multiqc_files = Channel.empty()
-    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config              = multiqc_config ? Channel.fromPath(multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_logo                       = multiqc_logo ? Channel.fromPath(multiqc_logo, checkIfExists: true) : Channel.empty()
+    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_custom_methods_description = multiqc_methods_description
+    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
 
     MULTIQC (
         ch_multiqc_files.collect(),
@@ -225,23 +197,10 @@ workflow CMGGWISECONDORX {
         ch_multiqc_custom_config.toList(),
         ch_multiqc_logo.toList()
     )
-    multiqc_report = MULTIQC.out.report.toList()
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    COMPLETION EMAIL AND SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
 
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
-    }
-    NfcoreTemplate.summary(workflow, params, log)
-    if (params.hook_url) {
-        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
-    }
+    emit:
+    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }
 
 /*
@@ -256,20 +215,17 @@ def get_gender(tsv) {
 }
 
 def create_metrics(genders) {
-    male = genders["male"]
-    female = genders["female"]
-    male_count = male.size()
-    female_count = female.size()
-    total_count = male_count + female_count
-    ratio_male_to_female = male_count / female_count
-
-    output = file("${params.outdir}/metrics.txt")
-    output.write("Ratio male to female: ${ratio_male_to_female}\n")
-    output.append("Male count: ${male_count}\n")
-    output.append("Female count: ${female_count}\n")
-    output.append("Total count: ${total_count}\n")
-    output.append("Males: ${male.join(',')}\n")
-    output.append("Females: ${female.join(',')}\n")
+    def List male = genders["male"]
+    def List female = genders["female"]
+    def Integer male_count = male.size()
+    def Integer female_count = female.size()
+    def Float male_to_female_ratio = male_count / female_count
+    def Integer total_count = male_count + female_count
+
+    return """# plot_type: 'table'
+Male to female ratio\tMale count\tFemale count\tTotal count\tMales\tFemales
+${male_to_female_ratio}\t${male_count}\t${female_count}\t${total_count}\t${male.join(",")}\t${female.join(",")}
+"""
 }
 
 /*