diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4ecfbfe3..b290e090 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -10,15 +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 b6b31907..dd9ffa53 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 d1d4012c..f5839259 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,24 +1,22 @@
-# tomte: Contributing Guidelines
+# genomic-medicine-sweden/tomte: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving tomte.
+Many thanks for taking an interest in improving genomic-medicine-sweden/tomte.
 
-We try to manage the required tasks for tomte using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for genomic-medicine-sweden/tomte 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!
 Contributions to the code are even more welcome ;)
 
-:::info
 If you need help using or modifying genomic-medicine-sweden/tomte then the best place to ask is by creating an [issue] (https://github.com/genomic-medicine-sweden/tomte/issues).
-:::
 
 ## Contribution workflow
 
-If you'd like to write some code for tomte, the standard workflow is as follows:
+If you'd like to write some code for genomic-medicine-sweden/tomte, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [tomte issues](https://github.com/genomic-medicine-sweden/tomte/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 [tomte repository](https://github.com/genomic-medicine-sweden/tomte) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/tomte issues](https://github.com/genomic-medicine-sweden/tomte/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 [genomic-medicine-sweden/tomte repository](https://github.com/genomic-medicine-sweden/tomte) 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
@@ -27,6 +25,12 @@ 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.
 
@@ -60,7 +64,7 @@ For further information/help, please consult the [tomte documentation](https://g
 
 ## Pipeline contribution conventions
 
-To make the tomte 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 genomic-medicine-sweden/tomte 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
 
@@ -87,7 +91,7 @@ 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
 
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 908a4a12..b47c0056 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,14 +2,6 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-  - type: markdown
-    attributes:
-      value: |
-        Before you post this issue, please check the documentation:
-
-        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [tomte pipeline documentation](https://github.com/genomic-medicine-sweden/tomte)
-
   - type: textarea
     id: description
     attributes:
@@ -17,34 +9,45 @@ body:
       description: A clear and concise description of what the bug is.
     validations:
       required: true
-
   - type: textarea
     id: command_used
     attributes:
       label: Command used and terminal output
-      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
       render: console
-      placeholder: |
-        $ nextflow run ...
+      placeholder: "$ nextflow run ...
 
         Some output where something broke
 
+        "
   - type: textarea
     id: files
     attributes:
       label: Relevant files
-      description: |
-        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
-        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
 
+        "
   - type: textarea
     id: system
     attributes:
       label: System information
-      description: |
-        * Nextflow version _(eg. 23.04.0)_
+      description: "* Nextflow version _(eg. 23.04.0)_
+
         * Hardware _(eg. HPC, Desktop, Cloud)_
+
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
+
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of tomte _(eg. 1.1, 1.5, 1.8.2)_
+
+        * Version of genomic-medicine-sweden/tomte _(eg. 1.1, 1.5, 1.8.2)_
+
+        "
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
deleted file mode 100644
index 8b6b66a0..00000000
--- a/.github/ISSUE_TEMPLATE/config.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-contact_links:
-  - name: Join nf-core
-    url: https://nf-co.re/join
-    about: Please join the nf-core community here
-  - name: "Slack #tomte channel"
-    url: https://nfcore.slack.com/channels/tomte
-    about: Discussion about the nf-core/tomte pipeline
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 6d5e47cf..8c2f125b 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 nf-core/tomte pipeline
+description: Suggest an idea for the genomic-medicine-sweden/tomte pipeline
 labels: enhancement
 body:
   - type: textarea
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index fd5308cc..a2bdb8e0 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,7 +1,7 @@
 <!--
-# tomte pull request
+# genomic-medicine-sweden/tomte pull request
 
-Many thanks for contributing to tomte!
+Many thanks for contributing to genomic-medicine-sweden/tomte!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
@@ -18,6 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/genomic-medi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/genomic-medicine-sweden/tomte/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>`).
+- [ ] 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/awsfulltest.yml b/.github/workflows/awsfulltest.yml
deleted file mode 100644
index cdff769a..00000000
--- a/.github/workflows/awsfulltest.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
-# It can be additionally triggered manually with GitHub actions workflow dispatch button.
-# It runs the -profile 'test_full' on AWS batch
-
-on:
-  release:
-    types: [published]
-  workflow_dispatch:
-jobs:
-  run-tower:
-    name: Run AWS full tests
-    if: github.repository == 'nf-core/tomte'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/tomte/work-${{ github.sha }}
-          parameters: |
-            {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/tomte/results-${{ github.sha }}"
-            }
-          profiles: test_full
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: Tower debug log file
-          path: |
-            tower_action_*.log
-            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
deleted file mode 100644
index 3b77fab7..00000000
--- a/.github/workflows/awstest.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: nf-core AWS test
-# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
-# It runs the -profile 'test' on AWS batch
-
-on:
-  workflow_dispatch:
-jobs:
-  run-tower:
-    name: Run AWS tests
-    if: github.repository == 'nf-core/tomte'
-    runs-on: ubuntu-latest
-    steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/tomte/work-${{ github.sha }}
-          parameters: |
-            {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/tomte/results-test-${{ github.sha }}"
-            }
-          profiles: test
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: Tower debug log file
-          path: |
-            tower_action_*.log
-            tower_action_*.json
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index df47d818..e9878c64 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 == 'nf-core/tomte'
+        if: github.repository == 'genomic-medicine-sweden/tomte'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/tomte ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == genomic-medicine-sweden/tomte ]] && [[ $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 45706d40..4ce866ff 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,7 +19,7 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/tomte') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/tomte') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -28,13 +28,16 @@ jobs:
           - "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
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run pipeline with test data
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 694e90ec..0b6b1f27 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v7
+      - uses: actions/stale@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."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
new file mode 100644
index 00000000..08622fd5
--- /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 d8d8a42f..e0c4d0ac 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 == 'nf-core/tomte'
+      github.repository == 'genomic-medicine-sweden/tomte'
     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/genomic-medicine-sweden/tomte/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index e16ae43e..748b4311 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,72 +11,33 @@ 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\|.bed\|.tsv')
-
-  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: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -99,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 0bbcd30f..b706875f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(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: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
new file mode 100644
index 00000000..d468aeaa
--- /dev/null
+++ b/.github/workflows/release-announcements.yml
@@ -0,0 +1,75 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - name: get topics and convert to hashtags
+        id: get_topics
+        run: |
+          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ 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/.gitpod.yml b/.gitpod.yml
index 25488dcc..105a1821 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,16 +4,17 @@ tasks:
     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 52171fad..3f2d1805 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,4 +1,3 @@
-repository_type: pipeline
 lint:
   files_exist: false
     - assets/nf-core-tomte_logo_light.png
@@ -7,6 +6,8 @@ lint:
     - docs/images/tomte_logo.eps
     - docs/images/tomte_pipeline_metromap.eps
     - docs/images/tomte_pipeline_metromap.png
+    - conf/modules.config
+    - .github/ISSUE_TEMPLATE/config.yml
   files_unchanged: false
     - assets/sendmail_template.txt
     - .github/CONTRIBUTING.md
@@ -19,7 +20,15 @@ lint:
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
     - docs/README.md
+    - pyproject.toml
+  multiqc_config:
+    - report_comment
   nextflow_config:
     - manifest.name
     - manifest.homePage
-  multiqc_config: false
+repository_type: pipeline
+template:
+  author: lucpen
+  description: Analyzing RNAseq data
+  name: tomte
+  prefix: genomic-medicine-sweden
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0c31cdb9..af57081f 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 f6777da5..f15b0f41 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,16 +1,63 @@
-# genomic-medicine-seden/tomte: Changelog
+# genomic-medicine-sweden/tomte: 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).
 
-## 1.0.0 - Nisse [2023-11-06]
+## 1.1.0 - Rudolph [2024-03-11]
 
-Initial release of genomic-medicine-sweden/tomte, created with the [nf-core](https://nf-co.re/) template.
+Release of genomic-medicine-sweden/tomte, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
+- switch_vep, switch_build_tracks and switch_stringtie to make the pipeline more versatile [#61](https://github.com/genomic-medicine-sweden/tomte/pull/61)
+- Updated template and nf-tools [#65](https://github.com/genomic-medicine-sweden/tomte/pull/65)
+- Use `nf-validation` plugin for parameter and samplesheet validation [#66](https://github.com/genomic-medicine-sweden/tomte/pull/66)
+- Installed the nf-core version of ensemblvep/vep module [#67](https://github.com/genomic-medicine-sweden/tomte/pull/67)
+- A new parameter `vep_plugin_files` to supply files required by vep plugins [#67](https://github.com/genomic-medicine-sweden/tomte/pull/67)
+- The possibility of using `igenomes_base` to point to a path where genome specific reference files are placed (fasta, fai, gtf, star_index, salmon_index, subsample_bed) [#76](https://github.com/genomic-medicine-sweden/tomte/pull/76)
+- Merging of case's vcf files [#80](https://github.com/genomic-medicine-sweden/tomte/pull/80)
+- Reference list to MultiQC report [#88](https://github.com/genomic-medicine-sweden/tomte/pull/88)
+- Added module to calculate insert size and added results to MultiQC report [#90](https://github.com/genomic-medicine-sweden/tomte/pull/90)
+
 ### `Fixed`
 
+- Renamed the other switches (subsample_region_switch, downsample_switch, run_drop_ae_switch and run_drop_as_switch) so that they all start with switch\* (switch_subsample_region, switch_downsample, switch_drop_ae and switch_drop_as) [#61](https://github.com/genomic-medicine-sweden/tomte/pull/61)
+- Separated modules.config into smaller configs [#61](https://github.com/genomic-medicine-sweden/tomte/pull/61)
+- Missing fasta_fai channel when fai file is given [#63](https://github.com/genomic-medicine-sweden/tomte/pull/63)
+- DROP output file columns, removing duplicate column and adding same ids to both AE and AS [#68](https://github.com/genomic-medicine-sweden/tomte/pull/68)
+- Patch tools update and case ID parsing [#71](https://github.com/genomic-medicine-sweden/tomte/pull/71)
+- Naming of DROP output files [#72](https://github.com/genomic-medicine-sweden/tomte/pull/72)
+- VEP plugin schema to allow for directories [#74](https://github.com/genomic-medicine-sweden/tomte/pull/74)
+- Made params.platform into a channel [#75](https://github.com/genomic-medicine-sweden/tomte/pull/75)
+- Changed name of salmon's quant.nf to include sample id [#78](https://github.com/genomic-medicine-sweden/tomte/pull/78)
+- Shortened name of DROP output files [#79](https://github.com/genomic-medicine-sweden/tomte/pull/79)
+- Merging of vcfs has been moved to after bootstrapAnn [#81](https://github.com/genomic-medicine-sweden/tomte/pull/81)
+- Substituted bgzip and tabix modules by bgzip_tabix module [#85](https://github.com/genomic-medicine-sweden/tomte/pull/85)
+- Updated module input channels in the GATK variant calling subworkflow [#89](https://github.com/genomic-medicine-sweden/tomte/pull/85)
+
 ### `Dependencies`
 
 ### `Deprecated`
+
+## 1.0.0 - Nisse [2023-11-06]
+
+### `Added`
+
+- Trim reads with FASTP
+- Read mapping with STAR
+- Transcript quantification with Salmon
+- Output junction tracks
+- Output bigwig
+- Choice to subsample overrepresented regions with Samtools
+- Choice to downsample number of reads with Samtools
+- Detection of aberrant expression with DROP
+- Detection of aberrant splicing with DROP
+- Filter aberrant expression and aberrant splicing results
+- Guided transcript assembly with StringTie
+- Filtering results of guided transcript assembly with GffCompare
+- SNVs calling with GATK or BCFtools Mpileups
+- Allele Specific Read Counter with ASEReadCounter
+- Assess allelic imbalance with BootstrapAnn
+- Annotation with VEP
+- Alignment QC with Picard CollectRnaSeqMetrics
+- Present QCs with MultiQC
diff --git a/CITATIONS.md b/CITATIONS.md
index 8869811f..86fa03a9 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -14,7 +14,7 @@
 
   > Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
 
-- [UCSC tools] (https://academic.oup.com/bioinformatics/article/26/17/2204/199001)
+- [UCSC tools](https://academic.oup.com/bioinformatics/article/26/17/2204/199001)
 
   > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351
 
@@ -26,10 +26,22 @@
 
   > McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4
 
+- [DROP](https://www.nature.com/articles/s41596-020-00462-5)
+
+  > Yépez, V.A., Mertes, C., Müller, M.F. et al. Detection of aberrant gene expression events in RNA sequencing data. Nat Protoc 16, 1276–1296 (2021). doi:10.1038/s41596-020-00462-5
+
+- [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/)
+
+  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [FRASER](https://www.nature.com/articles/s41467-020-20573-7)
+
+  > Mertes C, Scheller IF, Yépez VA, et al. Detection of aberrant splicing events in RNA-seq data using FRASER [published correction appears in Nat Commun. 2022 Jun 16;13(1):3474]. Nat Commun. 2021;12(1):529. Published 2021 Jan 22. doi:10.1038/s41467-020-20573-7
+
 - [GATK](https://genome.cshlp.org/content/20/9/1297)
 
   > McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-1303. doi:10.1101/gr.107524.110
@@ -42,6 +54,12 @@
 
   > 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.
 
+- [OUTRIDER](https://www.sciencedirect.com/science/article/pii/S0002929718304014?via%3Dihub)
+
+  > Brechtmann F, Mertes C, Matusevičiūtė A, et al. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. Am J Hum Genet. 2018;103(6):907-917. doi:10.1016/j.ajhg.2018.10.025
+
+- [picard-tools](http://broadinstitute.github.io/picard)
+
 - [StringTie](http://ccb.jhu.edu/software/stringtie/)
 
   > Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. PMID: 25690850; PMCID: PMC4643835.
@@ -50,6 +68,10 @@
 
   > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.
 
+- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)
+
+  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)
diff --git a/README.md b/README.md
index eb7d02df..dc15a44b 100644
--- a/README.md
+++ b/README.md
@@ -1,19 +1,18 @@
 # ![tomte](docs/images/tomte_logo_light.png#gh-light-mode-only) ![tomte](docs/images/tomte_logo_dark.png#gh-dark-mode-only)
 
-[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/tomte/workflows/nf-core%20CI/badge.svg)](https://github.com/genomic-medicine-sweden/tomte/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/tomte/workflows/nf-core%20linting/badge.svg)](https://github.com/genomic-medicine-sweden/tomte/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/tomte/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/tomte/actions/workflows/ci.yml/badge.svg)](https://github.com/genomic-medicine-sweden/tomte/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/tomte/actions/workflows/linting.yml/badge.svg)](https://github.com/genomic-medicine-sweden/tomte/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%A523.04.0-23aa62.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/genomic-medicine-sweden/tomte)
-
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![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/genomic-medicine-sweden/tomte)
 
 ## Introduction
 
-**tomte** is a bioinformatics best-practice analysis pipeline for Pipeline to analyse RNAseq from raredisease patients.
+**genomic-medicine-sweden/tomte** is a bioinformatics best-practice analysis pipeline to analyse RNAseq from raredisease patients.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
@@ -51,11 +50,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## 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.
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -111,7 +107,7 @@ If you use genomic-medicine-sweden/tomte for your analysis, please cite it using
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-You can cite the `nf-core` publication as follows:
+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).
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >
diff --git a/assets/email_template.html b/assets/email_template.html
index 58425729..f06f650b 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="tomte: Pipeline to analyse RNAseq from raredisease patients">
-  <title>tomte Pipeline Report</title>
+  <meta name="description" content="genomic-medicine-sweden/tomte: Pipeline to analyse RNAseq from raredisease patients">
+  <title>genomic-medicine-sweden/tomte 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>tomte v${version}</h1>
+<h1>genomic-medicine-sweden/tomte ${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;">tomte execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">genomic-medicine-sweden/tomte 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;">tomte execution completed unsuccessful
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        tomte execution completed successfully!
+        genomic-medicine-sweden/tomte execution completed successfully!
     </div>
     """
 }
@@ -44,7 +44,7 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>tomte</p>
+<p>genomic-medicine-sweden/tomte</p>
 <p><a href="https://github.com/genomic-medicine-sweden/tomte">https://github.com/genomic-medicine-sweden/tomte</a></p>
 
 </div>
diff --git a/assets/email_template.txt b/assets/email_template.txt
index a0e702bb..ae0301af 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -36,5 +36,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-tomte
+genomic-medicine-sweden/tomte
 https://github.com/genomic-medicine-sweden/tomte
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 41cc8786..00e12cf3 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -1,4 +1,4 @@
-id: "tomte-methods-description"
+id: "genomic-medicine-sweden/tomte-methods-description"
 description: "A best-practice analysis pipeline to analyse RNAseq data from rare disease patients."
 section_name: "tomte Methods Description"
 section_href: "https://github.com/genomic-medicine-sweden/tomte"
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 179510d0..7aa5892b 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,13 +1,15 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/1.0.0" target="_blank">genomic-medicine-sweden/tomte</a>
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/1.1.0" target="_blank">genomic-medicine-sweden/tomte</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/output.md" target="_blank">documentation</a>.
 report_section_order:
-  "nf-core-tomte-methods-description":
+  "genomic-medicine-sweden-tomte-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "nf-core-tomte-summary":
+  "genomic-medicine-sweden-tomte-summary":
     order: -1002
 
 export_plots: true
+
+disable_version_detection: true
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 0d5ea9b5..959e539c 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -7,13 +7,23 @@
     "items": {
         "type": "object",
         "properties": {
+            "case": {
+                "type": "string",
+                "meta": ["case"],
+                "pattern": "^\\S+$",
+                "errorMessage": "Case name must be provided and cannot contain spaces"
+            },
             "sample": {
                 "type": "string",
+                "exists": true,
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id", "sample"]
             },
             "fastq_1": {
                 "type": "string",
+                "format": "file-path",
+                "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
@@ -22,6 +32,8 @@
                 "anyOf": [
                     {
                         "type": "string",
+                        "format": "file-path",
+                        "exists": true,
                         "pattern": "^\\S+\\.f(ast)?q\\.gz$"
                     },
                     {
@@ -29,8 +41,14 @@
                         "maxLength": 0
                     }
                 ]
+            },
+            "strandedness": {
+                "type": "string",
+                "meta": ["strandedness"],
+                "enum": ["unstranded", "forward", "reverse"],
+                "errorMessage": "Sample strandness valid input is unstranded,forward or reverse"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["case", "sample", "fastq_1", "strandedness"]
     }
 }
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
index e64bf677..e8d6e831 100644
--- a/assets/sendmail_template.txt
+++ b/assets/sendmail_template.txt
@@ -9,7 +9,7 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="nf-core-tomte_logo.png"
+Content-Type: image/png;name="genomic-medicine-sweden-tomte_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
 Content-Disposition: inline; filename="tomte_logo_light.png"
diff --git a/assets/slackreport.json b/assets/slackreport.json
index 9b869412..9d890711 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": "genomic-medicine-sweden/tomte v${version} - ${runName}",
+            "author_name": "genomic-medicine-sweden/tomte ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [
diff --git a/assets/vep_plugin_files_schema.json b/assets/vep_plugin_files_schema.json
new file mode 100644
index 00000000..2456ec60
--- /dev/null
+++ b/assets/vep_plugin_files_schema.json
@@ -0,0 +1,28 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json",
+    "title": "Schema for VEP plugin files and their indices",
+    "description": "Schema for VEP plugin files and their indices",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "vep_files": {
+                "anyOf": [
+                    {
+                        "type": "string",
+                        "format": "file-path",
+                        "exists": true
+                    },
+                    {
+                        "type": "string",
+                        "format": "directory-path",
+                        "exists": true
+                    }
+                ],
+                "errorMessage": "The path to one of your vep plugin files could not be found"
+            }
+        },
+        "required": ["vep_files"]
+    }
+}
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
deleted file mode 100755
index c1533741..00000000
--- a/bin/check_samplesheet.py
+++ /dev/null
@@ -1,286 +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",
-    )
-
-    VALID_STRANDEDNESS = (
-        "unstranded",
-        "forward",
-        "reverse",
-    )
-
-    def __init__(
-        self,
-        case_col="case",
-        sample_col="sample",
-        first_col="fastq_1",
-        second_col="fastq_2",
-        single_col="single_end",
-        strand_col="strandedness",
-        **kwargs,
-    ):
-        """
-        Initialize the row checker with the expected column names.
-
-        Args:
-            case_col (str): The name of the column that contains the case name.
-            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").
-            strand_col (str): The name of the column that contains the strandedness
-                 of the reads.
-
-        """
-        super().__init__(**kwargs)
-        self._case_col = case_col
-        self._sample_col = sample_col
-        self._first_col = first_col
-        self._second_col = second_col
-        self._single_col = single_col
-        self._strand_col = strand_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_case(row)
-        self._validate_sample(row)
-        self._validate_first(row)
-        self._validate_second(row)
-        self._validate_pair(row)
-        self._validate_strand(row)
-        self._seen.add((row[self._sample_col], row[self._first_col]))
-        self.modified.append(row)
-
-    def _validate_case(self, row):
-        """Assert that a case name exist sand convert spaces to underscores."""
-        if len(row[self._case_col]) <= 0:
-            raise AssertionError("Case input is required.")
-        # Sanitize case name slightly.
-        row[self._case_col] = row[self._case_col].replace(" ", "_")
-
-    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_strand(self, row):
-        """Assert that strandedness entry follows valid entries"""
-        if not any(row[self._strand_col] == strandedness for strandedness in self.VALID_STRANDEDNESS):
-            raise AssertionError(f"Strandedness must be one of: {', '.join(self.VALID_STRANDEDNESS)}")
-
-    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`_::
-
-            case,sample,fastq_1,fastq_2,strandedness
-            CASE_1,SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz,reverse
-            CASE_1,SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz,reverse
-            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 = {"case", "sample", "fastq_1", "fastq_2", "strandedness"}
-    # 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/bin/drop_filter_results.py b/bin/drop_filter_results.py
index 64e4b95b..520797a5 100755
--- a/bin/drop_filter_results.py
+++ b/bin/drop_filter_results.py
@@ -1,18 +1,21 @@
 #!/usr/bin/env python3
 
 import argparse
-from pandas import DataFrame, read_csv, concat
+
 import pyreadr
+from pandas import DataFrame, concat, read_csv
 
-SCRIPT_VERSION = "v1.0"
+SCRIPT_VERSION = "v1.2"
 GENE_PANEL_HEADER = ["chromosome", "gene_start", "gene_stop", "hgnc_id", "hgnc_symbol"]
 GENE_PANEL_COLUMNS_TO_KEEP = ["hgnc_symbol", "hgnc_id"]
 
 
-def get_top_hits(sample_id: str, df_results_family_aberrant_expression: DataFrame) -> DataFrame:
+def get_top_hits(
+    sample_id: str, df_results_family_aberrant_expression: DataFrame
+) -> DataFrame:
     """
     Filter results to get only those with the id provided.
-    If there are >= 20 hits it will output all of them.
+    If there are <= 20 hits it will output all of them.
     If there are less than 20 hits, it will output the 20 with the lowest p-value.
     """
     df_id: DataFrame = df_results_family_aberrant_expression[
@@ -24,30 +27,56 @@ def get_top_hits(sample_id: str, df_results_family_aberrant_expression: DataFram
     return df_id[:20]
 
 
-def annotate_with_hgnc(df_family_aberrant_expression_top_hits: DataFrame, out_drop_gene_name: str) -> DataFrame:
-    """Annotate results from DROP Aberrant Expression with hgnc ids."""
+def annotate_with_drop_gene_name(
+    df_family_results: DataFrame, out_drop_gene_name: str
+) -> DataFrame:
+    """Annotate results from DROP with hgnc symbols."""
     df_genes: DataFrame = read_csv(out_drop_gene_name)
+    common_columns = list(set(df_genes.columns) & set(df_family_results.columns))
     df_genes.rename(columns={"gene_name": "hgncSymbol"}, inplace=True)
-    return df_genes.merge(df_family_aberrant_expression_top_hits, left_on="gene_id", right_on="geneID")
+    df_genes.rename(columns={"gene_id": "geneID"}, inplace=True)
+    if common_columns:
+        df_merged = df_genes.drop(common_columns, axis=1).merge(
+            df_family_results, left_on="hgncSymbol", right_on="hgncSymbol"
+        )
+    else:
+        df_merged = df_genes.merge(
+            df_family_results, left_on="geneID", right_on="geneID"
+        )
+    return df_merged
 
 
-def filter_by_gene_panel(df_family_top_hits: DataFrame, gene_panel: str, module_name: str) -> DataFrame:
+def filter_by_gene_panel(
+    df_family_top_hits: DataFrame, gene_panel: str, file_name_research: str
+) -> DataFrame:
     """Filter out from results any gene that is not present in the provided gene panel."""
     if gene_panel != "None":
         df_panel: DataFrame = read_csv(
-            gene_panel, sep="\t", names=GENE_PANEL_HEADER, header=None, comment="#", index_col=False
+            gene_panel,
+            sep="\t",
+            names=GENE_PANEL_HEADER,
+            header=None,
+            comment="#",
+            index_col=False,
         )
-        df_family_top_hits = df_family_top_hits.loc[df_family_top_hits["hgncSymbol"].isin(df_panel["hgnc_symbol"])]
+        df_family_top_hits = df_family_top_hits.loc[
+            df_family_top_hits["hgncSymbol"].isin(df_panel["hgnc_symbol"])
+        ]
         df_clinical: DataFrame = df_panel[GENE_PANEL_COLUMNS_TO_KEEP].merge(
             df_family_top_hits, left_on="hgnc_symbol", right_on="hgncSymbol"
         )
         df_clinical = df_clinical.drop(columns=["hgnc_symbol"])
-        file_name = f"{module_name}_provided_samples_top_hits_filtered.tsv"
-        df_clinical.to_csv(file_name, sep="\t", index=False, header=True)
+        file_name_clinical = file_name_research.replace("research.tsv", "clinical.tsv")
+        df_clinical.to_csv(file_name_clinical, sep="\t", index=False, header=True)
 
 
 def filter_outrider_results(
-    samples: list, gene_panel: str, out_drop_aberrant_expression_rds: str, out_drop_gene_name: str
+    samples: list,
+    gene_panel: str,
+    out_drop_aberrant_expression_rds: str,
+    out_drop_gene_name: str,
+    case_id: str,
+    output_name_fragment_ae: str,
 ):
     """
     Filter results to get only those from the sample(s) provided.
@@ -61,43 +90,70 @@ def filter_outrider_results(
     rds_aberrant_expression = pyreadr.read_r(out_drop_aberrant_expression_rds)
     df_results_aberrante_expression: DataFrame = rds_aberrant_expression[None]
     # Keep only samples provided to tomte
-    df_results_family_aberrant_expression: DataFrame = df_results_aberrante_expression.loc[
-        df_results_aberrante_expression["sampleID"].isin(samples)
-    ]
+    df_results_family_aberrant_expression: DataFrame = (
+        df_results_aberrante_expression.loc[
+            df_results_aberrante_expression["sampleID"].isin(samples)
+        ]
+    )
     df_family_aberrant_expression_top_hits = DataFrame()
     for id in samples:
-        df_sample_aberrant_expression_top_hits = get_top_hits(id, df_results_family_aberrant_expression)
+        df_sample_aberrant_expression_top_hits = get_top_hits(
+            id, df_results_family_aberrant_expression
+        )
         df_family_aberrant_expression_top_hits = concat(
-            [df_family_aberrant_expression_top_hits, df_sample_aberrant_expression_top_hits],
+            [
+                df_family_aberrant_expression_top_hits,
+                df_sample_aberrant_expression_top_hits,
+            ],
             ignore_index=True,
             sort=False,
         )
-        df_family_aberrant_expression_top_hits = df_family_aberrant_expression_top_hits.drop(columns=["index"])
-    df_family_annotated_aberrant_expression_top_hits = annotate_with_hgnc(
+        df_family_aberrant_expression_top_hits = (
+            df_family_aberrant_expression_top_hits.drop(columns=["index"])
+        )
+    df_family_annotated_aberrant_expression_top_hits = annotate_with_drop_gene_name(
         df_family_aberrant_expression_top_hits, out_drop_gene_name
     )
+    file_name_research = f"{case_id}{output_name_fragment_ae}_research.tsv"
     df_family_annotated_aberrant_expression_top_hits.to_csv(
-        "OUTRIDER_provided_samples_top_hits.tsv", sep="\t", index=False, header=True
+        file_name_research, sep="\t", index=False, header=True
+    )
+    filter_by_gene_panel(
+        df_family_annotated_aberrant_expression_top_hits, gene_panel, file_name_research
     )
-    filter_by_gene_panel(df_family_annotated_aberrant_expression_top_hits, gene_panel, "OUTRIDER")
 
 
-def filter_fraser_result(samples: list, gene_panel: str, out_drop_aberrant_splicing_tsv: str):
+def filter_fraser_result(
+    samples: list,
+    gene_panel: str,
+    out_drop_aberrant_splicing_tsv: str,
+    out_drop_gene_name: str,
+    case_id: str,
+    output_name_fragment_as: str,
+):
     """
     Filter results to get only those from the sample(s) provided.
     Two tsvs will be outputed:
-        - One filtered to keep gense in the gene panel (if provided).
-        - Another that is unfilterd.
+        - One filtered to keep genes in the gene panel (if provided).
+        - Another that is unfiltered.
     """
-    df_results_aberrant_splicing: DataFrame = read_csv(out_drop_aberrant_splicing_tsv, sep="\t")
+    df_results_aberrant_splicing: DataFrame = read_csv(
+        out_drop_aberrant_splicing_tsv, sep="\t"
+    )
     # Keep only samples provided to tomte
     df_results_family_aberrant_splicing: DataFrame = df_results_aberrant_splicing.loc[
         df_results_aberrant_splicing["sampleID"].isin(samples)
     ]
+    df_results_family_aberrant_splicing = annotate_with_drop_gene_name(
+        df_results_family_aberrant_splicing, out_drop_gene_name
+    )
+    file_name_research = f"{case_id}{output_name_fragment_as}_research.tsv"
     df_results_family_aberrant_splicing.to_csv(
-        "FRASER_provided_samples_top_hits.tsv", sep="\t", index=False, header=True
+        file_name_research, sep="\t", index=False, header=True
+    )
+    filter_by_gene_panel(
+        df_results_family_aberrant_splicing, gene_panel, file_name_research
     )
-    filter_by_gene_panel(df_results_family_aberrant_splicing, gene_panel, "FRASER")
 
 
 def parse_args(argv=None):
@@ -132,6 +188,20 @@ def parse_args(argv=None):
         type=str,
         default="None",
         help="Path to gene name annotion, output from DROP Aberrant Expression",
+        required=True,
+    )
+    parser.add_argument(
+        "--case_id",
+        type=str,
+        default="",
+        help="Case id",
+        required=False,
+    )
+    parser.add_argument(
+        "--output_name_fragment_ae",
+        type=str,
+        default="outrider_top_hits",
+        help="Central fragment of Aberrant Expression output file, case will be added at the beginning and clinical/research at end",
         required=False,
     )
     parser.add_argument(
@@ -141,6 +211,13 @@ def parse_args(argv=None):
         help="Path to tsv output from DROP Aberrant Splicing",
         required=False,
     )
+    parser.add_argument(
+        "--output_name_fragment_as",
+        type=str,
+        default="fraser_top_hits",
+        help="Central fragment of Aberrant Splicing output file, case will be added at the beginning and clinical/research at end",
+        required=False,
+    )
     parser.add_argument(
         "--version",
         action="version",
@@ -152,15 +229,26 @@ def parse_args(argv=None):
 def main():
     """Coordinate argument parsing and program execution."""
     args = parse_args()
-    filter_outrider_results(
-        samples=args.samples,
-        gene_panel=args.gene_panel,
-        out_drop_aberrant_expression_rds=args.drop_ae_rds,
-        out_drop_gene_name=args.out_drop_gene_name,
-    )
-    filter_fraser_result(
-        samples=args.samples, gene_panel=args.gene_panel, out_drop_aberrant_splicing_tsv=args.out_drop_as_tsv
-    )
+    if args.case_id != "":
+        args.case_id += "_"
+    if args.drop_ae_rds != "None":
+        filter_outrider_results(
+            samples=args.samples,
+            gene_panel=args.gene_panel,
+            out_drop_aberrant_expression_rds=args.drop_ae_rds,
+            out_drop_gene_name=args.out_drop_gene_name,
+            case_id=args.case_id,
+            output_name_fragment_ae=args.output_name_fragment_ae,
+        )
+    if args.out_drop_as_tsv != "None":
+        filter_fraser_result(
+            samples=args.samples,
+            gene_panel=args.gene_panel,
+            out_drop_aberrant_splicing_tsv=args.out_drop_as_tsv,
+            out_drop_gene_name=args.out_drop_gene_name,
+            case_id=args.case_id,
+            output_name_fragment_as=args.output_name_fragment_as,
+        )
 
 
 if __name__ == "__main__":
diff --git a/conf/base.config b/conf/base.config
index 169777b6..14782c73 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    tomte Nextflow base config file
+    genomic-medicine-sweden/tomte 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
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 3f114377..c53c559f 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -12,429 +12,20 @@ params {
     // illumina iGenomes reference file paths
     genomes {
         'GRCh37' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
+            fasta         = "${params.igenomes_base}/grch37_homo_sapiens_-gencode_pri-.fasta"
+            fai           = "${params.igenomes_base}/grch37_homo_sapiens_-gencode_pri-.fasta.fai"
+            gtf           = "${params.igenomes_base}/grch37_gencode_annotation_-v37-.gtf"
+            star_index    = "${params.igenomes_base}/grch37_homo_sapiens_star"
+            salmon_index  = "${params.igenomes_base}/grch37_homo_sapiens_salmon"
+            subsample_bed = "${params.igenomes_base}/grch37_homo_sapiens_hemoglobin_noncanonical.bed"
         }
         'GRCh38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'CHM13' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
-            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
-            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
-            mito_name   = "chrM"
-        }
-        'GRCm38' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
-        }
-        'TAIR10' {
-            fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
-            mito_name   = "Mt"
-        }
-        'EB2' {
-            fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
-        }
-        'UMD3.1' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'WBcel235' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
-            mito_name   = "MtDNA"
-            macs_gsize  = "9e7"
-        }
-        'CanFam3.1' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'GRCz10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'BDGP6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
-            mito_name   = "M"
-            macs_gsize  = "1.2e8"
-        }
-        'EquCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'EB1' {
-            fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
-        }
-        'Galgal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Gm01' {
-            fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
-        }
-        'Mmul_1' {
-            fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'IRGSP-1.0' {
-            fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'CHIMP2.1.4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'Rnor_5.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Rnor_6.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'R64-1-1' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-            macs_gsize  = "1.2e7"
-        }
-        'EF2' {
-            fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.21e7"
-        }
-        'Sbi1' {
-            fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
-        }
-        'Sscrofa10.2' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'AGPv3' {
-            fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'hg38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'hg19' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
-        }
-        'mm10' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
-        }
-        'bosTau8' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'ce10' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "9e7"
-        }
-        'canFam3' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'danRer10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.37e9"
-        }
-        'dm6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e8"
-        }
-        'equCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'galGal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'panTro4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'rn6' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'sacCer3' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
-            readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e7"
-        }
-        'susScr3' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
-            mito_name   = "chrM"
+            fasta         = "${params.igenomes_base}/grch38_homo_sapiens_-gencode_pri-.fasta"
+            fai           = "${params.igenomes_base}/grch38_homo_sapiens_-gencode_pri-.fasta.fai"
+            gtf           = "${params.igenomes_base}/grch38_gencode_annotation_-v37-.gtf"
+            star_index    = "${params.igenomes_base}/grch38_homo_sapiens_star"
+            salmon_index  = "${params.igenomes_base}/grch38_homo_sapiens_salmon"
+            subsample_bed = "${params.igenomes_base}/grch38_homo_sapiens_hemoglobin_noncanonical.bed"
         }
     }
 }
diff --git a/conf/modules.config b/conf/modules.config
deleted file mode 100644
index 10d5b68e..00000000
--- a/conf/modules.config
+++ /dev/null
@@ -1,522 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
-*/
-
-process {
-
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
-    withName: SAMPLESHEET_CHECK {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: FASTQC {
-        ext.args = '--quiet'
-    }
-
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
-    withName: 'MULTIQC' {
-        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-}
-
-//
-// Genome preparation options
-//
-
-process {
-
-    withName: '.*PREPARE_REFERENCES:GUNZIP_FASTA' {
-        ext.when = {params.fasta.endsWith(".gz")}
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-            pattern: "*.{fasta,fa}"
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME' {
-        ext.when = {!params.fai}
-        ext.args2 = " --no-same-owner "
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-            pattern: "*fai"
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:BUILD_DICT' {
-        ext.when = {!params.sequence_dict}
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-            pattern: "*dict"
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:GET_RRNA_TRANSCRIPTS' {
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:GET_CHROM_SIZES' {
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:UNTAR_STAR_INDEX' {
-        ext.when = {params.star_index && params.star_index.endsWith(".gz")}
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:BUILD_STAR_GENOME' {
-        ext.when = {!params.star_index}
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:GUNZIP_GTF' {
-        ext.when = { params.gtf && params.gtf.endsWith(".gz") }
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-            pattern: "*gtf"
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:GTF_TO_REFFLAT' {
-        ext.args = [
-            '-genePredExt',
-            '-geneNameAsName2'
-        ].join(' ').trim()
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-            pattern: "*refflat"
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:BEDTOINTERVALLIST' {
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:UNTAR_VEP_CACHE' {
-        ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) }
-        publishDir = [
-            enabled: false
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:GUNZIP_TRFASTA' {
-        ext.when = { params.transcript_fasta && params.transcript_fasta.endsWith(".gz") }
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-            pattern: "*.{fasta,fa}"
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:GFFREAD' {
-        ext.when = { (!params.transcript_fasta) }
-        ext.args = { '-w' }
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference,
-            pattern: "*.{fasta,fa}"
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:SALMON_INDEX' {
-        ext.when = {!params.salmon_index}
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
-    withName: '.*PREPARE_REFERENCES:UNTAR_SALMON_INDEX' {
-        ext.when = {params.salmon_index.endsWith(".gz")}
-        publishDir = [
-            path: { "${params.outdir}/references" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
-}
-
-//
-// Alignment options
-//
-
-process {
-    withName: '.*ALIGNMENT:FASTP' {
-        ext.args = [
-            params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
-            '--correction',
-            '--overrepresentation_analysis'
-        ].join(' ').trim()
-        publishDir = [
-            path: { "${params.outdir}/trimming" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ALIGNMENT:STAR_ALIGN' {
-        ext.args = [
-            "--twopassMode ${params.star_two_pass_mode}",
-            '--outReadsUnmapped None',
-            '--outSAMtype BAM SortedByCoordinate',
-            '--quantMode GeneCounts',
-            '--outSAMstrandField intronMotif',
-            '--peOverlapNbasesMin 10',
-            '--peOverlapMMp 0.1',
-            '--chimSegmentMin 12',
-            '--chimJunctionOverhangMin 12',
-            '--chimOutType WithinBAM',
-            '--readFilesCommand gunzip -c',
-            '--outWigType wiggle',
-            '--outWigStrand Unstranded'
-            ].join(' ')
-        publishDir = [
-            path: { "${params.outdir}/alignment" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ALIGNMENT:SAMTOOLS_INDEX' {
-        publishDir = [
-            path: { "${params.outdir}/trimming" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ALIGNMENT:SAMTOOLS_VIEW' {
-        ext.args = { '--output-fmt cram --write-index' }
-        ext.when = params.save_mapped_as_cram
-        publishDir = [
-            path: { "${params.outdir}/alignment" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-
-    withName: '.*ALIGNMENT:RNA_DOWNSAMPLE' {
-        publishDir = [
-            path: { "${params.outdir}/alignment" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ALIGNMENT:SALMON_QUANT' {
-        ext.args = [
-            '--gcBias',
-            '--validateMappings'
-            ].join(' ')
-        publishDir = [
-            path: { "${params.outdir}/alignment" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-}
-
-//
-// BAM_QC
-//
-
-process {
-    withName: '.*BAM_QC:PICARD_COLLECTRNASEQMETRICS' {
-        ext.args = { [
-            meta.strandedness.equals('unstranded') ? '--STRAND_SPECIFICITY NONE' : '',
-            meta.strandedness.equals('forward') ? '--STRAND_SPECIFICITY FIRST_READ_TRANSCRIPTION_STRAND' : '',
-            meta.strandedness.equals('reverse') ? '--STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND' : ''
-        ].join(' ').trim() }
-        publishDir = [
-            path: { "${params.outdir}/bam_qc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-}
-
-//
-// ANALYSE_TRANSCRIPTS
-//
-
-process {
-    withName: '.*ANALYSE_TRANSCRIPTS:DROP_SAMPLE_ANNOT' {
-        ext.when = {params.run_drop_ae_switch|params.run_drop_as_switch}
-        publishDir = [
-            path: { "${params.outdir}/analyse_transcripts/drop" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ANALYSE_TRANSCRIPTS:DROP_CONFIG_RUN_AE' {
-        ext.when = {params.run_drop_ae_switch}
-        publishDir = [
-            path: { "${params.outdir}/analyse_transcripts/drop/AE" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ANALYSE_TRANSCRIPTS:DROP_CONFIG_RUN_AS' {
-        ext.when = {params.run_drop_as_switch}
-        publishDir = [
-            path: { "${params.outdir}/analyse_transcripts/drop/AS" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ANALYSE_TRANSCRIPTS:DROP_FILTER_RESULTS' {
-        ext.when = {params.run_drop_ae_switch|params.run_drop_as_switch}
-        publishDir = [
-            path: { "${params.outdir}/analyse_transcripts/drop" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ANALYSE_TRANSCRIPTS:STRINGTIE_STRINGTIE' {
-        publishDir = [
-            path: { "${params.outdir}/analyse_transcripts" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*ANALYSE_TRANSCRIPTS:GFFCOMPARE' {
-        publishDir = [
-            path: { "${params.outdir}/analyse_transcripts" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-}
-
-//
-// CALL_VARIANTS
-//
-
-process {
-    withName: '.*CALL_VARIANTS_GATK:GATK4_SPLITNCIGARREADS' {
-        ext.prefix = { "${meta.id}_splitncigar" }
-        publishDir = [
-            enabled: false,
-        ]
-    }
-
-    withName: '.*CALL_VARIANTS_GATK:SAMTOOLS_INDEX' {
-        publishDir = [
-            enabled: false,
-        ]
-    }
-
-    withName: '.*CALL_VARIANTS_GATK:GATK4_HAPLOTYPECALLER' {
-        ext.args = [
-            '--dont-use-soft-clipped-bases',
-            '--create-output-variant-index',
-            '--standard-min-confidence-threshold-for-calling 20'
-        ].join(' ').trim()
-        ext.prefix = { "${meta.id}_gatk" }
-        publishDir = [
-            enabled: false,
-        ]
-    }
-
-    withName: '.*CALL_VARIANTS_GATK:GATK4_VARIANTFILTRATION' {
-        ext.args = [
-            '--window 3',
-            '--cluster 35',
-            '--filter-name "QD" --filter-expression "QD < 2.0"',
-            '--filter-name "FS" --filter-expression "FS > 30.0"'
-        ].join(' ').trim()
-        publishDir = [
-            path: { "${params.outdir}/call_variants" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*CALL_VARIANTS:BCFTOOLS_MPILEUP' {
-        ext.args = '--max-depth 2000'
-        ext.args2 = [
-            '--variants-only',
-            params.bcftools_caller_mode.equals('multiallelic')
-                ? '--multiallelic-caller'
-                : '--consensus-caller --pval-threshold 0.01',
-        ].join(' ').trim()
-        publishDir = [
-            path: { "${params.outdir}/call_variants" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
-    withName: '.*BCFTOOLS_STATS' {
-        publishDir = [
-            path: { "${params.outdir}/call_variants" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-}
-
-//
-// ALLELE_SPECIFIC_CALLING
-//
-
-process {
-    withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_VIEW' {
-        ext.prefix = { "${meta.id}_biallelic" }
-        ext.args = '--genotype het --max-alleles 2 --min-alleles 2 --types snps'
-    }
-
-    withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_INDEX' {
-        ext.args = '--tbi'
-    }
-
-    withName: '.*GATK4_ASEREADCOUNTER' {
-        publishDir = [
-            enabled: false
-        ]
-    }
-}
-
-//
-// ANNOTATE_SNV
-//
-
-process {
-    withName: '.*ANNOTATE_SNV:ENSEMBLVEP' {
-        ext.prefix = { "${vcf.simpleName}_vep" }
-        ext.args   = [
-            '--dir_plugins cache/Plugins',
-            '--plugin LoFtool,cache/Plugins/LoFtool_scores.txt',
-            '--plugin pLI,cache/Plugins/pLI_values_107.txt',
-            '--distance 5000',
-            '--buffer_size 20000',
-            '--format vcf --max_sv_size 248956422',
-            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
-            '--domains --exclude_predicted --force_overwrite',
-            '--hgvs --humdiv --no_progress --no_stats --numbers',
-            '--merged --polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
-            '--uniprot --vcf'
-        ].join(' ')
-        publishDir = [
-            path: { "${params.outdir}/annotate_vep" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*ANNOTATE_SNV:TABIX_VEP' {
-        publishDir = [
-            path: { "${params.outdir}/annotate_vep" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
-
-//
-// IGV_TRACKS
-//
-
-process {
-    withName: '.*IGV_TRACKS:UCSC_WIGTOBIGWIG' {
-        ext.args   = '-clip'
-    }
-
-    withName: '.*IGV_TRACKS:JUNCTION_TRACK' {
-        publishDir = [
-            path: { "${params.outdir}/ucsc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*IGV_TRACKS:TABIX_BGZIPTABIX' {
-        ext.args2   = '--preset bed'
-        publishDir = [
-            path: { "${params.outdir}/ucsc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/conf/modules/alignment.config b/conf/modules/alignment.config
new file mode 100644
index 00000000..73fc1690
--- /dev/null
+++ b/conf/modules/alignment.config
@@ -0,0 +1,97 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// Alignment options
+//
+
+process {
+    withName: '.*ALIGNMENT.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+    withName: '.*ALIGNMENT:FASTP' {
+        ext.args = { [
+            params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
+            '--correction',
+            '--overrepresentation_analysis'
+        ].join(' ').trim() }
+        publishDir = [
+            path: { "${params.outdir}/trimming" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ALIGNMENT:STAR_ALIGN' {
+        ext.args = { [
+            "--twopassMode ${params.star_two_pass_mode}",
+            '--outReadsUnmapped None',
+            '--outSAMtype BAM SortedByCoordinate',
+            '--quantMode GeneCounts',
+            '--outSAMstrandField intronMotif',
+            '--peOverlapNbasesMin 10',
+            '--peOverlapMMp 0.1',
+            '--chimSegmentMin 12',
+            '--chimJunctionOverhangMin 12',
+            '--chimOutType WithinBAM',
+            '--readFilesCommand gunzip -c',
+            '--outWigType wiggle',
+            '--outWigStrand Unstranded'
+            ].join(' ') }
+        publishDir = [
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ALIGNMENT:SAMTOOLS_INDEX' {
+        publishDir = [
+            path: { "${params.outdir}/trimming" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ALIGNMENT:SAMTOOLS_VIEW' {
+        ext.args = { '--output-fmt cram --write-index' }
+        ext.when = params.save_mapped_as_cram
+        publishDir = [
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*ALIGNMENT:RNA_DOWNSAMPLE' {
+        publishDir = [
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ALIGNMENT:SALMON_QUANT' {
+        ext.args = { [
+            '--gcBias',
+            '--validateMappings'
+            ].join(' ') }
+        publishDir = [
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+}
diff --git a/conf/modules/allele_specific_calling.config b/conf/modules/allele_specific_calling.config
new file mode 100644
index 00000000..65e12d9a
--- /dev/null
+++ b/conf/modules/allele_specific_calling.config
@@ -0,0 +1,59 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// ALLELE_SPECIFIC_CALLING
+//
+
+process {
+    withName: '.*ALLELE_SPECIFIC_CALLING.*' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_VIEW' {
+        ext.prefix = { "${meta.id}_biallelic" }
+        ext.args = { '--genotype het --max-alleles 2 --min-alleles 2 --types snps --output-type z' }
+    }
+
+    withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_INDEX' {
+        ext.args = { '--tbi' }
+    }
+
+    withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_MERGE' {
+        ext.args = '--output-type z'
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/bootstrapann" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ALLELE_SPECIFIC_CALLING:RENAME_FILES' {
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/bootstrapann" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ALLELE_SPECIFIC_CALLING:TABIX_TABIX' {
+        publishDir = [
+            path: { "${params.outdir}/bootstrapann" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+}
diff --git a/conf/modules/analyse_transcripts.config b/conf/modules/analyse_transcripts.config
new file mode 100644
index 00000000..c9ed8ed7
--- /dev/null
+++ b/conf/modules/analyse_transcripts.config
@@ -0,0 +1,71 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// ANALYSE_TRANSCRIPTS
+//
+
+process {
+    withName: '.*ANALYSE_TRANSCRIPTS:DROP_SAMPLE_ANNOT' {
+        ext.when = { params.switch_drop_ae | params.switch_drop_as }
+        publishDir = [
+            path: { "${params.outdir}/analyse_transcripts/drop" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ANALYSE_TRANSCRIPTS:DROP_CONFIG_RUN_AE' {
+        ext.when = { params.switch_drop_ae }
+        publishDir = [
+            path: { "${params.outdir}/analyse_transcripts/drop/AE" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ANALYSE_TRANSCRIPTS:DROP_CONFIG_RUN_AS' {
+        ext.when = { params.switch_drop_as }
+        publishDir = [
+            path: { "${params.outdir}/analyse_transcripts/drop/AS" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ANALYSE_TRANSCRIPTS:DROP_FILTER_RESULTS' {
+        ext.when = { params.switch_drop_ae | params.switch_drop_as }
+        publishDir = [
+            path: { "${params.outdir}/analyse_transcripts/drop" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ANALYSE_TRANSCRIPTS:STRINGTIE_STRINGTIE' {
+        ext.when = { params.switch_stringtie }
+        publishDir = [
+            path: { "${params.outdir}/analyse_transcripts" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*ANALYSE_TRANSCRIPTS:GFFCOMPARE' {
+        ext.when = { params.switch_stringtie }
+        publishDir = [
+            path: { "${params.outdir}/analyse_transcripts" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+}
diff --git a/conf/modules/annotate_snv.config b/conf/modules/annotate_snv.config
new file mode 100644
index 00000000..2b3c299e
--- /dev/null
+++ b/conf/modules/annotate_snv.config
@@ -0,0 +1,47 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// ANNOTATE_SNV
+//
+
+process {
+    withName: '.*ANNOTATE_SNV:ENSEMBLVEP_VEP' {
+        ext.when = { params.switch_vep }
+        ext.prefix = { "${vcf.simpleName}_vep" }
+        ext.args   = { [
+            '--dir_plugins vep_cache/Plugins',
+            '--plugin LoFtool,LoFtool_scores.txt',
+            '--plugin pLI,pLI_values.txt',
+            '--distance 5000',
+            '--buffer_size 20000',
+            '--format vcf --max_sv_size 248956422',
+            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
+            '--domains --exclude_predicted --force_overwrite',
+            '--hgvs --humdiv --no_progress --numbers',
+            '--merged --polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
+            '--uniprot --vcf'
+        ].join(' ') }
+        publishDir = [
+            path: { "${params.outdir}/annotate_vep" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: '.*ANNOTATE_SNV:TABIX_VEP' {
+        publishDir = [
+            path: { "${params.outdir}/annotate_vep" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
diff --git a/conf/modules/bam_qc.config b/conf/modules/bam_qc.config
new file mode 100644
index 00000000..1b612b2d
--- /dev/null
+++ b/conf/modules/bam_qc.config
@@ -0,0 +1,39 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// BAM_QC
+//
+
+process {
+    withName: '.*BAM_QC:PICARD_COLLECTRNASEQMETRICS' {
+        ext.args = { [
+            meta.strandedness.equals('unstranded') ? '--STRAND_SPECIFICITY NONE' : '',
+            meta.strandedness.equals('forward') ? '--STRAND_SPECIFICITY FIRST_READ_TRANSCRIPTION_STRAND' : '',
+            meta.strandedness.equals('reverse') ? '--STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND' : ''
+        ].join(' ').trim() }
+        publishDir = [
+            path: { "${params.outdir}/bam_qc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*BAM_QC:PICARD_COLLECTINSERTSIZEMETRICS' {
+        ext.prefix = { "${meta.id}_insert_size" }
+        publishDir = [
+            path: { "${params.outdir}/bam_qc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+}
diff --git a/conf/modules/call_variants.config b/conf/modules/call_variants.config
new file mode 100644
index 00000000..91d53a8c
--- /dev/null
+++ b/conf/modules/call_variants.config
@@ -0,0 +1,64 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// CALL_VARIANTS
+//
+
+process {
+    withName: '.*CALL_VARIANTS.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+    withName: '.*CALL_VARIANTS:CALL_VARIANTS_GATK:GATK4_SPLITNCIGARREADS' {
+        ext.prefix = { "${meta.id}_splitncigar" }
+    }
+
+    withName: '.*CALL_VARIANTS:CALL_VARIANTS_GATK:GATK4_HAPLOTYPECALLER' {
+        ext.args = { [
+            '--dont-use-soft-clipped-bases',
+            '--create-output-variant-index',
+            '--standard-min-confidence-threshold-for-calling 20'
+        ].join(' ').trim() }
+        ext.prefix = { "${meta.id}_gatk" }
+    }
+
+    withName: '.*CALL_VARIANTS:CALL_VARIANTS_GATK:GATK4_VARIANTFILTRATION' {
+        ext.args = { [
+            '--window 3',
+            '--cluster 35',
+            '--filter-name "QD" --filter-expression "QD < 2.0"',
+            '--filter-name "FS" --filter-expression "FS > 30.0"'
+        ].join(' ').trim() }
+    }
+
+    withName: '.*CALL_VARIANTS:BCFTOOLS_MPILEUP' {
+        ext.args = { '--max-depth 2000' }
+        ext.args2 = { [
+            '--variants-only',
+            params.bcftools_caller_mode.equals('multiallelic')
+                ? '--multiallelic-caller'
+                : '--consensus-caller --pval-threshold 0.01',
+        ].join(' ').trim() }
+    }
+
+    withName: '.*CALL_VARIANTS:CALL_VARIANTS_GATK:BCFTOOLS_STATS' {
+        publishDir = [
+            path: { "${params.outdir}/call_variants" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+}
diff --git a/conf/modules/general_tomte.config b/conf/modules/general_tomte.config
new file mode 100644
index 00000000..316c8bcd
--- /dev/null
+++ b/conf/modules/general_tomte.config
@@ -0,0 +1,41 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    withName: FASTQC {
+        ext.args = { '--quiet' }
+    }
+
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+
+    withName: 'MULTIQC' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
diff --git a/conf/modules/igv_tracks.config b/conf/modules/igv_tracks.config
new file mode 100644
index 00000000..a4dea5eb
--- /dev/null
+++ b/conf/modules/igv_tracks.config
@@ -0,0 +1,37 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// IGV_TRACKS
+//
+
+process {
+    withName: '.*IGV_TRACKS:UCSC_WIGTOBIGWIG' {
+        ext.when = { params.switch_build_tracks }
+        ext.args = { '-clip' }
+    }
+
+    withName: '.*IGV_TRACKS:JUNCTION_TRACK' {
+        ext.when = { params.switch_build_tracks }
+    }
+
+    withName: '.*IGV_TRACKS:TABIX_BGZIPTABIX' {
+        ext.when = { params.switch_build_tracks }
+        ext.args2  = { '--preset bed' }
+        ext.prefix = { "${meta.id}_junction" }
+        publishDir = [
+            path: { "${params.outdir}/ucsc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config
new file mode 100644
index 00000000..5f2932cd
--- /dev/null
+++ b/conf/modules/prepare_references.config
@@ -0,0 +1,174 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// Genome preparation options
+//
+
+process {
+
+    withName: '.*PREPARE_REFERENCES:GUNZIP_FASTA' {
+        ext.when = {params.fasta.endsWith(".gz")}
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+            pattern: "*.{fasta,fa}"
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME' {
+        ext.when = { !params.fai }
+        ext.args2 = { '--no-same-owner' }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+            pattern: "*fai"
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:BUILD_DICT' {
+        ext.when = { !params.sequence_dict }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+            pattern: "*dict"
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:GET_RRNA_TRANSCRIPTS' {
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:GET_CHROM_SIZES' {
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:UNTAR_STAR_INDEX' {
+        ext.when = { params.star_index && params.star_index.endsWith(".gz") }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:BUILD_STAR_GENOME' {
+        ext.when = { !params.star_index }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:GUNZIP_GTF' {
+        ext.when = { params.gtf && params.gtf.endsWith(".gz") }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+            pattern: "*gtf"
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:GTF_TO_REFFLAT' {
+        ext.args = { [
+            '-genePredExt',
+            '-geneNameAsName2'
+        ].join(' ').trim() }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+            pattern: "*refflat"
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:BEDTOINTERVALLIST' {
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:UNTAR_VEP_CACHE' {
+        ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:GUNZIP_TRFASTA' {
+        ext.when = { params.transcript_fasta && params.transcript_fasta.endsWith(".gz") }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+            pattern: "*.{fasta,fa}"
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:GFFREAD' {
+        ext.when = { !params.transcript_fasta }
+        ext.args = { '-w' }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference,
+            pattern: "*.{fasta,fa}"
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:SALMON_INDEX' {
+        ext.when = { !params.salmon_index }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
+        ]
+    }
+
+    withName: '.*PREPARE_REFERENCES:UNTAR_SALMON_INDEX' {
+        ext.when = { params.salmon_index.endsWith(".gz") }
+        publishDir = [
+            path: { "${params.outdir}/references" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
+        ]
+    }
+
+}
diff --git a/conf/test.config b/conf/test.config
index c7a9bcba..eeb61a26 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  genomic-medicine-sweden/tomte -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run genomic-medicine-sweden/tomte -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -38,6 +38,7 @@ params {
     vep_cache            = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz"
     vep_filters          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
     vep_cache_version    = 107
+    vep_plugin_files     = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv"
 
     // DROP
     reference_drop_count_file    = "${projectDir}/test_data/drop_data/geneCounts.tsv.gz"
@@ -45,6 +46,6 @@ params {
     reference_drop_annot_file    = "${projectDir}/test_data/drop_data/sampleAnnotation.tsv"
     gene_panel_clinical_filter   = "${projectDir}/test_data/drop_data/mock_gene_panel.tsv"
     drop_padjcutoff_ae           = 1
-    drop_padjcutoff_as           = 0.75
+    drop_padjcutoff_as           = 1
     drop_zscorecutoff            = 2.5
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index 23afe3e7..f2ddc76d 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run  genomic-medicine-sweden/tomte -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run genomic-medicine-sweden/tomte -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
diff --git a/docs/README.md b/docs/README.md
index 9d76d9e1..23be83a4 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,6 +1,10 @@
-# tomte: Documentation
+# genomic-medicine-sweden/tomte: Documentation
 
-The tomte documentation is split into the following pages:
+# The genomic-medicine-sweden/tomte documentation is split into the following pages:
+
+# genomic-medicine-sweden/tomte: Documentation
+
+The genomic-medicine-sweden/tomte 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 589cb62b..5e24b011 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,4 +1,4 @@
-# tomte: Output
+# genomic-medicine-sweden/tomte: Output
 
 ## Introduction
 
@@ -31,8 +31,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [`Variant annotation`](#variant-annotation)
   - [`VEP`](#vep) annotation
 - [`Pipeline information and QCs`](#pipeline-information-and-qcs)
-  - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+  - [Pipeline information](#pipeline-information) - report metrics generated during the workflow execution
   - [`Picard CollectRnaSeqMetrics`](#picard-collectrnaseqmetrics) alignment QC
+  - [`Picard CollectInsertSizeMetrics`](#picard-collectinsertsizemetrics) insert size
   - [`MultiQC`](#multiqc) presents QCs
 
 ### Trimming
@@ -242,6 +243,18 @@ to "gatk". Involves several steps: [`SplitN Cigar Reads`](https://gatk.broadinst
 
 - `bam_qc/`
   - `*rna_metrics`: metrics describing the distribution of the bases within the transcripts.
+  - `*_insert_size.txt`: metrics describing the insert size.
+
+#### Picard CollectInsertSizeMetrics
+
+[`Picard CollectInsertSizeMetrics`](https://broadinstitute.github.io/picard/)
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `bam_qc/`
+  - `*rna_metrics`: metrics describing the distribution of the bases within the transcripts.
+  - `sample.txt`: metrics describing the insert size.
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index ddabdb21..125e4339 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -121,17 +121,19 @@ If you would like to see more examples of what a typical samplesheet looks like
 
 #### Reference files and parameters
 
-In genomic-medicine-sweden/tomte, references can be supplied using parameters.
+In genomic-medicine-sweden/tomte, references can be supplied using parameters. We have also introduced the possiblility of using the `--igenomes_base` parameter to point to a path where genome specific reference files are placed (fasta, fai, gtf, star_index, salmon_index, subsample_bed). To make sure that the names of the reference files match those in your directory, check [igenomes.config](https://github.com/genomic-medicine-sweden/tomte/blob/master/conf/igenomes.config).
 
-Note that the pipeline is modular in architecture. It offers you the flexibility to choose between different tools. For example, you can call SNVs either with BCFtools or with GATK. You also have the option to turn off sections of the pipeline if you do not want to run them. For example, drop aberrant expression module can be turned off by setting `--run_drop_ae_switch FALSE`. This flexibility means that in any given analysis run, a combination of tools included in the pipeline will not be executed. So the pipeline is written in a way that can account for these differences while working with reference parameters. If a tool is not going to be executed during the course of a run, parameters used only by that tool need not be provided. For example, if you are not running DROP aberrant splicing, you do not need to provide `--reference_drop_splice_folder`.
+Note that the pipeline is modular in architecture. It offers you the flexibility to choose between different tools. For example, you can call SNVs either with BCFtools or with GATK. You also have the option to turn off sections of the pipeline if you do not want to run them. For example, drop aberrant expression module can be turned off by setting `--switch_drop_ae FALSE`. This flexibility means that in any given analysis run, a combination of tools included in the pipeline will not be executed. So the pipeline is written in a way that can account for these differences while working with reference parameters. If a tool is not going to be executed during the course of a run, parameters used only by that tool need not be provided. For example, if you are not running DROP aberrant splicing, you do not need to provide `--reference_drop_splice_folder`.
 
 genomic-medicine-sweden/tomte consists of several tools used for various purposes. For convenience, we have grouped those tools under the following categories:
 
 1. Alignment and pseudo quantification (STAR & Salmon)
-2. Subsample_region (Samtools)
-3. Variant calling - SNV (BCFTools or GATK's GermlineCNVCaller)
-4. SNV annotation (ensembl VEP)
-5. DROP
+2. Junction track and bigwig
+3. Subsample region (Samtools)
+4. Variant calling - SNV (BCFTools or GATK's HaplotypeCaller)
+5. SNV annotation (ensembl VEP)
+6. Stringtie & gffcompare
+7. DROP
 
 > We have only listed the groups that require at least one input from the user. For example, the pipeline also runs WigToBigWig, but it does not require any input other than the bam files passed by the pipeline. Hence, it is not mentioned in the list above. To know more about the tools used in the pipeline check the [README](../README.md).
 
@@ -153,80 +155,105 @@ The mandatory and optional parameters for each category are tabulated below.
 |           | min_trimmed_length<sup>4</sup> |
 |           | star_two_pass_mode<sup>4</sup> |
 
-<sup>1</sup> If the parameter is not provided by the user, it will be generated from the fasta and gtf files.
-<sup>2</sup> If it is not provided by the user, the default value is GRCh38.
-<sup>3</sup> If it is not provided by the user, the default value is illumina.
-<sup>4</sup> If it is not provided by the user, the default value is 40.
+<sup>1</sup> If the parameter is not provided by the user, it will be generated from the fasta and gtf files.<br />
+<sup>2</sup> If it is not provided by the user, the default value is GRCh38.<br />
+<sup>3</sup> If it is not provided by the user, the default value is illumina.<br />
+<sup>4</sup> If it is not provided by the user, the default value is 40.<br />
 <sup>5</sup> If it is not provided by the user, the default value is Basic.
 
-##### 2. Subsample region
+##### 2. Junction track and bigwig
 
-| Mandatory     | Optional                             |
-| ------------- | ------------------------------------ |
-| subsample_bed | subsample_region_switch <sup>1</sup> |
-|               | seed_frac<sup>2</sup>                |
+| Mandatory | Optional                         |
+| --------- | -------------------------------- |
+|           | switch_build_tracks <sup>1</sup> |
+
+<sup>1</sup> If it is not provided by the user, the default value is true
+
+##### 3. Subsample region
+
+| Mandatory     | Optional                            |
+| ------------- | ----------------------------------- |
+| subsample_bed | switch_subsample_region<sup>1</sup> |
+|               | seed_frac<sup>2</sup>               |
 
 <sup>1</sup> If it is not provided by the user, the default value is true
 <sup>2</sup> If it is not provided by the user, the default value is 0.001
 
-##### 3. Variant calling - SNV
+##### 4. Variant calling - SNV
 
 | Mandatory | Optional                         |
 | --------- | -------------------------------- |
 |           | variant_caller<sup>1</sup>       |
 |           | bcftools_caller_mode<sup>2</sup> |
 
-<sup>1</sup> If it is not provided by the user, the default value is bcftools
+<sup>1</sup> If it is not provided by the user, the default value is bcftools<br />
 <sup>2</sup> If it is not provided by the user, the default value is multiallelic
 
-#### 4. SNV annotation (ensembl VEP)
+#### 5. SNV annotation (ensembl VEP)
 
-| Mandatory | Optional                      |
-| --------- | ----------------------------- |
-| vep_cache | vep_cache_version<sup>1</sup> |
-|           | vep_filters                   |
+| Mandatory                    | Optional               |
+| ---------------------------- | ---------------------- |
+| vep_plugin_files<sup>1</sup> | switch_vep<sup>2</sup> |
+|                              | vep_cache<sup>3</sup>  |
+|                              | vep_cache_version      |
+|                              | vep_filters            |
 
-<sup>1</sup> For the time being, only 107 is suported
+<sup>1</sup> VEP caches can be downloaded [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache). VEP plugins may be installed in the cache directory, and the plugin pLI is mandatory to install. To supply files required by VEP plugins, use `vep_plugin_files` parameter. See example cache [here](https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz).<br />
+<sup>2</sup> If it is not provided by the user, the default value is true<br />
+<sup>3</sup> If it is not provided by the user, the default value is 110, supported values are 107 and 110 <br />
 
-#### 5. DROP
+#### 6. Stringtie & gffcompare
+
+| Mandatory | Optional                     |
+| --------- | ---------------------------- |
+| fasta     | switch_stringtie<sup>1</sup> |
+| gtf       |                              |
+
+<sup>1</sup> If it is not provided by the user, the default value is true
+
+#### 7. DROP
 
 DROP - aberrant expression
 
 | Mandatory                             | Optional                          |
 | ------------------------------------- | --------------------------------- |
-| reference_drop_annot_file<sup>1</sup> | run_drop_ae_switch<sup>2</sup>    |
+| reference_drop_annot_file<sup>1</sup> | switch_drop_ae<sup>2</sup>        |
 | reference_drop_count_file             | drop_group_samples_ae<sup>3</sup> |
-|                                       | drop_padjcutoff_ae<sup>4</sup>    |
-|                                       | drop_zscorecutoff<sup>5</sup>     |
+| fasta                                 | drop_padjcutoff_ae<sup>4</sup>    |
+| gtf                                   | drop_zscorecutoff<sup>5</sup>     |
 |                                       | gene_panel_clinical_filter        |
-|                                       | downsample_switch<sup>6</sup>     |
+|                                       | switch_downsample<sup>6</sup>     |
 |                                       | num_reads<sup>7</sup>             |
+|                                       | genome<sup>8</sup>                |
 
-<sup>1</sup> To get more information on how to format it, see below
-<sup>2</sup> If it is not provided by the user, the default value is true
-<sup>3</sup> If it is not provided by the user, the default value is outrider
-<sup>4</sup> If it is not provided by the user, the default value is 0.05
-<sup>5</sup> If it is not provided by the user, the default value is 0
-<sup>6</sup> If it is not provided by the user, the default value is true
-<sup>7</sup> If it is not provided by the user, the default value is 120000000
+<sup>1</sup> To get more information on how to format it, see below<br />
+<sup>2</sup> If it is not provided by the user, the default value is true<br />
+<sup>3</sup> If it is not provided by the user, the default value is outrider<br />
+<sup>4</sup> If it is not provided by the user, the default value is 0.05<br />
+<sup>5</sup> If it is not provided by the user, the default value is 0<br />
+<sup>6</sup> If it is not provided by the user, the default value is true<br />
+<sup>7</sup> If it is not provided by the user, the default value is 120000000<br />
+<sup>8</sup> If it is not provided by the user, the default value is GRCh38
 
 DROP - aberrant splicing
 
 | Mandatory                             | Optional                          |
 | ------------------------------------- | --------------------------------- |
-| reference_drop_annot_file<sup>1</sup> | run_drop_as_switch<sup>2</sup>    |
+| reference_drop_annot_file<sup>1</sup> | switch_drop_as<sup>2</sup>        |
 | reference_drop_splice_folder          | drop_group_samples_as<sup>3</sup> |
 |                                       | drop_padjcutoff_as<sup>4</sup>    |
 |                                       | gene_panel_clinical_filter        |
-|                                       | downsample_switch<sup>5</sup>     |
+|                                       | switch_downsample<sup>5</sup>     |
 |                                       | num_reads<sup>6</sup>             |
-
-<sup>1</sup> To get more information on how to format it, see below
-<sup>2</sup> If it is not provided by the user, the default value is true
-<sup>3</sup> If it is not provided by the user, the default value is fraser
-<sup>4</sup> If it is not provided by the user, the default value is 0.1
-<sup>5</sup> If it is not provided by the user, the default value is true
-<sup>6</sup> If it is not provided by the user, the default value is 120000000
+|                                       | genome<sup>7</sup>                |
+
+<sup>1</sup> To get more information on how to format it, see below<br />
+<sup>2</sup> If it is not provided by the user, the default value is true<br />
+<sup>3</sup> If it is not provided by the user, the default value is fraser<br />
+<sup>4</sup> If it is not provided by the user, the default value is 0.1<br />
+<sup>5</sup> If it is not provided by the user, the default value is true<br />
+<sup>6</sup> If it is not provided by the user, the default value is 120000000<br />
+<sup>7</sup> If it is not provided by the user, the default value is GRCh38
 
 ##### Preparing input for DROP
 
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
deleted file mode 100755
index 86119c9e..00000000
--- a/lib/NfcoreTemplate.groovy
+++ /dev/null
@@ -1,375 +0,0 @@
-//
-// This file holds several functions used within the nf-core pipeline template.
-//
-
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-
-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());
-        }
-    }
-
-    //
-    // Dump pipeline parameters in a json file
-    //
-    public static void dump_parameters(workflow, params) {
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-
-        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def output_pf  = new File(output_d, "params_${timestamp}.json")
-        def jsonStr    = JsonOutput.toJson(params)
-        output_pf.text = JsonOutput.prettyPrint(jsonStr)
-    }
-
-    //
-    // 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)}
-                                                    ${colors.green},--.${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} ${workflow_version}${colors.reset}
-            ${dashedLine(monochrome_logs)}
-            """.stripIndent()
-        )
-    }
-
-    //
-    // GMS tomte logo (WIP)
-    //
-    public static String gmsLogo(workflow, monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        String workflow_version = NfcoreTemplate.version(workflow)
-        String.format(
-            """\n
-            ${dashedLine(monochrome_logs)}
-            ${colors.blue}   _____ __  __  _____            _                  _${colors.reset}
-            ${colors.blue}  / ____|  \\/  |/ ____|          | |                | |${colors.reset}
-            ${colors.blue} | |  __| \\  / | (___    ______  | |_ ___  _ __ ___ | |_ ___${colors.reset}
-            ${colors.blue} | | |_ | |\\/| |\\___ \\  |______| | __/ _ \\| '_ ` _ \\| __/ _ \\${colors.reset}
-            ${colors.blue} | |__| | |  | |____) |          | || (_) | | | | | | ||  __/${colors.reset}
-            ${colors.blue}  \\_____|_|  |_|_____/            \\__\\___/|_| |_| |_|\\__\\___|${colors.reset}
-
-            ${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 8d030f4e..00000000
--- 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/WorkflowMain.groovy b/lib/WorkflowMain.groovy
deleted file mode 100755
index f437aa3c..00000000
--- a/lib/WorkflowMain.groovy
+++ /dev/null
@@ -1,63 +0,0 @@
-//
-// This file holds several functions specific to the main.nf workflow in the genomic-medicine-sweden/tomte pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowMain {
-
-    //
-    // Citation string for pipeline
-    //
-    public static String citation(workflow) {
-        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            // TODO nf-core: Add Zenodo DOI for pipeline after first release
-            //"* The pipeline\n" +
-            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
-            "* The nf-core framework\n" +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-            "* Software dependencies\n" +
-            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-    }
-
-
-    //
-    // Validate parameters and print summary to screen
-    //
-    public static void initialise(workflow, params, log) {
-
-        // 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)
-        }
-
-        // 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/WorkflowTomte.groovy b/lib/WorkflowTomte.groovy
deleted file mode 100755
index c06e060f..00000000
--- a/lib/WorkflowTomte.groovy
+++ /dev/null
@@ -1,122 +0,0 @@
-//
-// This file holds several functions specific to the workflow/tomte.nf in the nf-core/tomte pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowTomte {
-
-    //
-    // 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
-    }
-
-    //
-    // Generate methods description for MultiQC
-    //
-
-    public static String toolCitationText(params) {
-
-        // TODO 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
-    }
-
-    public static String toolBibliographyText(params) {
-
-        // TODO 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
-    }
-
-    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) {
-        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
-        def meta = [:]
-        meta.workflow = run_workflow.toMap()
-        meta["manifest_map"] = run_workflow.manifest.toMap()
-
-        // Pipeline DOI
-        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
-
-        // Tool references
-        meta["tool_citations"] = ""
-        meta["tool_bibliography"] = ""
-
-        // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-        //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-        //meta["tool_bibliography"] = toolBibliographyText(params)
-
-
-        def methods_text = mqc_methods_yaml.text
-
-        def engine =  new SimpleTemplateEngine()
-        def description_html = engine.createTemplate(methods_text).make(meta)
-
-        return description_html
-    }
-
-    //
-    // Exit pipeline if incorrect --genome key provided
-    //
-    private static void genomeExistsError(params, log) {
-        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  Genome '${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/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
deleted file mode 100644
index 805c8bb5..00000000
Binary files a/lib/nfcore_external_java_deps.jar and /dev/null differ
diff --git a/main.nf b/main.nf
index 0ee71456..c1cca78c 100644
--- a/main.nf
+++ b/main.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    tomte
+    genomic-medicine-sweden/tomte
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/genomic-medicine-sweden/tomte
 ----------------------------------------------------------------------------------------
@@ -11,84 +11,114 @@ nextflow.enable.dsl = 2
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    GENOME PARAMETER VALUES
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta                          = WorkflowMain.getGenomeAttribute(params, 'fasta')
-params.fai                            = WorkflowMain.getGenomeAttribute(params, 'fai')
-params.gtf                            = WorkflowMain.getGenomeAttribute(params, 'gtf')
-params.reference_drop_count_file      = WorkflowMain.getGenomeAttribute(params, 'reference_drop_count_file')
-params.reference_drop_splice_folder   = WorkflowMain.getGenomeAttribute(params, 'reference_drop_splice_folder')
-params.reference_drop_annot_file      = WorkflowMain.getGenomeAttribute(params, 'reference_drop_annot_file')
-params.gene_panel_clinical_filter     = WorkflowMain.getGenomeAttribute(params, 'gene_panel_clinical_filter')
-params.sequence_dict                  = WorkflowMain.getGenomeAttribute(params, 'sequence_dict')
-params.star_index                     = WorkflowMain.getGenomeAttribute(params, 'star_index')
-params.salmon_index                   = WorkflowMain.getGenomeAttribute(params, 'salmon_index')
-params.transcript_fasta               = WorkflowMain.getGenomeAttribute(params, 'transcript_fasta')
-params.vep_cache                      = WorkflowMain.getGenomeAttribute(params, 'vep_cache')
-params.vep_cache_version              = WorkflowMain.getGenomeAttribute(params, 'vep_cache_version')
-params.vep_filters                    = WorkflowMain.getGenomeAttribute(params, 'vep_filters')
+include { TOMTE                   } from './workflows/tomte'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_tomte_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_tomte_pipeline'
+
+include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_tomte_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    OTHER PARAMETER VALUES
+    GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.subsample_bed                  = WorkflowMain.getGenomeAttribute(params, 'subsample_bed')
+params.fasta                        = getGenomeAttribute('fasta')
+params.fai                          = getGenomeAttribute('fai')
+params.gtf                          = getGenomeAttribute('gtf')
+params.reference_drop_count_file    = getGenomeAttribute('reference_drop_count_file')
+params.reference_drop_splice_folder = getGenomeAttribute('reference_drop_splice_folder')
+params.reference_drop_annot_file    = getGenomeAttribute('reference_drop_annot_file')
+params.gene_panel_clinical_filter   = getGenomeAttribute('gene_panel_clinical_filter')
+params.sequence_dict                = getGenomeAttribute('sequence_dict')
+params.star_index                   = getGenomeAttribute('star_index')
+params.salmon_index                 = getGenomeAttribute('salmon_index')
+params.transcript_fasta             = getGenomeAttribute('transcript_fasta')
+params.vep_cache                    = getGenomeAttribute('vep_cache')
+params.vep_filters                  = getGenomeAttribute('vep_filters')
+params.vep_plugin_files             = getGenomeAttribute('vep_plugin_files')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE & PRINT PARAMETER SUMMARY
+    OTHER PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
-
-// Print help message if needed
-if (params.help) {
-    def logo = NfcoreTemplate.gmsLogo(workflow, params.monochrome_logs)
-    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
-
-WorkflowMain.initialise(workflow, params, log)
+params.subsample_bed                  = getGenomeAttribute('subsample_bed')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
+    NAMED WORKFLOWS FOR PIPELINE
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { TOMTE } from './workflows/tomte'
-
 //
-// WORKFLOW: Run main nf-core/tomte analysis pipeline
+// WORKFLOW: Run main analysis pipeline depending on type of input
 //
-workflow GMS_TOMTE {
-    TOMTE ()
-}
+workflow GENOMICMEDICINESWEDEN_TOMTE {
+
+    take:
+    samplesheet // channel: samplesheet read in from --input
+
+    main:
+
+    //
+    // WORKFLOW: Run pipeline
+    //
+    TOMTE (
+        samplesheet
+    )
 
+    emit:
+    multiqc_report = TOMTE.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 {
-    GMS_TOMTE ()
+
+    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
+    //
+    GENOMICMEDICINESWEDEN_TOMTE (
+        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,
+        GENOMICMEDICINESWEDEN_TOMTE.out.multiqc_report
+    )
 }
 
 /*
diff --git a/modules.json b/modules.json
index 24b93745..119ff993 100644
--- a/modules.json
+++ b/modules.json
@@ -1,165 +1,197 @@
 {
-    "name": "nf-core/tomte",
-    "homePage": "https://github.com/nf-core/tomte",
+    "name": "genomic-medicine-sweden/tomte",
+    "homePage": "https://github.com/genomic-medicine-sweden/tomte",
     "repos": {
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
                     "bcftools/index": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+                        "installed_by": ["modules"]
+                    },
+                    "bcftools/merge": {
+                        "branch": "master",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["modules"]
                     },
                     "bcftools/mpileup": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/mpileup/bcftools-mpileup.diff"
                     },
                     "bcftools/stats": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["modules"]
                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "1013101da4252623fd7acf19cc581bae91d4f839",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca",
                         "installed_by": ["modules"]
                     },
-                    "custom/dumpsoftwareversions": {
+                    "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f",
+                        "git_sha": "76a0696a60c41c57fc5f6040ac31b11ce5d4d8dd",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
                         "installed_by": ["modules"]
                     },
                     "gatk4/asereadcounter": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/haplotypecaller": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/splitncigarreads": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "8797a219dfdac9bfa08645a6ad234f104b96fb76",
                         "installed_by": ["modules"]
                     },
                     "gatk4/variantfiltration": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gffcompare": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "installed_by": ["modules"]
+                    },
+                    "picard/collectinsertsizemetrics": {
+                        "branch": "master",
+                        "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
                         "installed_by": ["modules"]
                     },
                     "picard/collectrnaseqmetrics": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
                         "installed_by": ["modules"]
                     },
                     "salmon/index": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "ffc101e1b84ef3df2e4e4a966e84b3c513ae5693",
                         "installed_by": ["modules"]
                     },
                     "salmon/quant": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
-                        "installed_by": ["modules"]
+                        "git_sha": "03a8562231d575c313266c193a980594b941e3ea",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/salmon/quant/salmon-quant.diff"
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb",
                         "installed_by": ["modules"]
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
                         "installed_by": ["modules"]
                     },
                     "stringtie/stringtie": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
+                        "installed_by": ["modules"]
+                    },
+                    "tabix/bgzip": {
+                        "branch": "master",
+                        "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1",
                         "installed_by": ["modules"]
                     },
                     "ucsc/wigtobigwig": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["modules"]
                     }
                 }
             },
             "subworkflows": {
-                "nf-core": {}
+                "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/drop_config_runAE.nf b/modules/local/drop_config_runAE.nf
index 26d39fe0..2822db46 100644
--- a/modules/local/drop_config_runAE.nf
+++ b/modules/local/drop_config_runAE.nf
@@ -38,6 +38,7 @@ process DROP_CONFIG_RUN_AE {
 
     """
     TMPDIR=\$PWD
+    HOME=\$PWD
 
     drop init
 
diff --git a/modules/local/drop_config_runAS.nf b/modules/local/drop_config_runAS.nf
index 8fa7349f..75ca76a0 100644
--- a/modules/local/drop_config_runAS.nf
+++ b/modules/local/drop_config_runAS.nf
@@ -24,6 +24,7 @@ process DROP_CONFIG_RUN_AS {
     path('config.yaml')             , emit: config_drop
     path('output')                  , emit: drop_as_out
     path('FRASER_results_fraser--*'), emit: drop_as_tsv
+    path('gene_name_mapping*')      , emit: drop_gene_name
     path "versions.yml"             , emit: versions
 
     when:
@@ -34,6 +35,8 @@ process DROP_CONFIG_RUN_AS {
     def drop_group = "${drop_group_samples_as}".replace(" ","")
     """
     TMPDIR=\$PWD
+    HOME=\$PWD
+
 
     drop init
 
@@ -49,6 +52,7 @@ process DROP_CONFIG_RUN_AS {
     snakemake aberrantSplicing --cores ${task.cpus} --rerun-triggers mtime
 
     cp output/html/AberrantSplicing/FRASER_results_fraser--*.tsv .
+    cp output/processed_data/preprocess/*/gene_name_mapping_*.tsv .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -61,6 +65,7 @@ process DROP_CONFIG_RUN_AS {
     """
     touch config.yaml
     touch FRASER_results_fraser--.tsv
+    touch gene_name_mapping_.tsv
     mkdir output
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/drop_filter_results.nf b/modules/local/drop_filter_results.nf
index 619c57c3..3f4e5cd0 100644
--- a/modules/local/drop_filter_results.nf
+++ b/modules/local/drop_filter_results.nf
@@ -10,24 +10,25 @@ process DROP_FILTER_RESULTS {
     container "docker.io/clinicalgenomics/drop:1.3.3"
 
     input:
-    val(samples)
+    val(case_info)
     path gene_panel_clinical_filter
     path out_drop_ae_rds_in
     path out_drop_gene_name_in
     path out_drop_as_tsv_in
 
     output:
-    path('OUTRIDER_provided_samples_top_hits.tsv')         , optional: true, emit: ae_out_unfiltered
-    path('OUTRIDER_provided_samples_top_hits_filtered.tsv'), optional: true, emit: ae_out_filtered
-    path('FRASER_provided_samples_top_hits.tsv')           , optional: true, emit: as_out_unfiltered
-    path('FRASER_provided_samples_top_hits_filtered.tsv')  , optional: true, emit: as_out_filtered
-    path "versions.yml"                                    , emit: versions
+    path('*outrider_top_hits_research.tsv') , optional: true, emit: ae_out_research
+    path('*outrider_top_hits_clinical.tsv') , optional: true, emit: ae_out_clinical
+    path('*fraser_top_hits_research.tsv')   , optional: true, emit: as_out_research
+    path('*fraser_top_hits_clinical.tsv')   , optional: true, emit: as_out_clinical
+    path "versions.yml"                                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def ids = "${samples.id}".replace("[","").replace("]","").replace(",","")
+    def ids = "${case_info.probands}".replace("[","").replace("]","").replace(",","")
+    def case_id = "${case_info.id}".replace("[","").replace("]","").replace(",","")
     def gene_panel_filter = gene_panel_clinical_filter ? "--gene_panel ${gene_panel_clinical_filter}" : ''
     def drop_ae_rds = out_drop_ae_rds_in ? "--drop_ae_rds ${out_drop_ae_rds_in}" : ''
     def out_drop_gene_name = out_drop_gene_name_in ? "--out_drop_gene_name ${out_drop_gene_name_in}" : ''
@@ -39,7 +40,8 @@ process DROP_FILTER_RESULTS {
         $gene_panel_filter \\
         $drop_ae_rds \\
         $out_drop_gene_name \\
-        $out_drop_as_tsv
+        $out_drop_as_tsv \\
+        --case $case_id \\
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -49,10 +51,10 @@ process DROP_FILTER_RESULTS {
 
     stub:
     """
-    touch OUTRIDER_provided_samples_top_hits.tsv
-    touch OUTRIDER_provided_samples_top_hits_filtered.tsv
-    touch FRASER_provided_samples_top_hits.tsv
-    touch FRASER_provided_samples_top_hits_filtered.tsv
+    touch outrider_top_hits_research.tsv
+    touch outrider_top_hits_clinical.tsv
+    touch fraser_top_hits_research.tsv
+    touch fraser_top_hits_clinical.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/rename_files.nf b/modules/local/rename_files.nf
new file mode 100644
index 00000000..571f8b9a
--- /dev/null
+++ b/modules/local/rename_files.nf
@@ -0,0 +1,45 @@
+process RENAME_FILES {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "conda-forge::coreutils=8.31"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--0' :
+        'biocontainers/gnu-wget:1.18--0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("${output}"), emit: output
+    path "versions.yml",                emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def simplename = input.getSimpleName()
+    output = input.toString().replace("${simplename}","${prefix}")
+    """
+    ln -s $input ${output}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ln: \$(echo \$(ln --version 2>&1 | head -n 1 | cut -d ' ' -f4))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def simplename = input.getSimpleName()
+    output = input.toString().replace("${simplename}","${prefix}")
+    """
+    touch ${output}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ln: \$(echo \$(ln --version 2>&1 | head -n 1 | cut -d ' ' -f4))
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
deleted file mode 100644
index 3e9ead06..00000000
--- 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, originally from nf-core
-    """
-    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/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml
index 57631f42..bbee37ad 100644
--- a/modules/nf-core/bcftools/index/environment.yml
+++ b/modules/nf-core/bcftools/index/environment.yml
@@ -1,6 +1,7 @@
+name: bcftools_index
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::bcftools=1.17
+  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
index b94e9b4e..4cd0dcbb 100644
--- a/modules/nf-core/bcftools/index/main.nf
+++ b/modules/nf-core/bcftools/index/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_INDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'biocontainers/bcftools:1.17--haef29d1_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/bcftools/merge/environment.yml
similarity index 57%
rename from modules/nf-core/custom/dumpsoftwareversions/environment.yml
rename to modules/nf-core/bcftools/merge/environment.yml
index 9d0e6b20..55de7cd3 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml
+++ b/modules/nf-core/bcftools/merge/environment.yml
@@ -1,6 +1,7 @@
+name: bcftools_merge
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.17
+  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
new file mode 100644
index 00000000..b85d3fec
--- /dev/null
+++ b/modules/nf-core/bcftools/merge/main.nf
@@ -0,0 +1,64 @@
+process BCFTOOLS_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
+
+    input:
+    tuple val(meta), path(vcfs), path(tbis)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    path(bed)
+
+    output:
+    tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: merged_variants
+    path "versions.yml"                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args   ?: ''
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+
+    def regions = bed ? "--regions-file $bed" : ""
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
+
+    """
+    bcftools merge \\
+        $args \\
+        $regions \\
+        --threads $task.cpus \\
+        --output ${prefix}.${extension} \\
+        $vcfs
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
+    """
+    touch ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml
new file mode 100644
index 00000000..87707140
--- /dev/null
+++ b/modules/nf-core/bcftools/merge/meta.yml
@@ -0,0 +1,88 @@
+name: bcftools_merge
+description: Merge VCF files
+keywords:
+  - variant calling
+  - merge
+  - VCF
+tools:
+  - merge:
+      description: |
+        Merge VCF files.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcfs:
+      type: file
+      description: |
+        List containing 2 or more vcf files
+        e.g. [ 'file1.vcf', 'file2.vcf' ]
+  - tbis:
+      type: file
+      description: |
+        List containing the tbi index files corresponding to the vcfs input files
+        e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
+  - fasta:
+      type: file
+      description: "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)"
+      pattern: "*.{fasta,fa}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
+  - fai:
+      type: file
+      description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)"
+      pattern: "*.fai"
+  - bed:
+      type: file
+      description: "(Optional) The bed regions to merge on"
+      pattern: "*.bed"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf_gz:
+      type: file
+      description: VCF merged output file (bgzipped) => when `--output-type z` is used
+      pattern: "*.vcf.gz"
+  - vcf:
+      type: file
+      description: VCF merged output file => when `--output-type v` is used
+      pattern: "*.vcf"
+  - bcf_gz:
+      type: file
+      description: BCF merged output file (bgzipped) => when `--output-type b` is used
+      pattern: "*.bcf.gz"
+  - bcf:
+      type: file
+      description: BCF merged output file => when `--output-type u` is used
+      pattern: "*.bcf"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@nvnieuwk"
+  - "@ramprasadn"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@nvnieuwk"
+  - "@ramprasadn"
diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml
index 57631f42..114390be 100644
--- a/modules/nf-core/bcftools/mpileup/environment.yml
+++ b/modules/nf-core/bcftools/mpileup/environment.yml
@@ -1,6 +1,7 @@
+name: bcftools_mpileup
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::bcftools=1.17
+  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
index 796713c1..ed138600 100644
--- a/modules/nf-core/bcftools/mpileup/main.nf
+++ b/modules/nf-core/bcftools/mpileup/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_MPILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'biocontainers/bcftools:1.17--haef29d1_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
 
     input:
     tuple val(meta), path(bam), path(intervals)
diff --git a/modules/nf-core/bcftools/mpileup/tests/main.nf.test b/modules/nf-core/bcftools/mpileup/tests/main.nf.test
new file mode 100644
index 00000000..6478bbc2
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/main.nf.test
@@ -0,0 +1,116 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_MPILEUP"
+    script "../main.nf"
+    process "BCFTOOLS_MPILEUP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/mpileup"
+
+    config "./nextflow.config"
+
+    test("sarscov2 - [bam, []], fasta, false") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.tbi,
+                    process.out.stats,
+                    process.out.mpileup,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [bam, []], fasta, true") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.tbi,
+                    process.out.stats,
+                    process.out.mpileup,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [bam, bed], fasta, false") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.tbi,
+                    process.out.stats,
+                    process.out.mpileup,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap
new file mode 100644
index 00000000..ef80ab1b
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap
@@ -0,0 +1,112 @@
+{
+    "sarscov2 - [bam, []], fasta, true": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz:md5,0f2f2c8488e97e7f13979380d5d3b6b5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi:md5,34cb2eeb73f4d2b98218acecebd92704"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bcftools_stats.txt:md5,a988fbcd2ea5d1ce30970dcb60a77ed7"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.mpileup.gz:md5,73b4a00398bddab2cd065b40d17ca4dc"
+                ]
+            ],
+            [
+                "versions.yml:md5,e09c59d941374bb293aadc36e2f29dbf"
+            ]
+        ],
+        "timestamp": "2023-11-29T14:11:54.549517279"
+    },
+    "sarscov2 - [bam, bed], fasta, false": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz:md5,687244dbf71d05b3b973ab08ecf05310"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi:md5,3785df15f3d7faf35f3ad70d167a50f7"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bcftools_stats.txt:md5,f8c5ab149c4bf0e5f51c518346cb87b5"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,e09c59d941374bb293aadc36e2f29dbf"
+            ]
+        ],
+        "timestamp": "2023-11-29T14:12:00.865439661"
+    },
+    "sarscov2 - [bam, []], fasta, false": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz:md5,0f2f2c8488e97e7f13979380d5d3b6b5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi:md5,34cb2eeb73f4d2b98218acecebd92704"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bcftools_stats.txt:md5,a988fbcd2ea5d1ce30970dcb60a77ed7"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,e09c59d941374bb293aadc36e2f29dbf"
+            ]
+        ],
+        "timestamp": "2023-11-29T14:11:47.814900494"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/mpileup/tests/nextflow.config b/modules/nf-core/bcftools/mpileup/tests/nextflow.config
new file mode 100644
index 00000000..a7ba19fe
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/nextflow.config
@@ -0,0 +1,4 @@
+process {
+    ext.args2 = '--no-version --ploidy 1 --multiallelic-caller'
+    ext.args3 = '--no-version'
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/mpileup/tests/tags.yml b/modules/nf-core/bcftools/mpileup/tests/tags.yml
new file mode 100644
index 00000000..07b91f98
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/tags.yml
@@ -0,0 +1,2 @@
+bcftools/mpileup:
+  - "modules/nf-core/bcftools/mpileup/**"
diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml
index 57631f42..1a969528 100644
--- a/modules/nf-core/bcftools/stats/environment.yml
+++ b/modules/nf-core/bcftools/stats/environment.yml
@@ -1,6 +1,7 @@
+name: bcftools_stats
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::bcftools=1.17
+  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf
index b3a5f23b..ffa1df64 100644
--- a/modules/nf-core/bcftools/stats/main.nf
+++ b/modules/nf-core/bcftools/stats/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_STATS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'biocontainers/bcftools:1.17--haef29d1_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
 
     input:
     tuple val(meta),  path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml
index 57631f42..8937c6da 100644
--- a/modules/nf-core/bcftools/view/environment.yml
+++ b/modules/nf-core/bcftools/view/environment.yml
@@ -1,6 +1,7 @@
+name: bcftools_view
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::bcftools=1.17
+  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf
index 6afdd134..5237adc8 100644
--- a/modules/nf-core/bcftools/view/main.nf
+++ b/modules/nf-core/bcftools/view/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_VIEW {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'biocontainers/bcftools:1.17--haef29d1_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
@@ -14,8 +14,8 @@ process BCFTOOLS_VIEW {
     path(samples)
 
     output:
-    tuple val(meta), path("*.gz") , emit: vcf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,9 +26,14 @@ process BCFTOOLS_VIEW {
     def regions_file  = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
     def samples_file =  samples ? "--samples-file ${samples}" : ""
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
     """
     bcftools view \\
-        --output ${prefix}.vcf.gz \\
+        --output ${prefix}.${extension} \\
         ${regions_file} \\
         ${targets_file} \\
         ${samples_file} \\
@@ -43,9 +48,15 @@ process BCFTOOLS_VIEW {
     """
 
     stub:
+    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
     """
-    touch ${prefix}.vcf.gz
+    touch ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml
index eaa12b56..6baa34a6 100644
--- a/modules/nf-core/bcftools/view/meta.yml
+++ b/modules/nf-core/bcftools/view/meta.yml
@@ -53,7 +53,7 @@ output:
   - vcf:
       type: file
       description: VCF normalized output file
-      pattern: "*.{vcf.gz}"
+      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test b/modules/nf-core/bcftools/view/tests/main.nf.test
new file mode 100644
index 00000000..c285674c
--- /dev/null
+++ b/modules/nf-core/bcftools/view/tests/main.nf.test
@@ -0,0 +1,103 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_VIEW"
+    script "../main.nf"
+    process "BCFTOOLS_VIEW"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/view"
+
+    config "./nextflow.config"
+
+    test("sarscov2 - [vcf, tbi], [], [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'out', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi], vcf, tsv, []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'out', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                ]
+                input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi], [], [], [] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'out', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.vcf[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test.snap b/modules/nf-core/bcftools/view/tests/main.nf.test.snap
new file mode 100644
index 00000000..b59be932
--- /dev/null
+++ b/modules/nf-core/bcftools/view/tests/main.nf.test.snap
@@ -0,0 +1,45 @@
+{
+    "sarscov2 - [vcf, tbi], vcf, tsv, []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "out",
+                        "single_end": false
+                    },
+                    "out.vcf:md5,1bcbd0eff25d316ba915d06463aab17b"
+                ]
+            ],
+            [
+                "versions.yml:md5,106d119dde844ec7fee1cdd30828bcdc"
+            ]
+        ],
+        "timestamp": "2024-02-05T17:12:20.799849895"
+    },
+    "sarscov2 - [vcf, tbi], [], [], [] - stub": {
+        "content": [
+            "out.vcf",
+            [
+                "versions.yml:md5,106d119dde844ec7fee1cdd30828bcdc"
+            ]
+        ],
+        "timestamp": "2024-02-05T16:53:34.652746985"
+    },
+    "sarscov2 - [vcf, tbi], [], [], []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "out",
+                        "single_end": false
+                    },
+                    "out.vcf:md5,8e722884ffb75155212a3fc053918766"
+                ]
+            ],
+            [
+                "versions.yml:md5,106d119dde844ec7fee1cdd30828bcdc"
+            ]
+        ],
+        "timestamp": "2024-02-05T17:12:14.247465409"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/view/tests/nextflow.config b/modules/nf-core/bcftools/view/tests/nextflow.config
new file mode 100644
index 00000000..932e3ba6
--- /dev/null
+++ b/modules/nf-core/bcftools/view/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = '--no-version --output-type v'
+}
diff --git a/modules/nf-core/bcftools/view/tests/tags.yml b/modules/nf-core/bcftools/view/tests/tags.yml
new file mode 100644
index 00000000..43b1f0aa
--- /dev/null
+++ b/modules/nf-core/bcftools/view/tests/tags.yml
@@ -0,0 +1,2 @@
+bcftools/view:
+  - "modules/nf-core/bcftools/view/**"
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
index 222b301f..8c69b121 100644
--- a/modules/nf-core/cat/fastq/environment.yml
+++ b/modules/nf-core/cat/fastq/environment.yml
@@ -1,6 +1,7 @@
+name: cat_fastq
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - conda-forge::sed=4.7
+  - conda-forge::coreutils=8.30
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index 3d963784..f132b2ad 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -76,5 +76,4 @@ process CAT_FASTQ {
             """
         }
     }
-
 }
diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test
index f5f94182..dab2e14c 100644
--- a/modules/nf-core/cat/fastq/tests/main.nf.test
+++ b/modules/nf-core/cat/fastq/tests/main.nf.test
@@ -16,11 +16,11 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [
-                            [ id:'test', single_end:true ], // meta map
-                            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
-                        ]
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
                 """
             }
         }
@@ -28,8 +28,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.reads).match() },
-                { assert path(process.out.versions.get(0)).getText().contains("cat") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -42,13 +41,13 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test', single_end:false ], // meta map
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)]
+                ])
                 """
             }
         }
@@ -56,8 +55,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.reads).match() },
-                { assert path(process.out.versions.get(0)).getText().contains("cat") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -70,11 +68,11 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test', single_end:true ], // meta map
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
                 """
             }
         }
@@ -82,8 +80,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.reads).match() },
-                { assert path(process.out.versions.get(0)).getText().contains("cat") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -96,13 +93,13 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test', single_end:false ], // meta map
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
                 """
             }
         }
@@ -110,8 +107,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.reads).match() },
-                { assert path(process.out.versions.get(0)).getText().contains("cat") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -124,10 +120,10 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test', single_end:true ], // meta map
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
                 """
             }
         }
@@ -135,8 +131,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.reads).match() },
-                { assert path(process.out.versions.get(0)).getText().contains("cat") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap
index ec2342e5..43dfe28f 100644
--- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap
+++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap
@@ -1,78 +1,169 @@
 {
     "test_cat_fastq_single_end": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "test.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-10-17T23:19:12.990284837"
+        "timestamp": "2024-01-17T17:30:39.816981"
     },
     "test_cat_fastq_single_end_same_name": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "test.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-10-17T23:19:31.554568147"
+        "timestamp": "2024-01-17T17:32:35.229332"
     },
     "test_cat_fastq_single_end_single_file": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "test.merged.fastq.gz:md5,e325ef7deb4023447a1f074e285761af"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-10-17T23:19:49.629360033"
+        "timestamp": "2024-01-17T17:34:00.058829"
     },
     "test_cat_fastq_paired_end_same_name": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
+            {
+                "0": [
                     [
-                        "test_1.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66",
-                        "test_2.merged.fastq.gz:md5,fe9f266f43a6fc3dcab690a18419a56e"
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
                     ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-10-17T23:19:40.711617539"
+        "timestamp": "2024-01-17T17:33:33.031555"
     },
     "test_cat_fastq_paired_end": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
                     [
-                        "test_1.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d",
-                        "test_2.merged.fastq.gz:md5,77c8e966e130d8c6b6ec9be52fcb2bda"
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
                     ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-10-18T07:53:20.923560211"
+        "timestamp": "2024-01-17T17:32:02.270935"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
deleted file mode 100644
index 7685b33c..00000000
--- 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 "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.17--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 9414c32d..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,37 +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"
-maintainers:
-  - "@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 da033408..00000000
--- 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/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
deleted file mode 100644
index eec1db10..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ /dev/null
@@ -1,38 +0,0 @@
-nextflow_process {
-
-    name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
-    script "../main.nf"
-    process "CUSTOM_DUMPSOFTWAREVERSIONS"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "custom"
-    tag "dumpsoftwareversions"
-    tag "custom/dumpsoftwareversions"
-
-    test("Should run without failures") {
-        when {
-            process {
-                """
-                def tool1_version = '''
-                TOOL1:
-                    tool1: 0.11.9
-                '''.stripIndent()
-
-                def tool2_version = '''
-                TOOL2:
-                    tool2: 1.9
-                '''.stripIndent()
-
-                input[0] = Channel.of(tool1_version, tool2_version).collectFile()
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
deleted file mode 100644
index 4274ed57..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ],
-                "1": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "2": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "mqc_yml": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "versions": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "yml": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-03T14:43:22.157011"
-    }
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
deleted file mode 100644
index 405aa24a..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-custom/dumpsoftwareversions:
-  - modules/nf-core/custom/dumpsoftwareversions/**
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
new file mode 100644
index 00000000..7a127746
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/environment.yml
@@ -0,0 +1,7 @@
+name: ensemblvep_vep
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ensembl-vep=110.0
diff --git a/modules/local/ensemblvep.nf b/modules/nf-core/ensemblvep/vep/main.nf
similarity index 51%
rename from modules/local/ensemblvep.nf
rename to modules/nf-core/ensemblvep/vep/main.nf
index 379769ea..a7fc5ad1 100644
--- a/modules/local/ensemblvep.nf
+++ b/modules/nf-core/ensemblvep/vep/main.nf
@@ -1,32 +1,27 @@
-process ENSEMBLVEP {
+process ENSEMBLVEP_VEP {
     tag "$meta.id"
     label 'process_medium'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Local VEP module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
-    container "docker.io/ensemblorg/ensembl-vep:release_107.0"
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' :
+        'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }"
 
     input:
-    tuple val(meta), path(vcf)
+    tuple val(meta), path(vcf), path(custom_extra_files)
     val   genome
     val   species
     val   cache_version
     path  cache
-    path  fasta
+    tuple val(meta2), path(fasta)
     path  extra_files
 
     output:
-    tuple val(meta), path("*.vcf")    , optional:true, emit: vcf
-    tuple val(meta), path("*.tab")    , optional:true, emit: tab
-    tuple val(meta), path("*.json")   , optional:true, emit: json
-    tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf_gz
-    tuple val(meta), path("*.tab.gz") , optional:true, emit: tab_gz
-    tuple val(meta), path("*.json.gz"), optional:true, emit: json_gz
-    path "*.summary.html"             , optional:true, emit: report
-    path "versions.yml"               , emit: versions
+    tuple val(meta), path("*.vcf.gz")  , optional:true, emit: vcf
+    tuple val(meta), path("*.tab.gz")  , optional:true, emit: tab
+    tuple val(meta), path("*.json.gz") , optional:true, emit: json
+    path "*.summary.html"              , optional:true, emit: report
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,25 +29,25 @@ process ENSEMBLVEP {
     script:
     def args = task.ext.args ?: ''
     def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf'
-    def compress_out = args.contains("--compress_output") ? '.gz' : ''
+    def compress_cmd = args.contains("--compress_output") ? '' : '--compress_output bgzip'
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def stats_file     = args.contains("--no_stats") ? '' : "--stats_file ${prefix}.summary.html"
     def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
     def reference = fasta ? "--fasta $fasta" : ""
-
     """
     vep \\
         -i $vcf \\
-        -o ${prefix}.${file_extension}${compress_out} \\
+        -o ${prefix}.${file_extension}.gz \\
         $args \\
+        $compress_cmd \\
         $reference \\
         --assembly $genome \\
         --species $species \\
         --cache \\
         --cache_version $cache_version \\
         --dir_cache $dir_cache \\
-        --fork $task.cpus \\
-        ${stats_file}
+        --fork $task.cpus
+
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
@@ -62,13 +57,11 @@ process ENSEMBLVEP {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf
-    touch ${prefix}.tab
-    touch ${prefix}.json
     touch ${prefix}.vcf.gz
     touch ${prefix}.tab.gz
     touch ${prefix}.json.gz
     touch ${prefix}.summary.html
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml
new file mode 100644
index 00000000..d8ff8d14
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/meta.yml
@@ -0,0 +1,92 @@
+name: ensemblvep_vep
+description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.
+keywords:
+  - annotation
+  - vcf
+  - json
+  - tab
+tools:
+  - ensemblvep:
+      description: |
+        VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs
+        or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
+      homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
+      documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
+      licence: ["Apache-2.0"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: |
+        vcf to annotate
+  - custom_extra_files:
+      type: file
+      description: |
+        extra sample-specific files to be used with the `--custom` flag to be configured with ext.args
+        (optional)
+  - genome:
+      type: string
+      description: |
+        which genome to annotate with
+  - species:
+      type: string
+      description: |
+        which species to annotate with
+  - cache_version:
+      type: integer
+      description: |
+        which version of the cache to annotate with
+  - cache:
+      type: file
+      description: |
+        path to VEP cache (optional)
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing fasta reference information
+        e.g. [ id:'test' ]
+  - fasta:
+      type: file
+      description: |
+        reference FASTA file (optional)
+      pattern: "*.{fasta,fa}"
+  - extra_files:
+      type: file
+      description: |
+        path to file(s) needed for plugins  (optional)
+output:
+  - vcf:
+      type: file
+      description: |
+        annotated vcf (optional)
+      pattern: "*.ann.vcf.gz"
+  - tab:
+      type: file
+      description: |
+        tab file with annotated variants (optional)
+      pattern: "*.ann.tab.gz"
+  - json:
+      type: file
+      description: |
+        json file with annotated variants (optional)
+      pattern: "*.ann.json.gz"
+  - report:
+      type: file
+      description: VEP report file
+      pattern: "*.html"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@maxulysse"
+  - "@matthdsm"
+  - "@nvnieuwk"
+maintainers:
+  - "@maxulysse"
+  - "@matthdsm"
+  - "@nvnieuwk"
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
new file mode 100644
index 00000000..f072dcab
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
@@ -0,0 +1,102 @@
+nextflow_process {
+
+    name "Test Process ENSEMBLVEP_VEP"
+    script "modules/nf-core/ensemblvep/vep/main.nf"
+    process "ENSEMBLVEP_VEP"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ensemblvep"
+    tag "ensemblvep/vep"
+    tag "ensemblvep/download"
+
+
+    test("test_ensemblvep_vep_fasta_vcf") {
+
+        config "./vcf.config"
+
+        setup {
+            run("ENSEMBLVEP_DOWNLOAD") {
+                script "../../download/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([[id:"${params.vep_cache_version}_${params.vep_genome}"], params.vep_genome, params.vep_species, params.vep_cache_version])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    []
+                ])
+                input[1] = params.vep_genome
+                input[2] = params.vep_species
+                input[3] = params.vep_cache_version
+                input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }
+                input[5] = Channel.value([
+                    [id:"fasta"],
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ])
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            {assert process.success},
+            {assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2")}
+            )
+        }
+
+    }
+
+    test("test_ensemblvep_vep_fasta_tab_gz") {
+
+        config "./tab.gz.config"
+
+        setup {
+            run("ENSEMBLVEP_DOWNLOAD") {
+                script "../../download/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([[id:"${params.vep_cache_version}_${params.vep_genome}"], params.vep_genome, params.vep_species, params.vep_cache_version])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    []
+                ])
+                input[1] = params.vep_genome
+                input[2] = params.vep_species
+                input[3] = params.vep_cache_version
+                input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }
+                input[5] = Channel.value([
+                    [id:"fasta"],
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ])
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            {assert process.success},
+            {assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v110.0")}
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
new file mode 100644
index 00000000..cfaef733
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
@@ -0,0 +1,13 @@
+params {
+    vep_cache_version = "110"
+    vep_genome = "WBcel235"
+    vep_species = "caenorhabditis_elegans"
+}
+
+process {
+
+    withName: ENSEMBLVEP_DOWNLOAD {
+        ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
+    }
+
+}
diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config
new file mode 100644
index 00000000..40eb03e5
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config
@@ -0,0 +1,5 @@
+process {
+        withName: ENSEMBLVEP_VEP {
+        ext.args = '--tab --compress_output bgzip'
+    }
+}
diff --git a/modules/nf-core/ensemblvep/vep/tests/tags.yml b/modules/nf-core/ensemblvep/vep/tests/tags.yml
new file mode 100644
index 00000000..4aa4aa45
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/tests/tags.yml
@@ -0,0 +1,2 @@
+ensemblvep/vep:
+  - "modules/nf-core/ensemblvep/vep/**"
diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config
new file mode 100644
index 00000000..ad8955a3
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/tests/vcf.config
@@ -0,0 +1,5 @@
+process {
+        withName: ENSEMBLVEP_VEP {
+        ext.args = '--vcf'
+    }
+}
diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
index 19ccec25..70389e66 100644
--- a/modules/nf-core/fastp/environment.yml
+++ b/modules/nf-core/fastp/environment.yml
@@ -1,3 +1,4 @@
+name: fastp
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index c8e815ae..2a3b679e 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -45,7 +45,7 @@ process FASTP {
             $adapter_list \\
             $fail_fastq \\
             $args \\
-            2> ${prefix}.fastp.log \\
+            2> >(tee ${prefix}.fastp.log >&2) \\
         | gzip -c > ${prefix}.fastp.fastq.gz
 
         cat <<-END_VERSIONS > versions.yml
@@ -66,7 +66,7 @@ process FASTP {
             $adapter_list \\
             $fail_fastq \\
             $args \\
-            2> ${prefix}.fastp.log
+            2> >(tee ${prefix}.fastp.log >&2)
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -91,7 +91,7 @@ process FASTP {
             --thread $task.cpus \\
             --detect_adapter_for_pe \\
             $args \\
-            2> ${prefix}.fastp.log
+            2> >(tee ${prefix}.fastp.log >&2)
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -99,4 +99,22 @@ process FASTP {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix              = task.ext.prefix ?: "${meta.id}"
+    def is_single_output    = task.ext.args?.contains('--interleaved_in') || meta.single_end
+    def touch_reads         = is_single_output ? "${prefix}.fastp.fastq.gz" : "${prefix}_1.fastp.fastq.gz ${prefix}_2.fastp.fastq.gz"
+    def touch_merged        = (!is_single_output && save_merged) ? "touch ${prefix}.merged.fastq.gz" : ""
+    """
+    touch $touch_reads
+    touch "${prefix}.fastp.json"
+    touch "${prefix}.fastp.html"
+    touch "${prefix}.fastp.log"
+    $touch_merged
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test
index f610b735..9b3f9a38 100644
--- a/modules/nf-core/fastp/tests/main.nf.test
+++ b/modules/nf-core/fastp/tests/main.nf.test
@@ -19,11 +19,10 @@ nextflow_process {
                 save_trimmed_fail = false
                 save_merged       = false
 
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test', single_end:true ],
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-                ]
-
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
                 input[1] = adapter_fasta
                 input[2] = save_trimmed_fail
                 input[3] = save_merged
@@ -57,7 +56,67 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) }
                     }
                 },
-                { assert snapshot(process.out.versions).match("versions") }
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_single_end-_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_single_end") }
+            )
+        }
+    }
+
+    test("test_fastp_single_end-stub") {
+
+        options '-stub'
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = adapter_fasta
+                input[2] = save_trimmed_fail
+                input[3] = save_merged
+                """
+            }
+        }
+
+        then {
+
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_single_end-for_stub_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_single_end_stub") }
             )
         }
     }
@@ -74,12 +133,11 @@ nextflow_process {
                 save_trimmed_fail = false
                 save_merged       = false
 
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test', single_end:false ], // meta map
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-                ]
-
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
                 input[1] = adapter_fasta
                 input[2] = save_trimmed_fail
                 input[3] = save_merged
@@ -127,7 +185,67 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) }
                     }
                 },
-                { assert snapshot(process.out.versions).match("versions") }
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { it[1].collect { item -> file(item).getName() } } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_paired_end_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_paired_end") }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end-stub") {
+
+        options '-stub'
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = adapter_fasta
+                input[2] = save_trimmed_fail
+                input[3] = save_merged
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { it[1].collect { item -> file(item).getName() } } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_paired_end-for_stub_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_paired_end-stub") }
             )
         }
     }
@@ -144,10 +262,10 @@ nextflow_process {
                 save_trimmed_fail = false
                 save_merged       = false
 
-                input[0] = [ [ id:'test', single_end:true ], // meta map
-                            [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ]
-                        ]
-
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ]
+                ])
                 input[1] = adapter_fasta
                 input[2] = save_trimmed_fail
                 input[3] = save_merged
@@ -181,7 +299,67 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) }
                     }
                 },
-                { assert snapshot(process.out.versions).match("versions") }
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_interleaved-_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_interleaved") }
+            )
+        }
+    }
+
+    test("fastp test_fastp_interleaved-stub") {
+
+        options '-stub'
+
+        config './nextflow.config'
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = adapter_fasta
+                input[2] = save_trimmed_fail
+                input[3] = save_merged
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_interleaved-for_stub_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_interleaved-stub") }
             )
         }
     }
@@ -198,9 +376,10 @@ nextflow_process {
                 save_trimmed_fail = true
                 save_merged       = false
 
-                input[0] = [ [ id:'test', single_end:true ], // meta map
-                            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-                        ]
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
                 input[1] = adapter_fasta
                 input[2] = save_trimmed_fail
                 input[3] = save_merged
@@ -241,7 +420,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) }
                     }
                 },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.versions).match("versions_single_end_trim_fail") }
             )
         }
     }
@@ -258,13 +437,11 @@ nextflow_process {
                 save_trimmed_fail = true
                 save_merged       = false
 
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test', single_end:false ], // meta map
-                    [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-                    ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
                 input[1] = adapter_fasta
                 input[2] = save_trimmed_fail
                 input[3] = save_merged
@@ -321,7 +498,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) }
                     }
                 },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.versions).match("versions_paired_end_trim_fail") }
             )
         }
     }
@@ -337,11 +514,11 @@ nextflow_process {
                 adapter_fasta     = []
                 save_trimmed_fail = false
                 save_merged       = true
-
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                               file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-                           ]
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
                 input[1] = adapter_fasta
                 input[2] = save_trimmed_fail
                 input[3] = save_merged
@@ -399,7 +576,67 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) }
                     }
                 },
-                { assert snapshot(process.out.versions).match("versions") }
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { it[1].collect { item -> file(item).getName() } } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_paired_end_merged_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_paired_end_merged") }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_merged-stub") {
+
+        options '-stub'
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = true
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = adapter_fasta
+                input[2] = save_trimmed_fail
+                input[3] = save_merged
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { it[1].collect { item -> file(item).getName() } } +
+                            process.out.json.collect { file(it[1]).getName() } +
+                            process.out.html.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() } +
+                            process.out.reads_fail.collect { file(it[1]).getName() } +
+                            process.out.reads_merged.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("test_fastp_paired_end_merged-for_stub_match")
+                },
+                { assert snapshot(process.out.versions).match("versions_paired_end_merged_stub") }
             )
         }
     }
@@ -412,14 +649,15 @@ nextflow_process {
             }
             process {
                 """
-                adapter_fasta     = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta", checkIfExists: true)
+                adapter_fasta     = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ])
                 save_trimmed_fail = false
                 save_merged       = true
 
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                               file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-                           ]
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
                 input[1] = adapter_fasta
                 input[2] = save_trimmed_fail
                 input[3] = save_merged
@@ -478,7 +716,7 @@ nextflow_process {
                     { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) }
                     }
                 },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.versions).match("versions_paired_end_merged_adapterlist") }
             )
         }
     }
diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap
index 0fa68c7d..b4c0e1dd 100644
--- a/modules/nf-core/fastp/tests/main.nf.test.snap
+++ b/modules/nf-core/fastp/tests/main.nf.test.snap
@@ -11,7 +11,43 @@
                 ]
             ]
         ],
-        "timestamp": "2023-10-17T11:04:45.794175881"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-17T18:08:06.123035"
+    },
+    "test_fastp_paired_end_merged-for_stub_match": {
+        "content": [
+            [
+                [
+                    "test_1.fastp.fastq.gz",
+                    "test_2.fastp.fastq.gz"
+                ],
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "test.merged.fastq.gz",
+                "{id=test, single_end=false}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-17T18:10:13.467574"
+    },
+    "versions_interleaved": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:56:24.615634793"
     },
     "test_fastp_single_end_json": {
         "content": [
@@ -25,15 +61,253 @@
                 ]
             ]
         ],
-        "timestamp": "2023-10-17T11:04:10.566343705"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-17T18:06:00.223817"
+    },
+    "versions_paired_end": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:55:42.333545689"
+    },
+    "test_fastp_paired_end_match": {
+        "content": [
+            [
+                [
+                    "test_1.fastp.fastq.gz",
+                    "test_2.fastp.fastq.gz"
+                ],
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "{id=test, single_end=false}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T12:03:06.431833729"
+    },
+    "test_fastp_interleaved-_match": {
+        "content": [
+            [
+                "test.fastp.fastq.gz",
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "{id=test, single_end=true}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T12:03:37.827323085"
+    },
+    "test_fastp_paired_end_merged_match": {
+        "content": [
+            [
+                [
+                    "test_1.fastp.fastq.gz",
+                    "test_2.fastp.fastq.gz"
+                ],
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "test.merged.fastq.gz",
+                "{id=test, single_end=false}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T12:08:44.496251446"
+    },
+    "versions_single_end_stub": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:55:27.354051299"
+    },
+    "versions_interleaved-stub": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:56:46.535528418"
+    },
+    "versions_single_end_trim_fail": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:59:03.724591407"
+    },
+    "test_fastp_paired_end-for_stub_match": {
+        "content": [
+            [
+                [
+                    "test_1.fastp.fastq.gz",
+                    "test_2.fastp.fastq.gz"
+                ],
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "{id=test, single_end=false}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-17T18:07:15.398827"
+    },
+    "versions_paired_end-stub": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:56:06.50017282"
+    },
+    "versions_single_end": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:55:07.67921647"
+    },
+    "versions_paired_end_merged_stub": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:59:47.350653154"
+    },
+    "test_fastp_interleaved-for_stub_match": {
+        "content": [
+            [
+                "test.fastp.fastq.gz",
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "{id=test, single_end=true}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-17T18:08:06.127974"
+    },
+    "versions_paired_end_trim_fail": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:59:18.140484878"
+    },
+    "test_fastp_single_end-for_stub_match": {
+        "content": [
+            [
+                "test.fastp.fastq.gz",
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "{id=test, single_end=true}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-17T18:06:00.244202"
+    },
+    "test_fastp_single_end-_match": {
+        "content": [
+            [
+                "test.fastp.fastq.gz",
+                "test.fastp.html",
+                "test.fastp.json",
+                "test.fastp.log",
+                "{id=test, single_end=true}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:57:30.791982648"
+    },
+    "versions_paired_end_merged_adapterlist": {
+        "content": [
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T12:05:37.845370554"
     },
-    "versions": {
+    "versions_paired_end_merged": {
         "content": [
             [
                 "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
             ]
         ],
-        "timestamp": "2023-10-17T11:04:10.582076024"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:59:32.860543858"
     },
     "test_fastp_single_end_trim_fail_json": {
         "content": [
@@ -47,6 +321,10 @@
                 ]
             ]
         ],
-        "timestamp": "2023-10-17T11:05:00.379878948"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-17T18:08:41.942317"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index f52a53a0..1787b38a 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,3 +1,4 @@
+name: fastqc
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 50e59f2b..9e19a74c 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -37,7 +37,7 @@ process FASTQC {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
     END_VERSIONS
     """
 
@@ -49,7 +49,7 @@ process FASTQC {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 6437a144..70edae4d 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -3,24 +3,20 @@ nextflow_process {
     name "Test Process FASTQC"
     script "../main.nf"
     process "FASTQC"
+
     tag "modules"
     tag "modules_nfcore"
     tag "fastqc"
 
-    test("Single-Read") {
+    test("sarscov2 single-end [fastq]") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id: 'test', single_end:true ],
-                    [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-                    ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
                 """
             }
         }
@@ -28,14 +24,189 @@ nextflow_process {
         then {
             assertAll (
             { assert process.success },
+
             // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
             // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
             // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-            { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" },
-            { assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert snapshot(process.out.versions).match("versions") },
-            { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" }
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
             )
         }
     }
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            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 process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastq] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id: 'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
+                                process.out.zip.collect { file(it[1]).getName() } +
+                                process.out.versions ).match("fastqc_stub") }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 636a32ce..10da7d9d 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,10 +1,88 @@
 {
-    "versions": {
+    "fastqc_versions_interleaved": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
-        "timestamp": "2023-10-09T23:40:54+0000"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:40:07.293713"
+    },
+    "fastqc_stub": {
+        "content": [
+            [
+                "test.html",
+                "test.zip",
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:31:01.425198"
+    },
+    "fastqc_versions_multiple": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:40:55.797907"
+    },
+    "fastqc_versions_bam": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:40:26.795862"
+    },
+    "fastqc_versions_single": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:39:27.043675"
+    },
+    "fastqc_versions_paired": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:39:47.584191"
+    },
+    "fastqc_versions_custom_prefix": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:41:14.576531"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml
index 16241b6d..d0c8c2e8 100644
--- a/modules/nf-core/gatk4/asereadcounter/environment.yml
+++ b/modules/nf-core/gatk4/asereadcounter/environment.yml
@@ -1,6 +1,7 @@
+name: gatk4_asereadcounter
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
+  - bioconda::gatk4=4.5.0.0
diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf
index 1be36cab..4a151d6c 100644
--- a/modules/nf-core/gatk4/asereadcounter/main.nf
+++ b/modules/nf-core/gatk4/asereadcounter/main.nf
@@ -4,8 +4,8 @@ process GATK4_ASEREADCOUNTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml
index 16241b6d..d6fbe2e7 100644
--- a/modules/nf-core/gatk4/bedtointervallist/environment.yml
+++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml
@@ -1,6 +1,7 @@
+name: gatk4_bedtointervallist
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
+  - bioconda::gatk4=4.5.0.0
diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf
index 88b24b1a..68863d67 100644
--- a/modules/nf-core/gatk4/bedtointervallist/main.nf
+++ b/modules/nf-core/gatk4/bedtointervallist/main.nf
@@ -4,8 +4,8 @@ process GATK4_BEDTOINTERVALLIST {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)
diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml
index 16241b6d..78822ad0 100644
--- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml
+++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml
@@ -1,6 +1,7 @@
+name: gatk4_createsequencedictionary
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
+  - bioconda::gatk4=4.5.0.0
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
index b47ad162..c7f1d75b 100644
--- a/modules/nf-core/gatk4/createsequencedictionary/main.nf
+++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf
@@ -4,8 +4,8 @@ process GATK4_CREATESEQUENCEDICTIONARY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml
index 16241b6d..d4e8d360 100644
--- a/modules/nf-core/gatk4/haplotypecaller/environment.yml
+++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml
@@ -1,6 +1,7 @@
+name: gatk4_haplotypecaller
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
+  - bioconda::gatk4=4.5.0.0
diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf
index fdecf5f8..3043ee07 100644
--- a/modules/nf-core/gatk4/haplotypecaller/main.nf
+++ b/modules/nf-core/gatk4/haplotypecaller/main.nf
@@ -4,16 +4,16 @@ process GATK4_HAPLOTYPECALLER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
-    path  fasta
-    path  fai
-    path  dict
-    path  dbsnp
-    path  dbsnp_tbi
+    tuple val(meta),  path(input), path(input_index), path(intervals), path(dragstr_model)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
+    tuple val(meta5), path(dbsnp)
+    tuple val(meta6), path(dbsnp_tbi)
 
     output:
     tuple val(meta), path("*.vcf.gz")       , emit: vcf
diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml
index f38dc37d..703b99a0 100644
--- a/modules/nf-core/gatk4/haplotypecaller/meta.yml
+++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml
@@ -35,21 +35,46 @@ input:
       type: file
       description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
       pattern: "*.txt"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test_reference' ]
   - fasta:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test_reference' ]
   - fai:
       type: file
       description: Index of reference fasta file
       pattern: "fasta.fai"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test_reference' ]
   - dict:
       type: file
       description: GATK sequence dictionary
       pattern: "*.dict"
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing dbsnp information
+        e.g. [ id:'test_dbsnp' ]
   - dbsnp:
       type: file
       description: VCF file containing known sites (optional)
+  - meta6:
+      type: map
+      description: |
+        Groovy Map containing dbsnp information
+        e.g. [ id:'test_dbsnp' ]
   - dbsnp_tbi:
       type: file
       description: VCF index of dbsnp (optional)
diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
new file mode 100644
index 00000000..a124bff5
--- /dev/null
+++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
@@ -0,0 +1,142 @@
+// nf-core modules test gatk4/haplotypecaller
+nextflow_process {
+
+    name "Test Process GATK4_HAPLOTYPECALLER"
+    script "../main.nf"
+    process "GATK4_HAPLOTYPECALLER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/haplotypecaller"
+
+    test("homo_sapiens - [bam, bai] - fasta - fai - dict") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_bam' ], // 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:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+                input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
+                input[4] = [ [], [] ]
+                input[5] = [ [], [] ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                // { assert snapshot(process.out).match() }, // Unstable hashes
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") },
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [cram, crai] - fasta - fai - dict") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_cram' ], // 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_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+                input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
+                input[4] = [ [], [] ]
+                input[5] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                // { assert snapshot(process.out).match() }, // Unstable hashes
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") },
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_cram_sites' ], // 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_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+                input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
+                input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ]
+                input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                // { assert snapshot(process.out).match() }, // Unstable hashes
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") },
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_cram_sites_dragstr' ], // 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),
+                    [],
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true)
+                ]
+                input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+                input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
+                input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ]
+                input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                // { assert snapshot(process.out).match() }, // Unstable hashes
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
new file mode 100644
index 00000000..375025ee
--- /dev/null
+++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
@@ -0,0 +1,82 @@
+{
+    "gatk_hc_vcf_cram_dragstr_input_with_sites": {
+        "content": [
+            "test_cram_sites_dragstr.vcf.gz"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:24:45.142682"
+    },
+    "gatk_hc_vcf_bam_input": {
+        "content": [
+            "test_bam.vcf.gz"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:23:19.203837"
+    },
+    "gatk_hc_vcf_cram_input": {
+        "content": [
+            "test_cram.vcf.gz"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:23:48.434615"
+    },
+    "gatk_hc_vcf_cram_input_with_sites": {
+        "content": [
+            "test_cram_sites.vcf.gz"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:24:17.147745"
+    },
+    "gatk_hc_vcf_tbi_bam_input": {
+        "content": [
+            "test_bam.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:23:19.23048"
+    },
+    "gatk_hc_vcf_tbi_cram_input": {
+        "content": [
+            "test_cram.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:23:48.45958"
+    },
+    "gatk_hc_vcf_tbi_cram_dragstr_input_with_sites": {
+        "content": [
+            "test_cram_sites_dragstr.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:24:45.154818"
+    },
+    "gatk_hc_vcf_tbi_cram_input_with_sites": {
+        "content": [
+            "test_cram_sites.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T13:24:17.158138"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/tags.yml b/modules/nf-core/gatk4/haplotypecaller/tests/tags.yml
new file mode 100644
index 00000000..d05bb655
--- /dev/null
+++ b/modules/nf-core/gatk4/haplotypecaller/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/haplotypecaller:
+  - "modules/nf-core/gatk4/haplotypecaller/**"
diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml
index 16241b6d..834d2486 100644
--- a/modules/nf-core/gatk4/splitncigarreads/environment.yml
+++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml
@@ -1,6 +1,7 @@
+name: gatk4_splitncigarreads
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
+  - bioconda::gatk4=4.5.0.0
diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf
index 9d32e748..e017a62e 100644
--- a/modules/nf-core/gatk4/splitncigarreads/main.nf
+++ b/modules/nf-core/gatk4/splitncigarreads/main.nf
@@ -4,8 +4,8 @@ process GATK4_SPLITNCIGARREADS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(intervals)
diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test
new file mode 100644
index 00000000..85acfd4c
--- /dev/null
+++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test
@@ -0,0 +1,80 @@
+nextflow_process {
+
+    name "Test Process GATK4_SPLITNCIGARREADS"
+    script "../main.nf"
+    process "GATK4_SPLITNCIGARREADS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/splitncigarreads"
+
+    test("test_gatk4_splitncigarreads") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), []]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads") }
+            )
+        }
+
+    }
+
+    test("test_gatk4_splitncigarreads_intervals") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_intervals") }
+            )
+        }
+
+    }
+
+    test("test_gatk4_splitncigarreads_stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), [], []]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_stub") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap
new file mode 100644
index 00000000..3e581ceb
--- /dev/null
+++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap
@@ -0,0 +1,32 @@
+{
+    "test_gatk4_splitncigarreads_intervals": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-15T08:26:10.91960579"
+    },
+    "test_gatk4_splitncigarreads_stub": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-15T08:26:32.322712467"
+    },
+    "test_gatk4_splitncigarreads": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-15T08:25:53.532205456"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/tags.yml b/modules/nf-core/gatk4/splitncigarreads/tests/tags.yml
new file mode 100644
index 00000000..b5d95313
--- /dev/null
+++ b/modules/nf-core/gatk4/splitncigarreads/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/splitncigarreads:
+  - "modules/nf-core/gatk4/splitncigarreads/**"
diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml
index 16241b6d..0812b6f2 100644
--- a/modules/nf-core/gatk4/variantfiltration/environment.yml
+++ b/modules/nf-core/gatk4/variantfiltration/environment.yml
@@ -1,6 +1,7 @@
+name: gatk4_variantfiltration
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
+  - bioconda::gatk4=4.5.0.0
diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf
index 1c4d8ad0..388c60ab 100644
--- a/modules/nf-core/gatk4/variantfiltration/main.nf
+++ b/modules/nf-core/gatk4/variantfiltration/main.nf
@@ -4,8 +4,8 @@ process GATK4_VARIANTFILTRATION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/gffcompare/environment.yml b/modules/nf-core/gffcompare/environment.yml
index 6213dde8..bcd633ea 100644
--- a/modules/nf-core/gffcompare/environment.yml
+++ b/modules/nf-core/gffcompare/environment.yml
@@ -1,3 +1,4 @@
+name: gffcompare
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
index 222b301f..25910b34 100644
--- a/modules/nf-core/gunzip/environment.yml
+++ b/modules/nf-core/gunzip/environment.yml
@@ -1,3 +1,4 @@
+name: gunzip
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
index d0317922..6406008e 100644
--- a/modules/nf-core/gunzip/tests/main.nf.test
+++ b/modules/nf-core/gunzip/tests/main.nf.test
@@ -15,10 +15,11 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [
-                                [],
-                                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-                            ]
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 9d0e6b20..ca39fb67 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,6 +1,7 @@
+name: multiqc
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.17
+  - bioconda::multiqc=1.21
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 2bbc3983..47ac352f 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.17--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 a61223ed..45a9bc35 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
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 00000000..f1c4242e
--- /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 00000000..bfebd802
--- /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 00000000..bea6c0d3
--- /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/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
new file mode 100644
index 00000000..73ba7dc6
--- /dev/null
+++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
@@ -0,0 +1,7 @@
+name: picard_collectinsertsizemetrics
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::picard=3.1.1
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
new file mode 100644
index 00000000..06c4bc17
--- /dev/null
+++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
@@ -0,0 +1,61 @@
+process PICARD_COLLECTINSERTSIZEMETRICS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
+        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: metrics
+    tuple val(meta), path("*.pdf"), emit: histogram
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[Picard CollectInsertSizeMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}M \\
+        CollectInsertSizeMetrics \\
+        $args \\
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.txt \\
+        --Histogram_FILE ${prefix}.pdf \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard CollectInsertSizeMetrics --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.pdf
+    touch ${prefix}.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard CollectInsertSizeMetrics --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
+
+
+}
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml
new file mode 100644
index 00000000..e2749cb6
--- /dev/null
+++ b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml
@@ -0,0 +1,47 @@
+name: "picard_collectinsertsizemetrics"
+description: Collect metrics about the insert size distribution of a paired-end library.
+keywords:
+  - metrics
+  - alignment
+  - insert
+  - statistics
+  - bam
+tools:
+  - "picard":
+      description: "Java tools for working with NGS data in the BAM format"
+      homepage: "https://broadinstitute.github.io/picard/"
+      documentation: "https://broadinstitute.github.io/picard/"
+      tool_dev_url: "https://github.com/broadinstitute/picard"
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - pdf:
+      type: file
+      description: Histogram plots of the insert size metrics computed by Picard
+      pattern: "*.pdf"
+  - metrics:
+      type: file
+      description: Values used by Picard to generate the insert size histograms
+      pattern: "*.txt"
+authors:
+  - "@FerriolCalvet"
+maintainers:
+  - "@FerriolCalvet"
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
index be923a32..542b2e82 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
+++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
@@ -1,6 +1,7 @@
+name: picard_collectrnaseqmetrics
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.0
+  - bioconda::picard=3.1.1
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
index af735a41..f833a105 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/main.nf
+++ b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTRNASEQMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
-        'biocontainers/picard:3.1.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
+        'biocontainers/picard:3.1.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml
index 9df9267b..8a7bd234 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml
+++ b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml
@@ -15,7 +15,7 @@ tools:
       homepage: "https://broadinstitute.github.io/picard/"
       documentation: "https://broadinstitute.github.io/picard/"
       tool_dev_url: "https://github.com/broadinstitute/picard"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml
index a0519dd2..a6607d96 100644
--- a/modules/nf-core/salmon/index/environment.yml
+++ b/modules/nf-core/salmon/index/environment.yml
@@ -1,3 +1,4 @@
+name: salmon_index
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/salmon/index/tests/main.nf.test b/modules/nf-core/salmon/index/tests/main.nf.test
new file mode 100644
index 00000000..538b231b
--- /dev/null
+++ b/modules/nf-core/salmon/index/tests/main.nf.test
@@ -0,0 +1,35 @@
+nextflow_process {
+
+    name "Test Process SALMON_INDEX"
+    script "../main.nf"
+    process "SALMON_INDEX"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "salmon"
+    tag "salmon/index"
+
+    test("sarscov2") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.index.get(0)).exists() },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/salmon/index/tests/main.nf.test.snap b/modules/nf-core/salmon/index/tests/main.nf.test.snap
new file mode 100644
index 00000000..94edf390
--- /dev/null
+++ b/modules/nf-core/salmon/index/tests/main.nf.test.snap
@@ -0,0 +1,14 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2023-11-22T14:26:33.32036"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/salmon/index/tests/tags.yml b/modules/nf-core/salmon/index/tests/tags.yml
new file mode 100644
index 00000000..02997890
--- /dev/null
+++ b/modules/nf-core/salmon/index/tests/tags.yml
@@ -0,0 +1,2 @@
+salmon/index:
+  - modules/nf-core/salmon/index/**
diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml
index a0519dd2..86266724 100644
--- a/modules/nf-core/salmon/quant/environment.yml
+++ b/modules/nf-core/salmon/quant/environment.yml
@@ -1,3 +1,4 @@
+name: salmon_quant
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf
index e115d39c..acad0cef 100644
--- a/modules/nf-core/salmon/quant/main.nf
+++ b/modules/nf-core/salmon/quant/main.nf
@@ -16,9 +16,10 @@ process SALMON_QUANT {
     val   lib_type
 
     output:
-    tuple val(meta), path("${prefix}") , emit: results
-    tuple val(meta), path("*info.json"), emit: json_info, optional: true
-    path  "versions.yml"               , emit: versions
+    tuple val(meta), path("${prefix}")         , emit: results
+    tuple val(meta), path("${prefix}_quant.sf"), emit: quant, optional: true
+    tuple val(meta), path("*info.json")        , emit: json_info, optional: true
+    path  "versions.yml"                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -69,6 +70,7 @@ process SALMON_QUANT {
 
     if [ -f $prefix/aux_info/meta_info.json ]; then
         cp $prefix/aux_info/meta_info.json "${prefix}_meta_info.json"
+        cp $prefix/quant.sf "${prefix}_quant.sf"
     fi
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml
index 49d7137b..a2faf589 100644
--- a/modules/nf-core/salmon/quant/meta.yml
+++ b/modules/nf-core/salmon/quant/meta.yml
@@ -31,7 +31,7 @@ input:
   - gtf:
       type: file
       description: GTF of the reference transcriptome
-  - transcriptome_fasta:
+  - transcript_fasta:
       type: file
       description: Fasta file of the reference transcriptome
   - alignment_mode:
diff --git a/modules/nf-core/salmon/quant/salmon-quant.diff b/modules/nf-core/salmon/quant/salmon-quant.diff
new file mode 100644
index 00000000..72a7e93d
--- /dev/null
+++ b/modules/nf-core/salmon/quant/salmon-quant.diff
@@ -0,0 +1,27 @@
+Changes in module 'nf-core/salmon/quant'
+--- modules/nf-core/salmon/quant/main.nf
++++ modules/nf-core/salmon/quant/main.nf
+@@ -16,9 +16,10 @@
+     val   lib_type
+ 
+     output:
+-    tuple val(meta), path("${prefix}") , emit: results
+-    tuple val(meta), path("*info.json"), emit: json_info, optional: true
+-    path  "versions.yml"               , emit: versions
++    tuple val(meta), path("${prefix}")         , emit: results
++    tuple val(meta), path("${prefix}_quant.sf"), emit: quant, optional: true
++    tuple val(meta), path("*info.json")        , emit: json_info, optional: true
++    path  "versions.yml"                        , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+@@ -69,6 +70,7 @@
+ 
+     if [ -f $prefix/aux_info/meta_info.json ]; then
+         cp $prefix/aux_info/meta_info.json "${prefix}_meta_info.json"
++        cp $prefix/quant.sf "${prefix}_quant.sf"
+     fi
+ 
+     cat <<-END_VERSIONS > versions.yml
+
+************************************************************
diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test b/modules/nf-core/salmon/quant/tests/main.nf.test
new file mode 100644
index 00000000..04e61e2b
--- /dev/null
+++ b/modules/nf-core/salmon/quant/tests/main.nf.test
@@ -0,0 +1,160 @@
+nextflow_process {
+
+    name "Test Process SALMON_QUANT"
+    script "../main.nf"
+    process "SALMON_QUANT"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "salmon"
+    tag "salmon/quant"
+    tag "salmon/index"
+
+    setup {
+        run("SALMON_INDEX") {
+            script "../../../salmon/index/main.nf"
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - single_end") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match("versions_single_end") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - single_end lib type A") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = 'A'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match("versions_single_end_lib_type_a") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - pair_end") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match("versions_pair_end") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - pair_end multiple") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test2_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match("versions_pair_end_multiple") }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test.snap b/modules/nf-core/salmon/quant/tests/main.nf.test.snap
new file mode 100644
index 00000000..a1ec792e
--- /dev/null
+++ b/modules/nf-core/salmon/quant/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "versions_single_end": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T11:51:01.865730832"
+    },
+    "versions_pair_end": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-06T17:10:56.121713"
+    },
+    "versions_single_end_lib_type_a": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-06T17:09:14.898351"
+    },
+    "versions_pair_end_multiple": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-06T17:11:07.846643"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/salmon/quant/tests/nextflow.config b/modules/nf-core/salmon/quant/tests/nextflow.config
new file mode 100644
index 00000000..37c08212
--- /dev/null
+++ b/modules/nf-core/salmon/quant/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SALMON_QUANT {
+        ext.args = '--minAssignedFrags 1'
+    }
+
+}
diff --git a/modules/nf-core/salmon/quant/tests/tags.yml b/modules/nf-core/salmon/quant/tests/tags.yml
new file mode 100644
index 00000000..048d8164
--- /dev/null
+++ b/modules/nf-core/salmon/quant/tests/tags.yml
@@ -0,0 +1,2 @@
+salmon/quant:
+  - modules/nf-core/salmon/quant/**
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
index 04c82f14..3e95dd71 100644
--- a/modules/nf-core/samtools/faidx/environment.yml
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -1,6 +1,8 @@
+name: samtools_faidx
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.17
+  - bioconda::samtools=1.19.2
+  - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index 3aa98822..cfe7ad95 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX {
 
     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/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
index 04c82f14..a5e50649 100644
--- a/modules/nf-core/samtools/index/environment.yml
+++ b/modules/nf-core/samtools/index/environment.yml
@@ -1,6 +1,8 @@
+name: samtools_index
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.17
+  - 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 256bd7c4..dc14f98d 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_INDEX {
 
     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/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config
new file mode 100644
index 00000000..0ed260ef
--- /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 00000000..bb7756d1
--- /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 00000000..3dc8e7de
--- /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 00000000..e0f58a7a
--- /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/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
index 04c82f14..b0676f33 100644
--- a/modules/nf-core/samtools/view/environment.yml
+++ b/modules/nf-core/samtools/view/environment.yml
@@ -1,6 +1,8 @@
+name: samtools_view
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.17
+  - bioconda::samtools=1.19.2
+  - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index ddf3f88a..5a8989d6 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_VIEW {
 
     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), path(index)
@@ -53,10 +53,19 @@ process SAMTOOLS_VIEW {
     """
 
     stub:
+    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def file_type = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt bam") ? "bam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    input.getExtension()
+    if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+
+    def index = args.contains("--write-index") ? "touch ${prefix}.csi" : ""
+
     """
-    touch ${prefix}.bam
-    touch ${prefix}.cram
+    touch ${prefix}.${file_type}
+    ${index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/view/tests/bam.config b/modules/nf-core/samtools/view/tests/bam.config
new file mode 100644
index 00000000..c10d1081
--- /dev/null
+++ b/modules/nf-core/samtools/view/tests/bam.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "--output-fmt bam"
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/view/tests/bam_index.config b/modules/nf-core/samtools/view/tests/bam_index.config
new file mode 100644
index 00000000..771ae033
--- /dev/null
+++ b/modules/nf-core/samtools/view/tests/bam_index.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "--output-fmt bam --write-index"
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test
new file mode 100644
index 00000000..45a0defb
--- /dev/null
+++ b/modules/nf-core/samtools/view/tests/main.nf.test
@@ -0,0 +1,212 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_VIEW"
+    script "../main.nf"
+    process "SAMTOOLS_VIEW"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/view"
+
+    test("bam") {
+
+        when {
+            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.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") },
+                { assert snapshot(process.out.bai).match("bam_bai") },
+                { assert snapshot(process.out.crai).match("bam_crai") },
+                { assert snapshot(process.out.cram).match("bam_cram") },
+                { assert snapshot(process.out.csi).match("bam_csi") },
+                { assert snapshot(process.out.sam).match("bam_sam") },
+                { assert snapshot(process.out.versions).match("bam_versions") }
+            )
+        }
+    }
+
+    test("cram") {
+
+        when {
+            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.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.cram[0][1]).name).match("cram_cram") },
+                { assert snapshot(process.out.bai).match("cram_bai") },
+                { assert snapshot(process.out.bam).match("cram_bam") },
+                { assert snapshot(process.out.crai).match("cram_crai") },
+                { assert snapshot(process.out.csi).match("cram_csi") },
+                { assert snapshot(process.out.sam).match("cram_sam") },
+                { assert snapshot(process.out.versions).match("cram_versions") }
+            )
+        }
+    }
+
+    test("cram_to_bam") {
+
+        config "./bam.config"
+
+        when {
+            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.sorted.cram', checkIfExists: true),
+                    []
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_bam") },
+                { assert snapshot(process.out.bai).match("cram_to_bam_bai") },
+                { assert snapshot(process.out.crai).match("cram_to_bam_crai") },
+                { assert snapshot(process.out.cram).match("cram_to_bam_cram") },
+                { assert snapshot(process.out.csi).match("cram_to_bam_csi") },
+                { assert snapshot(process.out.sam).match("cram_to_bam_sam") },
+                { assert snapshot(process.out.versions).match("cram_to_bam_versions") }
+            )
+        }
+    }
+
+    test("cram_to_bam_index") {
+
+        config "./bam_index.config"
+
+        when {
+            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.sorted.cram', checkIfExists: true),
+                    []
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_bam") },
+                { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_csi") },
+                { assert snapshot(process.out.bai).match("cram_to_bam_index_bai") },
+                { assert snapshot(process.out.crai).match("cram_to_bam_index_crai") },
+                { assert snapshot(process.out.cram).match("cram_to_bam_index_cram") },
+                { assert snapshot(process.out.sam).match("cram_to_bam_index_sam") },
+                { assert snapshot(process.out.versions).match("cram_to_bam_index_versions") }
+            )
+        }
+    }
+
+    test("cram_to_bam_index_qname") {
+
+        config "./bam_index.config"
+
+        when {
+            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.sorted.cram', checkIfExists: true),
+                    []
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_qname_bam") },
+                { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_qname_csi") },
+                { assert snapshot(process.out.bai).match("cram_to_bam_index_qname_bai") },
+                { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") },
+                { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") },
+                { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") },
+                { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") }
+            )
+        }
+    }
+
+    test("bam_stub") {
+
+        options "-stub"
+        config "./bam_index.config"
+
+        when {
+            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.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") },
+                { assert snapshot(file(process.out.csi[0][1]).name).match("bam_stub_csi") },
+                { assert snapshot(process.out.bai).match("bam_stub_bai") },
+                { assert snapshot(process.out.crai).match("bam_stub_crai") },
+                { assert snapshot(process.out.cram).match("bam_stub_cram") },
+                { assert snapshot(process.out.sam).match("bam_stub_sam") },
+                { assert snapshot(process.out.versions).match("bam_stub_versions") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap
new file mode 100644
index 00000000..f55943a7
--- /dev/null
+++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap
@@ -0,0 +1,488 @@
+{
+    "bam_bam": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:51.256068"
+    },
+    "cram_to_bam_index_csi": {
+        "content": [
+            "test.bam.csi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:12.958617"
+    },
+    "bam_stub_bam": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:32.065301"
+    },
+    "bam_bai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:51.258578"
+    },
+    "bam_stub_bai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:32.071284"
+    },
+    "bam_stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:13:09.713353823"
+    },
+    "cram_to_bam_index_cram": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:12.972288"
+    },
+    "cram_to_bam_sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:04.999247"
+    },
+    "cram_to_bam_index_sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:12.976457"
+    },
+    "cram_crai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:56.497581"
+    },
+    "cram_csi": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:56.50038"
+    },
+    "cram_to_bam_cram": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:04.992239"
+    },
+    "cram_to_bam_index_qname_csi": {
+        "content": [
+            "test.bam.csi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.325496"
+    },
+    "bam_stub_sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:32.079529"
+    },
+    "cram_cram": {
+        "content": [
+            "test.cram"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:56.490286"
+    },
+    "bam_csi": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:51.262882"
+    },
+    "cram_to_bam_crai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:04.989247"
+    },
+    "cram_to_bam_index_crai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:12.967681"
+    },
+    "cram_to_bam_index_qname_versions": {
+        "content": [
+            [
+                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:13:03.935041046"
+    },
+    "cram_to_bam_bam": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:04.982361"
+    },
+    "cram_to_bam_index_bam": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:12.95456"
+    },
+    "cram_to_bam_index_versions": {
+        "content": [
+            [
+                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:12:55.910685496"
+    },
+    "cram_to_bam_bai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:04.98601"
+    },
+    "cram_to_bam_versions": {
+        "content": [
+            [
+                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:12:47.715221169"
+    },
+    "cram_bam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:56.495512"
+    },
+    "bam_stub_cram": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:32.076908"
+    },
+    "cram_to_bam_index_qname_bai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.328458"
+    },
+    "cram_to_bam_index_qname_crai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.330789"
+    },
+    "cram_bai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:56.493129"
+    },
+    "bam_stub_crai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:32.074313"
+    },
+    "cram_to_bam_index_qname_bam": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.322874"
+    },
+    "bam_versions": {
+        "content": [
+            [
+                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:12:31.692607421"
+    },
+    "cram_to_bam_index_qname_cram": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.333248"
+    },
+    "bam_crai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:51.259774"
+    },
+    "bam_cram": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:51.261287"
+    },
+    "cram_to_bam_csi": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:04.995454"
+    },
+    "cram_sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:56.502625"
+    },
+    "cram_versions": {
+        "content": [
+            [
+                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-13T16:12:39.913411036"
+    },
+    "bam_sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:37:51.264651"
+    },
+    "cram_to_bam_index_bai": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:12.962863"
+    },
+    "cram_to_bam_index_qname_sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.337634"
+    },
+    "bam_stub_csi": {
+        "content": [
+            "test.csi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:32.068596"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/view/tests/tags.yml b/modules/nf-core/samtools/view/tests/tags.yml
new file mode 100644
index 00000000..4fdf1dd1
--- /dev/null
+++ b/modules/nf-core/samtools/view/tests/tags.yml
@@ -0,0 +1,2 @@
+samtools/view:
+  - "modules/nf-core/samtools/view/**"
diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml
index a61d2f6d..8bd58cff 100644
--- a/modules/nf-core/star/align/environment.yml
+++ b/modules/nf-core/star/align/environment.yml
@@ -1,8 +1,10 @@
+name: star_align
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   - bioconda::star=2.7.10a
-  - bioconda::samtools=1.16.1
+  - bioconda::samtools=1.18
+  - bioconda::htslib=1.18
   - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index fa645a6d..8e9c48b1 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -4,8 +4,8 @@ process STAR_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' :
-        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' :
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test
new file mode 100644
index 00000000..6ecd7786
--- /dev/null
+++ b/modules/nf-core/star/align/tests/main.nf.test
@@ -0,0 +1,268 @@
+nextflow_process {
+
+    name "Test Process STAR_ALIGN"
+    script "../main.nf"
+    process "STAR_ALIGN"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "star"
+    tag "star/align"
+    tag "star/genomegenerate"
+
+    setup {
+        run("STAR_GENOMEGENERATE") {
+            script "../../../star/genomegenerate/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+    }
+
+    test("homo_sapiens - single_end") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") },
+                { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") },
+                { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") },
+                { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") },
+                { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") },
+                { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") },
+                { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") },
+                { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") },
+                { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") },
+                { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") },
+                { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") },
+                { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") },
+                { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") },
+                { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") },
+                { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") },
+                { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") },
+                { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") },
+                { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") },
+                { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") },
+                { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") },
+                { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") },
+                { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") },
+                { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") },
+                { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") },
+                { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") },
+                { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") },
+                { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") },
+                { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") },
+                { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") },
+                { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") },
+                { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - arriba") {
+        config "./nextflow.arriba.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") },
+                { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") },
+                { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") },
+                { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") },
+                { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") },
+                { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") },
+                { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") },
+                { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") },
+                { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") },
+                { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") },
+                { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") },
+                { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") },
+                { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") },
+                { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") },
+                { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") },
+                { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - starfusion") {
+        config "./nextflow.starfusion.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") },
+                { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") },
+                { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") },
+                { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") },
+                { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") },
+                { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") },
+                { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") },
+                { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") },
+                { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") },
+                { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") },
+                { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") },
+                { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") },
+                { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") },
+                { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") },
+                { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") },
+                { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - multiple") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") },
+                { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") },
+                { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") },
+                { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") },
+                { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") },
+                { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") },
+                { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") },
+                { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") },
+                { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") },
+                { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") },
+                { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") },
+                { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") },
+                { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") },
+                { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") },
+                { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") },
+                { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap
new file mode 100644
index 00000000..08edb914
--- /dev/null
+++ b/modules/nf-core/star/align/tests/main.nf.test.snap
@@ -0,0 +1,769 @@
+{
+    "homo_sapiens - paired_end - multiple - bam_sorted": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T18:01:19.968225733"
+    },
+    "homo_sapiens - paired_end - multiple - wig": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:29:01.857804"
+    },
+    "homo_sapiens - paired_end - arriba - tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:56:12.347549723"
+    },
+    "homo_sapiens - single_end - wig": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:22:55.24701"
+    },
+    "homo_sapiens - paired_end - sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:23:33.383818"
+    },
+    "homo_sapiens - paired_end - arriba - versions": {
+        "content": [
+            [
+                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+            ]
+        ],
+        "timestamp": "2023-12-04T17:56:12.431212643"
+    },
+    "homo_sapiens - paired_end - multiple - bedgraph": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.Signal.Unique.str1.out.bg:md5,d7bf8b70b436ca048a62513e1d0ece3a",
+                        "test.Signal.UniqueMultiple.str1.out.bg:md5,686d58493b9eb445b56ace4d67f76ef6"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T18:01:20.07119229"
+    },
+    "homo_sapiens - paired_end - read_per_gene_tab": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:23:33.368841"
+    },
+    "homo_sapiens - paired_end - arriba - bedgraph": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:07.102537"
+    },
+    "homo_sapiens - single_end - junction": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:22:55.185369"
+    },
+    "homo_sapiens - paired_end - arriba - spl_junc_tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:56:12.268388251"
+    },
+    "homo_sapiens - single_end - sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:22:55.216183"
+    },
+    "homo_sapiens - paired_end - fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:23:33.327236"
+    },
+    "homo_sapiens - single_end - versions": {
+        "content": [
+            [
+                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+            ]
+        ],
+        "timestamp": "2023-12-04T17:53:26.664210196"
+    },
+    "homo_sapiens - paired_end - multiple - log_out": {
+        "content": [
+            "test.Log.out"
+        ],
+        "timestamp": "2023-11-23T13:29:01.022176"
+    },
+    "homo_sapiens - paired_end - arriba - fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:07.15277"
+    },
+    "homo_sapiens - paired_end - multiple - junction": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:29:01.52923"
+    },
+    "homo_sapiens - paired_end - multiple - spl_junc_tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,069877e053714e23010fe4e1c003b4a2"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T18:01:20.189486201"
+    },
+    "homo_sapiens - paired_end - starfusion - log_final": {
+        "content": [
+            "test.Log.final.out"
+        ],
+        "timestamp": "2023-11-23T13:27:55.905883"
+    },
+    "homo_sapiens - paired_end - starfusion - fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.192302"
+    },
+    "homo_sapiens - paired_end - multiple - sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:29:01.661837"
+    },
+    "homo_sapiens - paired_end - multiple - log_final": {
+        "content": [
+            "test.Log.final.out"
+        ],
+        "timestamp": "2023-11-23T13:29:00.966417"
+    },
+    "homo_sapiens - paired_end - starfusion - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.out.bam:md5,bcad07b838f6762fc01eea52b5cd3f84"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:59:58.53235164"
+    },
+    "homo_sapiens - paired_end - arriba - junction": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:07.202776"
+    },
+    "homo_sapiens - single_end - bedgraph": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    [
+                        "test.Signal.Unique.str1.out.bg:md5,c56fc1472776fb927eaf62d973da5f9a",
+                        "test.Signal.UniqueMultiple.str1.out.bg:md5,e93373cf6f2a2a9506e2efdb260cdd4f"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:53:26.394863748"
+    },
+    "homo_sapiens - paired_end - arriba - read_per_gene_tab": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:07.251962"
+    },
+    "homo_sapiens - paired_end - starfusion - bam_sorted": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.040843"
+    },
+    "homo_sapiens - single_end - bam_unsorted": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:22:55.154172"
+    },
+    "homo_sapiens - paired_end - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:54:11.934832258"
+    },
+    "homo_sapiens - paired_end - arriba - bam_transcript": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:06.998817"
+    },
+    "homo_sapiens - paired_end - log_out": {
+        "content": [
+            "test.Log.out"
+        ],
+        "timestamp": "2023-11-23T13:23:33.259699"
+    },
+    "homo_sapiens - paired_end - arriba - log_out": {
+        "content": [
+            "test.Log.out"
+        ],
+        "timestamp": "2023-11-23T13:25:06.849451"
+    },
+    "homo_sapiens - paired_end - multiple - versions": {
+        "content": [
+            [
+                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+            ]
+        ],
+        "timestamp": "2023-12-04T18:01:20.393705142"
+    },
+    "homo_sapiens - paired_end - starfusion - bam_transcript": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.082408"
+    },
+    "homo_sapiens - paired_end - starfusion - tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:59:58.818041322"
+    },
+    "homo_sapiens - single_end - fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:22:55.175307"
+    },
+    "homo_sapiens - paired_end - tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:54:12.255481058"
+    },
+    "homo_sapiens - paired_end - starfusion - bedgraph": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.155413"
+    },
+    "homo_sapiens - single_end - bam_transcript": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:22:55.144852"
+    },
+    "homo_sapiens - paired_end - versions": {
+        "content": [
+            [
+                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+            ]
+        ],
+        "timestamp": "2023-12-04T17:54:12.343840482"
+    },
+    "homo_sapiens - paired_end - multiple - tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,069877e053714e23010fe4e1c003b4a2"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T18:01:20.291692062"
+    },
+    "homo_sapiens - single_end - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:53:26.265642675"
+    },
+    "homo_sapiens - paired_end - arriba - wig": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:07.444214"
+    },
+    "homo_sapiens - paired_end - log_progress": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:54:12.126063825"
+    },
+    "homo_sapiens - paired_end - arriba - log_final": {
+        "content": [
+            "test.Log.final.out"
+        ],
+        "timestamp": "2023-11-23T13:25:06.829799"
+    },
+    "homo_sapiens - paired_end - bam_unsorted": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:23:33.300509"
+    },
+    "homo_sapiens - paired_end - arriba - sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:07.300383"
+    },
+    "homo_sapiens - paired_end - multiple - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T18:01:19.851247126"
+    },
+    "homo_sapiens - paired_end - multiple - fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:29:01.462257"
+    },
+    "homo_sapiens - single_end - bam_sorted": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:53:26.335457371"
+    },
+    "homo_sapiens - paired_end - arriba - bam_sorted": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:06.94699"
+    },
+    "homo_sapiens - paired_end - starfusion - junction": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Chimeric.out.junction:md5,c10ef219f4a30e83711b995bc5e40dba"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:59:58.641115828"
+    },
+    "homo_sapiens - single_end - tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.SJ.out.tab:md5,75a516ab950fb958f40b29996474949c"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:53:26.580593434"
+    },
+    "homo_sapiens - paired_end - starfusion - versions": {
+        "content": [
+            [
+                "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+            ]
+        ],
+        "timestamp": "2023-12-04T17:59:58.907317103"
+    },
+    "homo_sapiens - paired_end - multiple - bam_unsorted": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:29:01.330463"
+    },
+    "homo_sapiens - paired_end - arriba - log_progress": {
+        "content": [
+            "test.Log.progress.out"
+        ],
+        "timestamp": "2023-11-23T13:25:06.86866"
+    },
+    "homo_sapiens - paired_end - bedgraph": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.Signal.Unique.str1.out.bg:md5,d7bf8b70b436ca048a62513e1d0ece3a",
+                        "test.Signal.UniqueMultiple.str1.out.bg:md5,686d58493b9eb445b56ace4d67f76ef6"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:54:12.064121304"
+    },
+    "homo_sapiens - paired_end - starfusion - bam_unsorted": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.118974"
+    },
+    "homo_sapiens - paired_end - starfusion - read_per_gene_tab": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.264699"
+    },
+    "homo_sapiens - paired_end - multiple - log_progress": {
+        "content": [
+            "test.Log.progress.out"
+        ],
+        "timestamp": "2023-11-23T13:29:01.076947"
+    },
+    "homo_sapiens - paired_end - arriba - bam_unsorted": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:25:07.050409"
+    },
+    "homo_sapiens - paired_end - bam_sorted": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:54:12.002180537"
+    },
+    "homo_sapiens - single_end - spl_junc_tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.SJ.out.tab:md5,75a516ab950fb958f40b29996474949c"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:53:26.50932751"
+    },
+    "homo_sapiens - paired_end - starfusion - spl_junc_tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:59:58.731699486"
+    },
+    "homo_sapiens - single_end - log_out": {
+        "content": [
+            "test.Log.out"
+        ],
+        "timestamp": "2023-11-23T13:22:55.126286"
+    },
+    "homo_sapiens - paired_end - log_final": {
+        "content": [
+            "test.Log.final.out"
+        ],
+        "timestamp": "2023-11-23T13:23:33.253884"
+    },
+    "homo_sapiens - single_end - log_final": {
+        "content": [
+            "test.Log.final.out"
+        ],
+        "timestamp": "2023-11-23T13:22:55.11799"
+    },
+    "homo_sapiens - paired_end - bam_transcript": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:23:33.287684"
+    },
+    "homo_sapiens - paired_end - starfusion - log_progress": {
+        "content": [
+            "test.Log.progress.out"
+        ],
+        "timestamp": "2023-11-23T13:27:55.971484"
+    },
+    "homo_sapiens - paired_end - multiple - bam_transcript": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:29:01.264176"
+    },
+    "homo_sapiens - paired_end - multiple - read_per_gene_tab": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:29:01.596406"
+    },
+    "homo_sapiens - single_end - read_per_gene_tab": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:22:55.205936"
+    },
+    "homo_sapiens - paired_end - junction": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:23:33.340653"
+    },
+    "homo_sapiens - paired_end - spl_junc_tab": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:54:12.185730856"
+    },
+    "homo_sapiens - paired_end - starfusion - sam": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.300637"
+    },
+    "homo_sapiens - paired_end - arriba - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:56:12.190560178"
+    },
+    "homo_sapiens - single_end - log_progress": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-04T17:53:26.450352138"
+    },
+    "homo_sapiens - paired_end - starfusion - wig": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:27:56.422018"
+    },
+    "homo_sapiens - paired_end - wig": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-11-23T13:23:33.429457"
+    },
+    "homo_sapiens - paired_end - starfusion - log_out": {
+        "content": [
+            "test.Log.out"
+        ],
+        "timestamp": "2023-11-23T13:27:55.93945"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config
new file mode 100644
index 00000000..2324b9e5
--- /dev/null
+++ b/modules/nf-core/star/align/tests/nextflow.arriba.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config
new file mode 100644
index 00000000..c4ac5808
--- /dev/null
+++ b/modules/nf-core/star/align/tests/nextflow.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config
new file mode 100644
index 00000000..467b6497
--- /dev/null
+++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/nf-core/star/align/tests/tags.yml b/modules/nf-core/star/align/tests/tags.yml
new file mode 100644
index 00000000..8beace16
--- /dev/null
+++ b/modules/nf-core/star/align/tests/tags.yml
@@ -0,0 +1,2 @@
+star/align:
+  - modules/nf-core/star/align/**
diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml
index a61d2f6d..791f255e 100644
--- a/modules/nf-core/star/genomegenerate/environment.yml
+++ b/modules/nf-core/star/genomegenerate/environment.yml
@@ -1,8 +1,10 @@
+name: star_genomegenerate
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
+  - bioconda::samtools=1.18
+  - bioconda::htslib=1.18
   - bioconda::star=2.7.10a
-  - bioconda::samtools=1.16.1
   - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
index 473e62a6..b8855715 100644
--- a/modules/nf-core/star/genomegenerate/main.nf
+++ b/modules/nf-core/star/genomegenerate/main.nf
@@ -4,8 +4,8 @@ process STAR_GENOMEGENERATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' :
-        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' :
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -19,9 +19,10 @@ process STAR_GENOMEGENERATE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def args_list = args.tokenize()
-    def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    def args        = task.ext.args ?: ''
+    def args_list   = args.tokenize()
+    def memory      = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    def include_gtf = gtf ? "--sjdbGTFfile $gtf" : ''
     if (args_list.contains('--genomeSAindexNbases')) {
         """
         mkdir star
@@ -29,7 +30,7 @@ process STAR_GENOMEGENERATE {
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             $memory \\
             $args
@@ -51,7 +52,7 @@ process STAR_GENOMEGENERATE {
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             --genomeSAindexNbases \$NUM_BASES \\
             $memory \\
@@ -67,30 +68,52 @@ process STAR_GENOMEGENERATE {
     }
 
     stub:
-    """
-    mkdir star
-    touch star/Genome
-    touch star/Log.out
-    touch star/SA
-    touch star/SAindex
-    touch star/chrLength.txt
-    touch star/chrName.txt
-    touch star/chrNameLength.txt
-    touch star/chrStart.txt
-    touch star/exonGeTrInfo.tab
-    touch star/exonInfo.tab
-    touch star/geneInfo.tab
-    touch star/genomeParameters.txt
-    touch star/sjdbInfo.txt
-    touch star/sjdbList.fromGTF.out.tab
-    touch star/sjdbList.out.tab
-    touch star/transcriptInfo.tab
+    if (gtf) {
+        """
+        mkdir star
+        touch star/Genome
+        touch star/Log.out
+        touch star/SA
+        touch star/SAindex
+        touch star/chrLength.txt
+        touch star/chrName.txt
+        touch star/chrNameLength.txt
+        touch star/chrStart.txt
+        touch star/exonGeTrInfo.tab
+        touch star/exonInfo.tab
+        touch star/geneInfo.tab
+        touch star/genomeParameters.txt
+        touch star/sjdbInfo.txt
+        touch star/sjdbList.fromGTF.out.tab
+        touch star/sjdbList.out.tab
+        touch star/transcriptInfo.tab
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
-    """
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        mkdir star
+        touch star/Genome
+        touch star/Log.out
+        touch star/SA
+        touch star/SAindex
+        touch star/chrLength.txt
+        touch star/chrName.txt
+        touch star/chrNameLength.txt
+        touch star/chrStart.txt
+        touch star/genomeParameters.txt
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    }
 }
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test
new file mode 100644
index 00000000..c17c8ba4
--- /dev/null
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test
@@ -0,0 +1,115 @@
+nextflow_process {
+
+    name "Test Process STAR_GENOMEGENERATE"
+    script "../main.nf"
+    process "STAR_GENOMEGENERATE"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "star"
+    tag "star/genomegenerate"
+
+    test("fasta_gtf") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") },
+                { assert snapshot(process.out.versions).match("fasta_gtf_versions") }
+            )
+        }
+    }
+
+    test("fasta_gtf_stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") },
+                { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") }
+            )
+        }
+    }
+
+    test("fasta") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") },
+                { assert snapshot(process.out.versions).match("fasta_versions") }
+            )
+        }
+
+    }
+
+    test("fasta_stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") },
+                { assert snapshot(process.out.versions).match("fasta_stub_versions") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
new file mode 100644
index 00000000..5653d6e6
--- /dev/null
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
@@ -0,0 +1,90 @@
+{
+    "fasta_gtf_versions": {
+        "content": [
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:31.798555"
+    },
+    "fasta_stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:55:07.521209"
+    },
+    "fasta_gtf_stub_index": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:46.478098"
+    },
+    "fasta_gtf_stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:46.491657"
+    },
+    "fasta_index": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:57.552329"
+    },
+    "fasta_versions": {
+        "content": [
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:57.560541"
+    },
+    "fasta_gtf_index": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:31.786814"
+    },
+    "fasta_stub_index": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:55:07.517472"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/star/genomegenerate/tests/tags.yml b/modules/nf-core/star/genomegenerate/tests/tags.yml
new file mode 100644
index 00000000..79f619bf
--- /dev/null
+++ b/modules/nf-core/star/genomegenerate/tests/tags.yml
@@ -0,0 +1,2 @@
+star/genomegenerate:
+  - modules/nf-core/star/genomegenerate/**
diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml
index 376fba8c..7a0eccdb 100644
--- a/modules/nf-core/stringtie/stringtie/environment.yml
+++ b/modules/nf-core/stringtie/stringtie/environment.yml
@@ -1,3 +1,4 @@
+name: stringtie_stringtie
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test
new file mode 100644
index 00000000..00efe8f1
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test
@@ -0,0 +1,116 @@
+nextflow_process {
+
+    name "Test Process STRINGTIE_STRINGTIE"
+    script "../main.nf"
+    process "STRINGTIE_STRINGTIE"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "stringtie"
+    tag "stringtie/stringtie"
+
+    test("sarscov2 [bam] - forward strandedness") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'forward' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") },
+                { assert snapshot(process.out.abundance).match("fs_abundance") },
+                { assert snapshot(process.out.versions).match("fs_versions") }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - forward strandedness + reference annotation") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', strandedness:'forward' ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+                { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") },
+                { assert snapshot(process.out.abundance).match("fs_gtf_abundance") },
+                { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") },
+                { assert snapshot(process.out.versions).match("fs_gtf_versions") }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse strandedness") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'reverse' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") },
+                { assert snapshot(process.out.abundance).match("rs_abundance") },
+                { assert snapshot(process.out.versions).match("rs_versions") }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse strandedness + reference annotation") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'reverse' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") },
+                { assert snapshot(process.out.abundance).match("rs_gtf_abundance") },
+                { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") },
+                { assert snapshot(process.out.versions).match("rs_gtf_versions") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
new file mode 100644
index 00000000..bf751636
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
@@ -0,0 +1,186 @@
+{
+    "fs_abundance": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:55:41.032044613"
+    },
+    "fs_transcript_gtf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.transcripts.gtf:md5,569137af5be452413086b50653a97203"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:55:41.017978904"
+    },
+    "rs_abundance": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:13.601112933"
+    },
+    "fs_gtf_versions": {
+        "content": [
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:00.523797974"
+    },
+    "fs_gtf_transcript_gtf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:00.475164879"
+    },
+    "rs_versions": {
+        "content": [
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:13.623892691"
+    },
+    "rs_gtf_transcript_gtf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:22.693599559"
+    },
+    "fs_gtf_abundance": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:00.482135418"
+    },
+    "rs_gtf_ballgown": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    [
+                        "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540",
+                        "e_data.ctab:md5,879b6696029d19c4737b562e9d149218",
+                        "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4",
+                        "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f",
+                        "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:22.715698347"
+    },
+    "rs_transcript_gtf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:13.590054035"
+    },
+    "rs_gtf_versions": {
+        "content": [
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:22.725513476"
+    },
+    "fs_gtf_ballgown": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    [
+                        "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540",
+                        "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471",
+                        "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4",
+                        "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f",
+                        "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:00.494299817"
+    },
+    "fs_versions": {
+        "content": [
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "timestamp": "2023-11-23T13:55:41.049417582"
+    },
+    "rs_gtf_abundance": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-23T13:56:22.701059059"
+    }
+}
diff --git a/modules/nf-core/stringtie/stringtie/tests/nextflow.config b/modules/nf-core/stringtie/stringtie/tests/nextflow.config
new file mode 100644
index 00000000..e3aaa099
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'STRINGTIE_STRINGTIE' {
+        ext.args = ''
+    }
+}
diff --git a/modules/nf-core/stringtie/stringtie/tests/tags.yml b/modules/nf-core/stringtie/stringtie/tests/tags.yml
new file mode 100644
index 00000000..da9b051c
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/tests/tags.yml
@@ -0,0 +1,2 @@
+stringtie/stringtie:
+  - modules/nf-core/stringtie/stringtie/**
diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml
new file mode 100644
index 00000000..361c078b
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/environment.yml
@@ -0,0 +1,8 @@
+name: tabix_bgzip
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::tabix=1.11
+  - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf
new file mode 100644
index 00000000..3065dab0
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/main.nf
@@ -0,0 +1,55 @@
+process TABIX_BGZIP {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
+        'biocontainers/htslib:1.19.1--h81da01d_1' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("${output}")    , emit: output
+    tuple val(meta), path("${output}.gzi"), emit: gzi, optional: true
+    path  "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension())
+    extension = in_bgzip ? input.getBaseName().tokenize(".")[-1] : input.getExtension()
+    output   = in_bgzip ? "${prefix}.${extension}" : "${prefix}.${extension}.gz"
+    command = in_bgzip ? '-d' : ''
+    // Name the index according to $prefix, unless a name has been requested
+    if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) {
+        args = args + " -I ${output}.gzi"
+    }
+    """
+    bgzip $command -c $args -@${task.cpus} $input > ${output}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension())
+    output   = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz"
+
+    """
+    echo "" | gzip > ${output}
+    touch ${output}.gzi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml
new file mode 100644
index 00000000..621d49ea
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/meta.yml
@@ -0,0 +1,52 @@
+name: tabix_bgzip
+description: Compresses/decompresses files
+keywords:
+  - compress
+  - decompress
+  - bgzip
+  - tabix
+tools:
+  - bgzip:
+      description: |
+        Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: http://www.htslib.org/doc/bgzip.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: file to compress or to decompress
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - output:
+      type: file
+      description: Output compressed/decompressed file
+      pattern: "*."
+  - gzi:
+      type: file
+      description: Optional gzip index file for compressed inputs
+      pattern: "*.gzi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@maxulysse"
+  - "@nvnieuwk"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@maxulysse"
+  - "@nvnieuwk"
diff --git a/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config
new file mode 100644
index 00000000..6b6ff55f
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_BGZIP {
+        ext.args = ' -i'
+    }
+}
diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test
new file mode 100644
index 00000000..95fd4c50
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test
@@ -0,0 +1,111 @@
+nextflow_process {
+
+    name "Test Process TABIX_BGZIP"
+    script "modules/nf-core/tabix/bgzip/main.nf"
+    process "TABIX_BGZIP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabix"
+    tag "tabix/bgzip"
+
+    test("sarscov2_vcf_bgzip_compress") {
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'bgzip_test' ],
+                                [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.output[0][1]).name
+                                ).match("bgzip_test")
+                }
+            )
+        }
+    }
+
+    test("homo_genome_bedgz_compress") {
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'bedgz_test' ],
+                            [ file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.output[0][1]).name
+                                ).match("bedgz_test")
+                }
+            )
+        }
+    }
+
+    test("sarscov2_vcf_bgzip_compress_stub") {
+        options '-stub'
+        config "./bgzip_compress.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:"test_stub" ],
+                                [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.output[0][1]).name
+                                ).match("test_stub")
+                }
+            )
+        }
+    }
+
+    test("sarscov2_vcf_bgzip_compress_gzi") {
+        config "./bgzip_compress.config"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:"gzi_compress_test" ],
+                                [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.gzi[0][1]).name
+                                ).match("gzi_compress_test")
+                }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
new file mode 100644
index 00000000..53d59932
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
@@ -0,0 +1,186 @@
+{
+    "gzi_compress_test": {
+        "content": [
+            "gzi_compress_test.vcf.gz.gzi"
+        ],
+        "timestamp": "2024-02-19T14:52:29.328146"
+    },
+    "homo_genome_bedgz_compress": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "bedgz_test"
+                        },
+                        "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ],
+                "gzi": [
+                    
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "bedgz_test"
+                        },
+                        "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:52:12.422209"
+    },
+    "test_stub": {
+        "content": [
+            "test_stub.vcf.gz"
+        ],
+        "timestamp": "2024-02-19T14:52:20.811489"
+    },
+    "sarscov2_vcf_bgzip_compress": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "bgzip_test"
+                        },
+                        "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ],
+                "gzi": [
+                    
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "bgzip_test"
+                        },
+                        "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:52:03.706028"
+    },
+    "sarscov2_vcf_bgzip_compress_gzi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:52:29.271494"
+    },
+    "bgzip_test": {
+        "content": [
+            "bgzip_test.vcf.gz"
+        ],
+        "timestamp": "2024-02-19T14:52:03.768295"
+    },
+    "bedgz_test": {
+        "content": [
+            "bedgz_test.bed"
+        ],
+        "timestamp": "2024-02-19T14:52:12.453855"
+    },
+    "sarscov2_vcf_bgzip_compress_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e023292de6ee109a44fc67475d658174"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:52:20.769619"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/bgzip/tests/tags.yml b/modules/nf-core/tabix/bgzip/tests/tags.yml
new file mode 100644
index 00000000..de0eec86
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/tags.yml
@@ -0,0 +1,2 @@
+tabix/bgzip:
+  - "modules/nf-core/tabix/bgzip/**"
diff --git a/modules/nf-core/tabix/bgzip/tests/vcf_none.config b/modules/nf-core/tabix/bgzip/tests/vcf_none.config
new file mode 100644
index 00000000..f3a3c467
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/vcf_none.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_BGZIP {
+        ext.args = ''
+    }
+}
diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml
index fdd84057..c4235872 100644
--- a/modules/nf-core/tabix/bgziptabix/environment.yml
+++ b/modules/nf-core/tabix/bgziptabix/environment.yml
@@ -1,6 +1,8 @@
+name: tabix_bgziptabix
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   - bioconda::tabix=1.11
+  - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index f9482690..bcdcf2a6 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
-        'biocontainers/tabix:1.11--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
+        'biocontainers/htslib:1.19.1--h81da01d_1' }"
 
     input:
     tuple val(meta), path(input)
@@ -35,7 +35,7 @@ process TABIX_BGZIPTABIX {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.${input.getExtension()}.gz
+    echo "" | gzip > ${prefix}.${input.getExtension()}.gz
     touch ${prefix}.${input.getExtension()}.gz.tbi
     touch ${prefix}.${input.getExtension()}.gz.csi
 
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
new file mode 100644
index 00000000..87ea2c84
--- /dev/null
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
@@ -0,0 +1,94 @@
+nextflow_process {
+
+    name "Test Process TABIX_BGZIPTABIX"
+    script "modules/nf-core/tabix/bgziptabix/main.nf"
+    process "TABIX_BGZIPTABIX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabix"
+    tag "tabix/bgziptabix"
+
+    test("sarscov2_bed_tbi") {
+        config "./tabix_tbi.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'tbi_test' ],
+                                [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.gz_tbi[0][1]).name
+                                ).match("tbi_test")
+                }
+            )
+        }
+    }
+
+    test("sarscov2_bed_csi") {
+        config "./tabix_csi.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'csi_test' ],
+                                [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.gz_csi[0][1]).name
+                                ).match("csi_test")
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2_bed_csi_stub") {
+        config "./tabix_csi.config"
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test' ],
+                                [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.gz_csi[0][1]).name
+                                ).match("csi_stub")
+                }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
new file mode 100644
index 00000000..fcecb2e4
--- /dev/null
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
@@ -0,0 +1,143 @@
+{
+    "sarscov2_bed_tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tbi_test"
+                        },
+                        "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
+                        "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+                ],
+                "gz_csi": [
+                    
+                ],
+                "gz_tbi": [
+                    [
+                        {
+                            "id": "tbi_test"
+                        },
+                        "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
+                        "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:50:51.513838"
+    },
+    "sarscov2_bed_csi": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "csi_test"
+                        },
+                        "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
+                        "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+                ],
+                "gz_csi": [
+                    [
+                        {
+                            "id": "csi_test"
+                        },
+                        "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
+                        "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43"
+                    ]
+                ],
+                "gz_tbi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:51:00.513777"
+    },
+    "csi_test": {
+        "content": [
+            "csi_test.bed.gz"
+        ],
+        "timestamp": "2024-02-19T14:51:00.548801"
+    },
+    "csi_stub": {
+        "content": [
+            "test.bed.gz"
+        ],
+        "timestamp": "2024-02-19T14:51:09.218454"
+    },
+    "tbi_test": {
+        "content": [
+            "tbi_test.bed.gz"
+        ],
+        "timestamp": "2024-02-19T14:50:51.579654"
+    },
+    "sarscov2_bed_csi_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+                ],
+                "gz_csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gz_tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:51:09.164254"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config
new file mode 100644
index 00000000..fb41a314
--- /dev/null
+++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_BGZIPTABIX {
+        ext.args2 = '-p vcf --csi'
+    }
+}
diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config
new file mode 100644
index 00000000..c1915dc4
--- /dev/null
+++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_BGZIPTABIX {
+        ext.args2 = '-p vcf'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/bgziptabix/tests/tags.yml b/modules/nf-core/tabix/bgziptabix/tests/tags.yml
new file mode 100644
index 00000000..5052b4d7
--- /dev/null
+++ b/modules/nf-core/tabix/bgziptabix/tests/tags.yml
@@ -0,0 +1,2 @@
+tabix/bgziptabix:
+  - "modules/nf-core/tabix/bgziptabix/**"
diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml
index fdd84057..76b45e16 100644
--- a/modules/nf-core/tabix/tabix/environment.yml
+++ b/modules/nf-core/tabix/tabix/environment.yml
@@ -1,6 +1,8 @@
+name: tabix_tabix
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   - bioconda::tabix=1.11
+  - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index c304a8a3..1737141d 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -4,8 +4,8 @@ process TABIX_TABIX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
-        'biocontainers/tabix:1.11--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
+        'biocontainers/htslib:1.19.1--h81da01d_1' }"
 
     input:
     tuple val(meta), path(tab)
@@ -30,9 +30,9 @@ process TABIX_TABIX {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${tab}.tbi
+    touch ${tab}.csi
     cat <<-END_VERSIONS > versions.yml
 
     "${task.process}":
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
new file mode 100644
index 00000000..3a150c70
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -0,0 +1,142 @@
+nextflow_process {
+
+    name "Test Process TABIX_TABIX"
+    script "modules/nf-core/tabix/tabix/main.nf"
+    process "TABIX_TABIX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabix"
+    tag "tabix/tabix"
+
+    test("sarscov2_bedgz_tbi") {
+        config "./tabix_bed.config"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'tbi_bed' ],
+                                [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.tbi[0][1]).name
+                                ).match("tbi_bed")
+                }
+            )
+        }
+    }
+
+    test("sarscov2_gff_tbi") {
+        config "./tabix_gff.config"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'tbi_gff' ],
+                                [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.tbi[0][1]).name
+                                ).match("tbi_gff")
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2_vcf_tbi") {
+        config "./tabix_vcf_tbi.config"
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'tbi_vcf' ],
+                                [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.tbi[0][1]).name
+                                ).match("tbi_vcf")
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2_vcf_csi") {
+        config "./tabix_vcf_csi.config"
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'vcf_csi' ],
+                                [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.csi[0][1]).name
+                                ).match("vcf_csi")
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2_vcf_csi_stub") {
+        config "./tabix_vcf_csi.config"
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'vcf_csi_stub' ],
+                                [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.csi[0][1]).name
+                                ).match("vcf_csi_stub")
+                }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
new file mode 100644
index 00000000..034e38b6
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -0,0 +1,217 @@
+{
+    "vcf_csi_stub": {
+        "content": [
+            "test.vcf.gz.csi"
+        ],
+        "timestamp": "2024-03-04T14:51:59.788002"
+    },
+    "tbi_gff": {
+        "content": [
+            "genome.gff3.gz.tbi"
+        ],
+        "timestamp": "2024-02-19T14:53:37.420216"
+    },
+    "sarscov2_gff_tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tbi_gff"
+                        },
+                        "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "tbi_gff"
+                        },
+                        "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:53:37.388157"
+    },
+    "sarscov2_bedgz_tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tbi_bed"
+                        },
+                        "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "tbi_bed"
+                        },
+                        "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:53:28.879408"
+    },
+    "tbi_vcf": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "timestamp": "2024-02-19T14:53:46.402522"
+    },
+    "vcf_csi": {
+        "content": [
+            "test.vcf.gz.csi"
+        ],
+        "timestamp": "2024-02-19T14:53:54.921189"
+    },
+    "sarscov2_vcf_tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tbi_vcf"
+                        },
+                        "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "tbi_vcf"
+                        },
+                        "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:53:46.370358"
+    },
+    "sarscov2_vcf_csi_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,3d45df6d80883bad358631069a2940fd"
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3d45df6d80883bad358631069a2940fd"
+                ]
+            }
+        ],
+        "timestamp": "2024-03-04T14:51:59.766184"
+    },
+    "sarscov2_vcf_csi": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "vcf_csi"
+                        },
+                        "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "vcf_csi"
+                        },
+                        "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03"
+                    ]
+                ],
+                "tbi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-19T14:53:54.886876"
+    },
+    "tbi_bed": {
+        "content": [
+            "test.bed.gz.tbi"
+        ],
+        "timestamp": "2024-02-19T14:53:28.947628"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config
new file mode 100644
index 00000000..7ff05905
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_bed.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p bed'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config
new file mode 100644
index 00000000..20c0a1e3
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_gff.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p gff'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config
new file mode 100644
index 00000000..eb4f2d7e
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p vcf --csi'
+    }
+}
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config
new file mode 100644
index 00000000..2774c8a9
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p vcf'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml
new file mode 100644
index 00000000..6eda0653
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tags.yml
@@ -0,0 +1,2 @@
+tabix/tabix:
+  - "modules/nf-core/tabix/tabix/**"
diff --git a/modules/nf-core/ucsc/wigtobigwig/environment.yml b/modules/nf-core/ucsc/wigtobigwig/environment.yml
index 51bcac63..3e88a5dd 100644
--- a/modules/nf-core/ucsc/wigtobigwig/environment.yml
+++ b/modules/nf-core/ucsc/wigtobigwig/environment.yml
@@ -1,3 +1,4 @@
+name: ucsc_wigtobigwig
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
index 2d52ce64..0c9cbb10 100644
--- a/modules/nf-core/untar/environment.yml
+++ b/modules/nf-core/untar/environment.yml
@@ -1,8 +1,11 @@
+name: untar
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - conda-forge::sed=4.7
   - conda-forge::grep=3.11
+  - conda-forge::sed=4.7
   - conda-forge::tar=1.34
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
new file mode 100644
index 00000000..2a7c97bf
--- /dev/null
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -0,0 +1,47 @@
+nextflow_process {
+
+    name "Test Process UNTAR"
+    script "../main.nf"
+    process "UNTAR"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untar"
+    test("test_untar") {
+
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.untar).match("test_untar") },
+            )
+        }
+
+    }
+
+    test("test_untar_onlyfiles") {
+
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.untar).match("test_untar_onlyfiles") },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
new file mode 100644
index 00000000..64550292
--- /dev/null
+++ b/modules/nf-core/untar/tests/main.nf.test.snap
@@ -0,0 +1,42 @@
+{
+    "test_untar_onlyfiles": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    [
+                        "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:49:41.320643"
+    },
+    "test_untar": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    [
+                        "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+                        "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+                        "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:49:33.795172"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml
new file mode 100644
index 00000000..feb6f15c
--- /dev/null
+++ b/modules/nf-core/untar/tests/tags.yml
@@ -0,0 +1,2 @@
+untar:
+  - modules/nf-core/untar/**
diff --git a/nextflow.config b/nextflow.config
index cbedd9f3..97c29801 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,11 +11,18 @@ params {
 
     // Input options
     input                      = null
+
     // References
     genome                     = 'GRCh38'
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
     save_reference             = true
+    fasta                      = null
+    fai                        = null
+    star_index                 = null
+    transcript_fasta           = null
+    salmon_index               = null
+    sequence_dict              = null
 
     // Main options
     platform                   = 'illumina'
@@ -25,8 +32,8 @@ params {
 
     // Alignment
     star_two_pass_mode         = 'Basic'
-    subsample_region_switch    = true
-    downsample_switch          = true
+    switch_subsample_region    = true
+    switch_downsample          = true
     num_reads                  = 120000000
     seed_frac                  = 0.001
     save_mapped_as_cram        = true
@@ -34,18 +41,24 @@ params {
     // Variant calling
     variant_caller             = 'bcftools'
     bcftools_caller_mode       = 'multiallelic'
-    run_drop_ae_switch         = true
-    run_drop_as_switch         = true
+    switch_build_tracks        = true
+    switch_stringtie           = true
+    switch_drop_ae             = true
+    switch_drop_as             = true
     drop_group_samples_ae      = 'outrider'
     drop_group_samples_as      = 'fraser'
     drop_padjcutoff_ae         = 0.05
     drop_padjcutoff_as         = 0.1
     drop_zscorecutoff          = 0
+    switch_vep                 = true
+
+    // Variant annotation
+    vep_cache_version          = 110
 
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
-    multiqc_logo               = null
+    multiqc_logo               = "${projectDir}/assets/tomte_logo_light.png"
     max_multiqc_email_size     = '25.MB'
     multiqc_methods_description = null
 
@@ -93,8 +106,8 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-// Load nf-core/tomte custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
+// Load genomic-medicine-sweden/tomte 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/tomte.config"
 // } catch (Exception e) {
@@ -105,6 +118,7 @@ profiles {
         dumpHashes             = true
         process.beforeScript   = 'echo $HOSTNAME'
         cleanup                = false
+        nextflow.enable.configProcessNamesValidation = true
     }
     conda {
         conda.enabled          = true
@@ -113,6 +127,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        channels               = ['conda-forge', 'bioconda', 'defaults']
         apptainer.enabled      = false
     }
     mamba {
@@ -127,16 +142,16 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        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
@@ -204,7 +219,7 @@ singularity.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {
-    id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 // Load igenomes.config if required
@@ -227,6 +242,9 @@ 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
@@ -252,12 +270,20 @@ manifest {
     description     = """Pipeline to analyse RNAseq from raredisease patients"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '1.0.0'
+    version         = '1.1.0'
     doi             = ''
 }
 
 // Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+includeConfig 'conf/modules/alignment.config'
+includeConfig 'conf/modules/allele_specific_calling.config'
+includeConfig 'conf/modules/analyse_transcripts.config'
+includeConfig 'conf/modules/annotate_snv.config'
+includeConfig 'conf/modules/bam_qc.config'
+includeConfig 'conf/modules/call_variants.config'
+includeConfig 'conf/modules/igv_tracks.config'
+includeConfig 'conf/modules/general_tomte.config'
+includeConfig 'conf/modules/prepare_references.config'
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b8cfd4c9..75c51bd0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,7 +1,7 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/tomte/master/nextflow_schema.json",
-    "title": "nf-core/tomte pipeline parameters",
+    "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/tomte/master/nextflow_schema.json",
+    "title": "genomic-medicine-sweden/tomte pipeline parameters",
     "description": "Pipeline to analyse RNAseq from raredisease patients",
     "type": "object",
     "definitions": {
@@ -16,10 +16,11 @@
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
+                    "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "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. See [usage docs](https://nf-co.re/tomte/usage#samplesheet-input).",
+                    "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 5 columns (case, sample, fastq1, fastq2 and strandedness), and a header row.",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "outdir": {
@@ -147,10 +148,10 @@
                 },
                 "vep_cache_version": {
                     "type": "integer",
-                    "default": 107,
+                    "default": 110,
                     "description": "Specifies version of vep cache to use.",
                     "fa_icon": "fas fa-folder-open",
-                    "enum": [107]
+                    "enum": [107, 110]
                 },
                 "vep_filters": {
                     "type": "string",
@@ -158,6 +159,17 @@
                     "fa_icon": "fas fa-file-csv",
                     "description": "File containing HGNC_IDs of interest on separate lines.",
                     "hidden": true
+                },
+                "vep_plugin_files": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "file-path",
+                    "description": "Databases used by both named and custom plugins to annotate variants.",
+                    "fa_icon": "fas fa-file-csv",
+                    "help_text": "Path to a file containing the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file. One line per resource.",
+                    "pattern": "^\\S+\\.csv$",
+                    "mimetype": "text/csv",
+                    "schema": "assets/vep_plugin_files_schema.json"
                 }
             },
             "required": ["fasta", "gtf"]
@@ -193,13 +205,13 @@
                     "enum": ["Basic", "None"],
                     "fa_icon": "fas fa-tachometer-alt"
                 },
-                "subsample_region_switch": {
+                "switch_subsample_region": {
                     "type": "boolean",
                     "default": true,
                     "description": "Do you want to subsample the region subsample_bed to the fraction given in seed_frac?",
                     "fa_icon": "fas fa-toggle-off"
                 },
-                "downsample_switch": {
+                "switch_downsample": {
                     "type": "boolean",
                     "default": true,
                     "description": "Do you want to downsample the number of reads to num_reads?",
@@ -207,7 +219,6 @@
                 },
                 "subsample_bed": {
                     "type": "string",
-                    "default": "None",
                     "format": "file-path",
                     "fa_icon": "far fa-file-code",
                     "description": "Bed with regions to subsample"
@@ -249,13 +260,31 @@
                     "enum": ["consensus", "multiallelic"],
                     "help_text": "Bcftools call can eitherbe run in multiallelic mode or in consensus mode. In consensus mode a p-value threshold of 0.01 is applied."
                 },
-                "run_drop_ae_switch": {
+                "switch_build_tracks": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Should tracks be build?",
+                    "fa_icon": "fas fa-toggle-off"
+                },
+                "switch_stringtie": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Should stringtie module be run?",
+                    "fa_icon": "fas fa-toggle-off"
+                },
+                "switch_vep": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Should VEP module be run?",
+                    "fa_icon": "fas fa-toggle-off"
+                },
+                "switch_drop_ae": {
                     "type": "boolean",
                     "default": true,
                     "description": "Should DROP Aberrant Expression module be run?",
                     "fa_icon": "fas fa-toggle-off"
                 },
-                "run_drop_as_switch": {
+                "switch_drop_as": {
                     "type": "boolean",
                     "default": true,
                     "description": "Should DROP Aberrant Splicing module be run?",
@@ -293,7 +322,6 @@
                 },
                 "reference_drop_annot_file": {
                     "type": "string",
-                    "default": "None",
                     "description": "Path to a tsv file containing sample annotation for DROP. Must be provided to run DROP.",
                     "fa_icon": "fas fa-file",
                     "format": "file-path",
@@ -301,7 +329,6 @@
                 },
                 "reference_drop_count_file": {
                     "type": "string",
-                    "default": "None",
                     "description": "If you are running DROP Aberrant Expression, provide the path to a tsv or tsv.gz with counts from at least 50 samples to use as controls",
                     "fa_icon": "fas fa-file",
                     "format": "file-path",
@@ -309,7 +336,6 @@
                 },
                 "reference_drop_splice_folder": {
                     "type": "string",
-                    "default": "None",
                     "description": "If you are running DROP Aberrant Splicing, provide the path to a folder with splice counts from at least 30 samples to use as controls, files inside folder must be tsv.gz",
                     "fa_icon": "fas fa-folder-open"
                 },
diff --git a/pyproject.toml b/pyproject.toml
index 0d62beb6..56110621 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/alignment.nf b/subworkflows/local/alignment.nf
index b6f26f72..a18c7cae 100644
--- a/subworkflows/local/alignment.nf
+++ b/subworkflows/local/alignment.nf
@@ -20,8 +20,8 @@ workflow ALIGNMENT {
         subsample_bed
         seed_frac
         num_reads
-        subsample_region_switch
-        downsample_switch
+        switch_subsample_region
+        switch_downsample
         salmon_index
         ch_genome_fasta
 
@@ -31,12 +31,12 @@ workflow ALIGNMENT {
         ch_fastq = branchFastqToSingleAndMulti(reads)
 
         CAT_FASTQ(ch_fastq.multiple_fq)
-        .reads.mix(ch_fastq.single_fq)
-        .set { ch_cat_fastq }
+            .reads.mix(ch_fastq.single_fq)
+            .set { ch_cat_fastq }
 
         FASTP(ch_cat_fastq, [], false, false)
 
-        ch_gtf = gtf.map { it -> [[:], it] }
+        ch_gtf = gtf.map { it -> [[:], it] }.collect()
         STAR_ALIGN(FASTP.out.reads, star_index, ch_gtf, false, platform, false)
 
         SAMTOOLS_INDEX( STAR_ALIGN.out.bam )
@@ -44,10 +44,10 @@ workflow ALIGNMENT {
         ch_bam_bai = Channel.empty()
         ch_bam_bai_out = Channel.empty()
 
-        if (subsample_region_switch) {
+        if (switch_subsample_region) {
             RNA_SUBSAMPLE_REGION( STAR_ALIGN.out.bam, subsample_bed, seed_frac)
             ch_bam_bai = ch_bam_bai.mix(RNA_SUBSAMPLE_REGION.out.bam_bai)
-            if (!downsample_switch) {
+            if (!switch_downsample) {
                 ch_bam_bai_out = RNA_SUBSAMPLE_REGION.out.bam_bai
             } else {
                 RNA_DOWNSAMPLE( ch_bam_bai, num_reads)
@@ -55,7 +55,7 @@ workflow ALIGNMENT {
             }
         } else {
             ch_bam_bai = ch_bam_bai.mix(STAR_ALIGN.out.bam.join(SAMTOOLS_INDEX.out.bai))
-             if (!downsample_switch) {
+            if (!switch_downsample) {
                 ch_bam_bai_out = STAR_ALIGN.out.bam.join(SAMTOOLS_INDEX.out.bai)
             } else {
                 RNA_DOWNSAMPLE( ch_bam_bai, num_reads)
@@ -65,7 +65,6 @@ workflow ALIGNMENT {
 
         SAMTOOLS_VIEW( STAR_ALIGN.out.bam.join(SAMTOOLS_INDEX.out.bai), ch_genome_fasta, [] )
 
-
         SALMON_QUANT( FASTP.out.reads, salmon_index, gtf, [], false, 'A')
 
         ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first())
@@ -106,17 +105,15 @@ workflow ALIGNMENT {
 def branchFastqToSingleAndMulti(ch_reads) {
 
     return ch_reads
-        .map {
-            meta, fastq ->
-                original_id = meta.id.split('_T')[0..-2].join('_')
-                [ meta + [id: original_id], fastq ]
+        .map { meta, fastqs ->
+            return [ groupKey( meta + [id:meta.sample], meta.fq_pairs ), fastqs ]
         }
         .groupTuple()
         .branch {
-            meta, fastq ->
-                single_fq: fastq.size() == 1
-                    return [ meta, fastq.flatten() ]
-                multiple_fq: fastq.size() > 1
-                    return [ meta, fastq.flatten() ]
+            meta, fastqs ->
+                single_fq: fastqs.size() == 1
+                    return [ meta, fastqs.flatten() ]
+                multiple_fq: fastqs.size() > 1
+                    return [ meta, fastqs.flatten() ]
         }
 }
diff --git a/subworkflows/local/allele_specific_calling.nf b/subworkflows/local/allele_specific_calling.nf
index b19d1418..95ece4a4 100644
--- a/subworkflows/local/allele_specific_calling.nf
+++ b/subworkflows/local/allele_specific_calling.nf
@@ -2,57 +2,109 @@
 // Allele specific variant calling
 //
 
-include { BCFTOOLS_VIEW        } from '../../modules/nf-core/bcftools/view/main' 
+include { BCFTOOLS_VIEW        } from '../../modules/nf-core/bcftools/view/main'
 include { BCFTOOLS_INDEX       } from '../../modules/nf-core/bcftools/index/main'
 include { GATK4_ASEREADCOUNTER } from '../../modules/nf-core/gatk4/asereadcounter/main'
 include { BOOTSTRAPANN         } from '../../modules/local/bootstrapann'
+include { TABIX_BGZIPTABIX     } from '../../modules/nf-core/tabix/bgziptabix/main'
+include { BCFTOOLS_MERGE       } from '../../modules/nf-core/bcftools/merge/main'
+include { RENAME_FILES         } from '../../modules/local/rename_files'
+include { TABIX_TABIX          } from '../../modules/nf-core/tabix/tabix/main'
 
 
 workflow ALLELE_SPECIFIC_CALLING {
     take:
-        vcf_tbi
-        bam_bai
-        fasta
-        fai
-        dict
-        intervals
+        ch_ind_vcf_tbi // channel (mandatory): [ val(meta), [ path(vcf), path(tbi) ] ]
+        ch_bam_bai     // channel (mandatory): [ val(meta), [ path(bam), path(bai) ] ]
+        ch_fasta       // channel (mandatory): [ path(fasta) ]
+        ch_fai         // channel (mandatory): [ path(fai) ]
+        ch_dict        // channel (mandatory): [ val(meta), [ path(dict) ] ]
+        ch_intervals   // channel (mandatory): [ path(intervals) ]
+        ch_case_info   // channel (mandatory): [ val(case_info) ]
 
     main:
         ch_versions = Channel.empty()
 
         // Keep only does variants in the vcf that are SNVs and are heterozygote
         BCFTOOLS_VIEW(
-            vcf_tbi,
+            ch_ind_vcf_tbi,
             [],
             [],
             []
         )
-        ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions.first())
 
         BCFTOOLS_INDEX(
             BCFTOOLS_VIEW.out.vcf
         )
-        ch_versions = ch_versions.mix(BCFTOOLS_INDEX.out.versions.first())
-        
-        dict_no_meta = dict.map{ meta, it -> [it] }.collect()
+
+        ch_dict_no_meta = ch_dict.map{ meta, it -> [it] }.collect()
         GATK4_ASEREADCOUNTER(
-            bam_bai,
-            BCFTOOLS_VIEW.out.vcf.join(BCFTOOLS_INDEX.out.tbi), 
-            fasta,
-            fai,
-            dict_no_meta,
-            intervals
+            ch_bam_bai,
+            BCFTOOLS_VIEW.out.vcf.join(BCFTOOLS_INDEX.out.tbi),
+            ch_fasta,
+            ch_fai,
+            ch_dict_no_meta,
+            ch_intervals
         )
-        ch_versions = ch_versions.mix(GATK4_ASEREADCOUNTER.out.versions.first())
 
         BOOTSTRAPANN(
-            vcf_tbi,
+            ch_ind_vcf_tbi,
             GATK4_ASEREADCOUNTER.out.csv
         )
-        ch_versions = ch_versions.mix(BOOTSTRAPANN.out.versions.first())
 
+        TABIX_BGZIPTABIX(BOOTSTRAPANN.out.vcf)
+
+        TABIX_BGZIPTABIX.out.gz_tbi
+                    .collect{it[1]}
+                    .ifEmpty([])
+                    .toList()
+                    .set { file_list_vcf }
+
+        TABIX_BGZIPTABIX.out.gz_tbi
+                    .collect{it[2]}
+                    .ifEmpty([])
+                    .toList()
+                    .set { file_list_tbi }
+
+        ch_case_info
+            .combine(file_list_vcf)
+            .combine(file_list_tbi)
+            .set { ch_vcf_tbi }
+
+        ch_vcf_tbi.branch {
+            meta, vcf, tbi ->
+                single: vcf.size() == 1
+                    return [meta, vcf]
+                multiple: vcf.size() > 1
+                    return [meta, vcf, tbi]
+            }.set { ch_case_vcf }
+
+        BCFTOOLS_MERGE( ch_case_vcf.multiple,
+            ch_fasta.map { it -> [[:], it] },
+            ch_fai.map { it -> [[:], it] },
+            []
+        )
+
+        RENAME_FILES( ch_case_vcf.single)
+
+        BCFTOOLS_MERGE.out.merged_variants
+            .mix( RENAME_FILES.out.output )
+            .set { ch_vcf }
+
+        TABIX_TABIX( ch_vcf )
+        ch_tbi = TABIX_TABIX.out.tbi
+
+        ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions.first())
+        ch_versions = ch_versions.mix(BCFTOOLS_INDEX.out.versions.first())
+        ch_versions = ch_versions.mix(GATK4_ASEREADCOUNTER.out.versions.first())
+        ch_versions = ch_versions.mix(BOOTSTRAPANN.out.versions.first())
+        ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions.first())
+        ch_versions = ch_versions.mix( BCFTOOLS_MERGE.out.versions.first() )
+        ch_versions = ch_versions.mix( RENAME_FILES.out.versions.first() )
+        ch_versions = ch_versions.mix( TABIX_TABIX.out.versions.first() )
 
     emit:
-        vcf  = BOOTSTRAPANN.out.vcf
+        vcf      = ch_vcf      // channel: [ val(meta), [ path(vcf) ] ]
+        tbi      = ch_tbi      // channel: [ val(meta), [ path(tbi) ] ]
         versions = ch_versions // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/local/analyse_transcripts.nf b/subworkflows/local/analyse_transcripts.nf
index 10c9927a..6035e4ca 100644
--- a/subworkflows/local/analyse_transcripts.nf
+++ b/subworkflows/local/analyse_transcripts.nf
@@ -2,12 +2,12 @@
 // ANALYSE TRANSCRITPS
 //
 
- include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie/main'
- include { GFFCOMPARE          } from '../../modules/nf-core/gffcompare/main'
- include { DROP_SAMPLE_ANNOT   } from '../../modules/local/drop_sample_annot'
- include { DROP_CONFIG_RUN_AE  } from '../../modules/local/drop_config_runAE'
- include { DROP_CONFIG_RUN_AS  } from '../../modules/local/drop_config_runAS'
- include { DROP_FILTER_RESULTS } from '../../modules/local/drop_filter_results'
+include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie/main'
+include { GFFCOMPARE          } from '../../modules/nf-core/gffcompare/main'
+include { DROP_SAMPLE_ANNOT   } from '../../modules/local/drop_sample_annot'
+include { DROP_CONFIG_RUN_AE  } from '../../modules/local/drop_config_runAE'
+include { DROP_CONFIG_RUN_AS  } from '../../modules/local/drop_config_runAS'
+include { DROP_FILTER_RESULTS } from '../../modules/local/drop_filter_results'
 
 workflow ANALYSE_TRANSCRIPTS {
     take:
@@ -15,7 +15,7 @@ workflow ANALYSE_TRANSCRIPTS {
         ch_bam_ds_bai                 // channel (mandatory): [ val(meta), [ path(bam) ],[ path(bai) ] ]
         ch_gtf                        // channel (mandatory): [ path(gtf) ]
         ch_fasta_fai_meta             // channel (mandatory): [ val(meta), [ path(fasta), path(fai) ]
-        gene_counts                   // channel [val(meta), path(tsv)] 
+        gene_counts                   // channel [val(meta), path(tsv)]
         ch_ref_drop_count_file        // channel [ path(tsv) ]
         ch_ref_drop_annot_file        // channel [ path(tsv) ]
         ch_ref_drop_splice_folder     // channel [ path(folder) ]
@@ -26,13 +26,14 @@ workflow ANALYSE_TRANSCRIPTS {
         drop_padjcutoff_as            // channel [val(drop_padjcutoff_as)]
         drop_zscorecutoff             // channel [val(drop_zscorecutoff)]
         ch_gene_panel_clinical_filter // channel [ path(tsv) ]
+        case_info                     // channel [val(case_id)]
 
     main:
         ch_versions = Channel.empty()
 
         // DROP
         // Generates count files for samples and merges them with reference count file
-        
+
         // Generates sample annotation
         star_samples = gene_counts.map{ meta, cnt_file -> meta }.collect()
         ch_bam_files = ch_bam_ds_bai.collect{it[1]}
@@ -49,8 +50,8 @@ workflow ANALYSE_TRANSCRIPTS {
         ch_bai_files = ch_bam_ds_bai.collect{ it[2] }.toList()
         ch_bam_bai_files = ch_bam_files.toList().combine(ch_bai_files)
         DROP_CONFIG_RUN_AE(
-            ch_fasta_fai_meta, 
-            ch_gtf, 
+            ch_fasta_fai_meta,
+            ch_gtf,
             DROP_SAMPLE_ANNOT.out.drop_annot,
             ch_bam_bai_files,
             ch_ref_drop_count_file,
@@ -60,11 +61,11 @@ workflow ANALYSE_TRANSCRIPTS {
             drop_padjcutoff_ae,
             drop_zscorecutoff
         )
-        
+
         // Generates  config file and runs Aberrant splicing module
         DROP_CONFIG_RUN_AS(
-            ch_fasta_fai_meta, 
-            ch_gtf, 
+            ch_fasta_fai_meta,
+            ch_gtf,
             DROP_SAMPLE_ANNOT.out.drop_annot,
             ch_bam_bai_files,
             ch_ref_drop_count_file,
@@ -74,19 +75,22 @@ workflow ANALYSE_TRANSCRIPTS {
             drop_padjcutoff_as
         )
 
-        ch_out_drop_ae_rds    = DROP_CONFIG_RUN_AE.out.drop_ae_rds    ? DROP_CONFIG_RUN_AE.out.drop_ae_rds.collect()
-                                                                        : Channel.empty()
-        ch_out_drop_gene_name = DROP_CONFIG_RUN_AE.out.drop_gene_name ? DROP_CONFIG_RUN_AE.out.drop_gene_name.collect()
-                                                                        : Channel.empty()
-        ch_out_drop_as_tsv    = DROP_CONFIG_RUN_AS.out.drop_as_tsv    ? DROP_CONFIG_RUN_AS.out.drop_as_tsv.collect()
-                                                                        : Channel.empty()
+        ch_out_drop_ae_rds       = DROP_CONFIG_RUN_AE.out.drop_ae_rds       ? DROP_CONFIG_RUN_AE.out.drop_ae_rds.collect()
+                                                                            : Channel.empty()
+        ch_out_drop_gene_name_ae = DROP_CONFIG_RUN_AE.out.drop_gene_name    ? DROP_CONFIG_RUN_AE.out.drop_gene_name.collect()
+                                                                            : Channel.empty()
+        ch_out_drop_gene_name_as = DROP_CONFIG_RUN_AS.out.drop_gene_name    ? DROP_CONFIG_RUN_AS.out.drop_gene_name.collect()
+                                                                            : Channel.empty()
+        ch_out_drop_as_tsv       = DROP_CONFIG_RUN_AS.out.drop_as_tsv       ? DROP_CONFIG_RUN_AS.out.drop_as_tsv.collect()
+                                                                            : Channel.empty()
+        ch_out_drop_gene_name    = params.switch_drop_ae ? ch_out_drop_gene_name_ae : ch_out_drop_gene_name_as
 
         DROP_FILTER_RESULTS(
-            star_samples,
+            case_info,
             ch_gene_panel_clinical_filter,
-            ch_out_drop_ae_rds,
+            ch_out_drop_ae_rds.ifEmpty([]),
             ch_out_drop_gene_name,
-            ch_out_drop_as_tsv
+            ch_out_drop_as_tsv.ifEmpty([])
         )
 
         // Stringtie
@@ -106,23 +110,24 @@ workflow ANALYSE_TRANSCRIPTS {
         ch_versions = ch_versions.mix(DROP_SAMPLE_ANNOT.out.versions)
         ch_versions = ch_versions.mix(DROP_CONFIG_RUN_AE.out.versions)
         ch_versions = ch_versions.mix(DROP_CONFIG_RUN_AS.out.versions)
+        ch_versions = ch_versions.mix(DROP_FILTER_RESULTS.out.versions)
         ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions.first())
         ch_versions = ch_versions.mix(GFFCOMPARE.out.versions.first())
 
     emit:
-        transcript_gtf        = STRINGTIE_STRINGTIE.out.transcript_gtf     // channel: [ val(meta), [ path(transctript_gtf)] ]
-        abundance             = STRINGTIE_STRINGTIE.out.abundance          // channel: [ val(meta), [ path(abundance) ] ]
-        coverage_gtf          = STRINGTIE_STRINGTIE.out.coverage_gtf       // channel: [ val(meta), [ path(coverage_gtf) ] ]
-        annotated_gtf         = GFFCOMPARE.out.annotated_gtf               // channel: [ val(meta), [ path(annotated_gtf) ] ]
-        stats_gtf             = GFFCOMPARE.out.stats                       // channel: [ val(meta), [ path(stats) ] ]
-        annotation_drop       = DROP_SAMPLE_ANNOT.out.drop_annot           // channel: [ path(sample_annotation.tsv) ]
-        config_drop_ae        = DROP_CONFIG_RUN_AE.out.config_drop         // channel: [ path(confg_file.yml) ]
-        drop_ae_out           = DROP_CONFIG_RUN_AE.out.drop_ae_out         // channel: [ path(drop_output_AE) ]
-        config_drop_as        = DROP_CONFIG_RUN_AS.out.config_drop         // channel: [ path(confg_file.yml) ]
-        drop_as_out           = DROP_CONFIG_RUN_AS.out.drop_as_out         // channel: [ path(drop_output_AS) ]
-        drop_filter_ae_res    = DROP_FILTER_RESULTS.out.ae_out_filtered    // channel: [ path(drop_AE_filtered.tsv) ]
-        drop_unfilter_ae_res  = DROP_FILTER_RESULTS.out.ae_out_unfiltered  // channel: [ path(drop_AE_unfiltered.tsv) ]
-        drop_filter_as_res    = DROP_FILTER_RESULTS.out.as_out_filtered    // channel: [ path(drop_AS_filtered.tsv) ]
-        drop_unfilter_as_res  = DROP_FILTER_RESULTS.out.as_out_unfiltered  // channel: [ path(drop_AS_unfiltered.tsv) ]
-        versions              = ch_versions                                // channel: [ path(versions.yml) ]
+        transcript_gtf        = STRINGTIE_STRINGTIE.out.transcript_gtf   // channel: [ val(meta), [ path(transctript_gtf)] ]
+        abundance             = STRINGTIE_STRINGTIE.out.abundance        // channel: [ val(meta), [ path(abundance) ] ]
+        coverage_gtf          = STRINGTIE_STRINGTIE.out.coverage_gtf     // channel: [ val(meta), [ path(coverage_gtf) ] ]
+        annotated_gtf         = GFFCOMPARE.out.annotated_gtf             // channel: [ val(meta), [ path(annotated_gtf) ] ]
+        stats_gtf             = GFFCOMPARE.out.stats                     // channel: [ val(meta), [ path(stats) ] ]
+        annotation_drop       = DROP_SAMPLE_ANNOT.out.drop_annot         // channel: [ path(sample_annotation.tsv) ]
+        config_drop_ae        = DROP_CONFIG_RUN_AE.out.config_drop       // channel: [ path(confg_file.yml) ]
+        drop_ae_out           = DROP_CONFIG_RUN_AE.out.drop_ae_out       // channel: [ path(drop_output_AE) ]
+        config_drop_as        = DROP_CONFIG_RUN_AS.out.config_drop       // channel: [ path(confg_file.yml) ]
+        drop_as_out           = DROP_CONFIG_RUN_AS.out.drop_as_out       // channel: [ path(drop_output_AS) ]
+        drop_ae_out_clinical  = DROP_FILTER_RESULTS.out.ae_out_clinical  // channel: [ path(drop_AE_clinical.tsv) ]
+        drop_ae_out_research  = DROP_FILTER_RESULTS.out.ae_out_research  // channel: [ path(drop_AE_research.tsv) ]
+        drop_as_out_clinical  = DROP_FILTER_RESULTS.out.as_out_clinical  // channel: [ path(drop_AS_clinical.tsv) ]
+        drop_as_out_research  = DROP_FILTER_RESULTS.out.as_out_research  // channel: [ path(drop_AS_research.tsv) ]
+        versions              = ch_versions                              // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/local/annotate_snv.nf b/subworkflows/local/annotate_snv.nf
index dd14be4d..40698a6b 100644
--- a/subworkflows/local/annotate_snv.nf
+++ b/subworkflows/local/annotate_snv.nf
@@ -2,43 +2,44 @@
 // Annotating SNVs
 //
 
-include { ENSEMBLVEP               } from '../../modules/local/ensemblvep'
+include { ENSEMBLVEP_VEP           } from '../../modules/nf-core/ensemblvep/vep/main'
 include { TABIX_TABIX as TABIX_VEP } from '../../modules/nf-core/tabix/tabix/main'
 
 
 workflow ANNOTATE_SNV {
     take:
-    vcf
-    val_vep_genome
-    val_vep_cache_version
-    ch_vep_cache
-    ch_fasta
+    vcf                   // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ]
+    val_vep_genome        // string: [mandatory] GRCh37 or GRCh38
+    val_vep_cache_version // string: [mandatory] default: 107
+    ch_vep_cache          // channel: [mandatory] [ path(cache) ]
+    ch_fasta              // channel: [mandatory] [ val(meta), path(fasta) ]
+    ch_vep_extra_files    // channel: [mandatory] [ path(files) ]
 
     main:
         ch_versions = Channel.empty()
 
         // Annotate with VEP
-        ENSEMBLVEP(
-            vcf,
+        ENSEMBLVEP_VEP(
+            vcf.map{ meta, vcf -> [ meta, vcf, [] ] },
             val_vep_genome,
             "homo_sapiens",
             val_vep_cache_version,
             ch_vep_cache,
             ch_fasta,
-            []
+            ch_vep_extra_files
         )
-        ch_versions = ch_versions.mix(ENSEMBLVEP.out.versions.first())
+        ch_versions = ch_versions.mix(ENSEMBLVEP_VEP.out.versions.first())
 
-        TABIX_VEP(ENSEMBLVEP.out.vcf_gz)
+        TABIX_VEP(ENSEMBLVEP_VEP.out.vcf)
         ch_versions = ch_versions.mix(TABIX_VEP.out.versions.first())
 
     emit:
-        json     = ENSEMBLVEP.out.json
-        vcf_gz   = ENSEMBLVEP.out.vcf_gz
+        json     = ENSEMBLVEP_VEP.out.json
+        vcf_gz   = ENSEMBLVEP_VEP.out.vcf
         tbi_gz   = TABIX_VEP.out.tbi
-        tab_gz   = ENSEMBLVEP.out.tab_gz
-        json_gz  = ENSEMBLVEP.out.json_gz
-        report   = ENSEMBLVEP.out.report
+        tab_gz   = ENSEMBLVEP_VEP.out.tab
+        json_gz  = ENSEMBLVEP_VEP.out.json
+        report   = ENSEMBLVEP_VEP.out.report
         versions = ch_versions // channel: [ path(versions.yml) ]
 }
 
diff --git a/subworkflows/local/bam_qc.nf b/subworkflows/local/bam_qc.nf
index eec002b4..715b50f6 100644
--- a/subworkflows/local/bam_qc.nf
+++ b/subworkflows/local/bam_qc.nf
@@ -2,27 +2,35 @@
 // BAM QC
 //
 
-include { PICARD_COLLECTRNASEQMETRICS } from '../../modules/nf-core/picard/collectrnaseqmetrics/main'
+include { PICARD_COLLECTRNASEQMETRICS     } from '../../modules/nf-core/picard/collectrnaseqmetrics/main'
+include { PICARD_COLLECTINSERTSIZEMETRICS } from '../../modules/nf-core/picard/collectinsertsizemetrics/main'
 
 workflow BAM_QC {
     take:
-        bam
-        fasta_no_meta
-        refflat
-        rrna_intervals
+        ch_bam            // channel (mandatory): [ val(meta), path(bam) ]
+        ch_fasta_no_meta  // channel (mandatory): [ path(fasta) ]
+        ch_refflat        // channel (mandatory): [ path(refflat) ]
+        ch_rrna_intervals // channel (mandatory): [ path(intervals) ]
 
     main:
         ch_versions = Channel.empty()
 
         PICARD_COLLECTRNASEQMETRICS(
-            bam,
-            refflat,
-            fasta_no_meta,
-            rrna_intervals
+            ch_bam,
+            ch_refflat,
+            ch_fasta_no_meta,
+            ch_rrna_intervals
         )
+
+        PICARD_COLLECTINSERTSIZEMETRICS(
+            ch_bam
+        )
+
         ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions.first())
+        ch_versions = ch_versions.mix(PICARD_COLLECTINSERTSIZEMETRICS.out.versions.first())
 
     emit:
-        metrics  = PICARD_COLLECTRNASEQMETRICS.out.metrics
+        metrics_general_rna = PICARD_COLLECTRNASEQMETRICS.out.metrics
+        metrics_insert_size = PICARD_COLLECTINSERTSIZEMETRICS.out.metrics
         versions = ch_versions
 }
diff --git a/subworkflows/local/call_variants.nf b/subworkflows/local/call_variants.nf
index 35a4ab6e..dfcedb73 100644
--- a/subworkflows/local/call_variants.nf
+++ b/subworkflows/local/call_variants.nf
@@ -13,7 +13,7 @@ workflow CALL_VARIANTS {
         ch_bam_bai     // channel (mandatory): [ val(meta), [ path(bam), path(bai) ] ]
         ch_fasta       // channel (mandatory): [ path(fasta) ]
         ch_fai         // channel (mandatory): [ path(fai) ]
-        ch_dict        // channel (mandatory): [ path(dict) ]
+        ch_dict        // channel (mandatory): [ val(meta), path(dict) ]
         variant_caller // string (mandatory)
 
     main:
@@ -33,6 +33,7 @@ workflow CALL_VARIANTS {
                     ch_fai,
                     ch_dict,
                 )
+
                 ch_vcf = ch_vcf.mix(CALL_VARIANTS_GATK.out.vcf)
                 ch_tbi = ch_tbi.mix(CALL_VARIANTS_GATK.out.tbi)
                 ch_stats = ch_stats.mix(CALL_VARIANTS_GATK.out.stats)
@@ -48,9 +49,9 @@ workflow CALL_VARIANTS {
                     false
                 )
 
-                ch_vcf = ch_vcf.mix(BCFTOOLS_MPILEUP.out.vcf.first())
-                ch_tbi = ch_tbi.mix(BCFTOOLS_MPILEUP.out.tbi.first())
-                ch_stats = ch_stats.mix(BCFTOOLS_MPILEUP.out.stats.first())
+                ch_vcf = ch_vcf.mix(BCFTOOLS_MPILEUP.out.vcf)
+                ch_tbi = ch_tbi.mix(BCFTOOLS_MPILEUP.out.tbi)
+                ch_stats = ch_stats.mix(BCFTOOLS_MPILEUP.out.stats)
                 ch_versions = ch_versions.mix(BCFTOOLS_MPILEUP.out.versions.first())
 
                 break
diff --git a/subworkflows/local/call_variants_gatk.nf b/subworkflows/local/call_variants_gatk.nf
index 5c53401e..50450457 100644
--- a/subworkflows/local/call_variants_gatk.nf
+++ b/subworkflows/local/call_variants_gatk.nf
@@ -14,17 +14,17 @@ workflow CALL_VARIANTS_GATK {
         ch_bam_bai // channel (mandatory): [ val(meta), [ path(bam), path(bai) ] ]
         ch_fasta   // channel (mandatory): [ path(fasta) ]
         ch_fai     // channel (mandatory): [ path(fai) ]
-        ch_dict    // channel (mandatory): [ path(dict) ]
+        ch_dict    // channel (mandatory): [ val(meta), path(dict) ]
 
     main:
 
         ch_versions = Channel.empty()
 
         GATK4_SPLITNCIGARREADS(
-            ch_bam_bai.map{ meta, bam, bai -> [ meta, bam, bai, [] ]},
+            ch_bam_bai.map{ meta, bam, bai -> [meta, bam, bai, []] },
             ch_fasta,
             ch_fai,
-            ch_dict
+            ch_dict.map{ meta, dict -> dict }
         )
         ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions.first())
 
@@ -34,29 +34,32 @@ workflow CALL_VARIANTS_GATK {
         ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
 
         ch_split_bam_bai = GATK4_SPLITNCIGARREADS.out.bam.join(SAMTOOLS_INDEX.out.bai)
+
         GATK4_HAPLOTYPECALLER(
-            ch_split_bam_bai.map{ meta, bam, bai -> [ meta, bam, bai, [], [] ] },
-            ch_fasta,
-            ch_fai,
+            ch_split_bam_bai.map{ meta, bam, bai -> [meta, bam, bai, [], []] },
+            ch_fasta.map{ fasta -> [[:], fasta] },
+            ch_fai.map{ fai -> [[:], fai] },
             ch_dict,
-            [],
-            [],
+            [[],[]],
+            [[],[]],
         )
         ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first())
 
         GATK4_VARIANTFILTRATION(
             GATK4_HAPLOTYPECALLER.out.vcf.join(GATK4_HAPLOTYPECALLER.out.tbi),
-            [ [:], ch_fasta],
-            [ [:], ch_fai],
-            [ [:], ch_dict]
+            ch_fasta.map{ fasta -> [[:], fasta] },
+            ch_fai.map{ fai -> [[:], fai] },
+            ch_dict
         )
-        ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first())
+        ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first())
 
         BCFTOOLS_STATS(
             GATK4_HAPLOTYPECALLER.out.vcf.join(GATK4_HAPLOTYPECALLER.out.tbi),
-            [],
-            [],
-            [],
+            [[],[]],
+            [[],[]],
+            [[],[]],
+            [[],[]],
+            [[],[]],
         )
         ch_versions = ch_versions.mix(BCFTOOLS_STATS.out.versions.first())
 
diff --git a/subworkflows/local/igv_tracks.nf b/subworkflows/local/igv_tracks.nf
index a41b5554..f6b4d7b9 100644
--- a/subworkflows/local/igv_tracks.nf
+++ b/subworkflows/local/igv_tracks.nf
@@ -3,8 +3,8 @@
 //
 
 include { JUNCTION_TRACK   } from '../../modules/local/junction_track'
-include { UCSC_WIGTOBIGWIG } from '../../modules/nf-core/ucsc/wigtobigwig/main'                                                                          
-include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main'                                                                          
+include { UCSC_WIGTOBIGWIG } from '../../modules/nf-core/ucsc/wigtobigwig/main'
+include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main'
 
 workflow IGV_TRACKS {
     take:
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
deleted file mode 100644
index 1b8f9283..00000000
--- a/subworkflows/local/input_check.nf
+++ /dev/null
@@ -1,57 +0,0 @@
-//
-// Check input samplesheet and get read channels
-//
-
-include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
-
-workflow CHECK_INPUT {
-    take:
-    samplesheet // file: /path/to/samplesheet.csv
-
-    main:
-        SAMPLESHEET_CHECK ( samplesheet )
-            .csv
-            .splitCsv ( header:true, sep:',' )
-            .set { sheet }
-
-        case_info    = sheet.first()
-                            .map { create_case_channel(it) }
-        reads     = sheet.map { create_fastq_channel(it) }
-
-    emit:
-        case_info                                 // channel: [ case_id ]
-        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()
-    meta.strandedness = row.strandedness
-
-    // 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
-}
-
-// Function to get a list of metadata (e.g. case id) for the case [ meta ]
-def create_case_channel(LinkedHashMap row) {
-    def case_info   = [:]
-    case_info.id    = row.case_id
-
-    return case_info
-}
diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf
index 12492991..a3a57c6c 100644
--- a/subworkflows/local/prepare_references.nf
+++ b/subworkflows/local/prepare_references.nf
@@ -38,7 +38,7 @@ workflow PREPARE_REFERENCES {
 
         // If no genome indices, create it
         SAMTOOLS_FAIDX_GENOME(ch_fasta,[[],[]])
-        ch_fai = Channel.empty().mix(fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect()
+        ch_fai = fai.mix(SAMTOOLS_FAIDX_GENOME.out.fai).collect()
 
         BUILD_DICT(ch_fasta)
         ch_dict = BUILD_DICT.out.dict.collect()
@@ -53,23 +53,27 @@ workflow PREPARE_REFERENCES {
         ch_fasta_no_meta = ch_fasta.map{ meta, fasta -> [ fasta ] }
 
         ch_gtf=ch_gtf_no_meta.map { it -> [[:], it] }
-        ch_star = star_index ? Channel.fromPath(star_index).collect() : Channel.empty()
+        ch_star = star_index ?
+            Channel.fromPath(star_index).collect().map { it -> [ [id:it[0].simpleName], it ] }
+            : Channel.empty()
+
         BUILD_STAR_GENOME (ch_fasta, ch_gtf )
-        UNTAR_STAR_INDEX( ch_star.map { it -> [[:], it] } )
-        ch_star_index = (!star_index) ?  BUILD_STAR_GENOME.out.index.collect() : 
-                                        (star_index.endsWith(".gz") ? UNTAR_STAR_INDEX.out.untar.map { it[1] } : star_index)
+        UNTAR_STAR_INDEX( ch_star.map { it -> [[:], it[1]] } )
+        ch_star_index = (!star_index) ?  BUILD_STAR_GENOME.out.index.collect() :
+                                        (star_index.endsWith(".gz") ? UNTAR_STAR_INDEX.out.untar.map { it[1] } : ch_star)
         // Convert gtf to refflat for picard
         GTF_TO_REFFLAT(ch_gtf_no_meta)
 
         // Get rRNA transcripts and convert to interval_list format
         GET_RRNA_TRANSCRIPTS(ch_gtf_no_meta)
-       
+
         BEDTOINTERVALLIST( GET_RRNA_TRANSCRIPTS.out.bed.map { it -> [ [id:it.name], it ] }, ch_dict )
 
         UNTAR_VEP_CACHE (ch_vep_cache)
-        
+
         // Preparing transcript fasta
-        ch_fasta_fai = ch_fasta.join(ch_fai).collect()
+        ch_fasta_fai = ch_fasta.mix(ch_fai.map{meta, fai -> fai}).collect()
+
         GFFREAD(ch_gtf_no_meta.map{ it -> [ [id:it[0].simpleName], it ] },ch_fasta_fai)
         transcript_fasta_no_meta = (!transcript_fasta) ? GFFREAD.out.tr_fasta.collect() :
                                     (transcript_fasta.endsWith(".gz") ? GUNZIP_TRFASTA.out.gunzip.collect().map{ meta, fasta -> [ fasta ] } : transcript_fasta)
@@ -79,9 +83,9 @@ workflow PREPARE_REFERENCES {
         UNTAR_SALMON_INDEX( ch_salmon.map { it -> [[:], it] } )
         SALMON_INDEX(ch_fasta_no_meta, transcript_fasta_no_meta)
 
-        ch_salmon_index = (!salmon_index) ? SALMON_INDEX.out.index.collect() : 
+        ch_salmon_index = (!salmon_index) ? SALMON_INDEX.out.index.collect() :
                                             (salmon_index.endsWith(".gz") ? UNTAR_SALMON_INDEX.out.untar.map { it[1] } : salmon_index)
-        
+
         ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions)
         ch_versions = ch_versions.mix(BUILD_DICT.out.versions)
@@ -100,7 +104,7 @@ workflow PREPARE_REFERENCES {
         fasta_no_meta    = ch_fasta_no_meta
         fai              = ch_fai
         fai_no_meta      = ch_fai.map{ meta, fai -> [fai] }.collect()
-        fasta_fai_meta   = ch_fasta.join(ch_fai).collect()
+        fasta_fai_meta   = ch_fasta_fai
         sequence_dict    = BUILD_DICT.out.dict.collect()
         gtf              = ch_gtf_no_meta
         star_index       = ch_star_index
diff --git a/subworkflows/local/utils_nfcore_tomte_pipeline/main.nf b/subworkflows/local/utils_nfcore_tomte_pipeline/main.nf
new file mode 100644
index 00000000..5fa61166
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_tomte_pipeline/main.nf
@@ -0,0 +1,346 @@
+//
+// Subworkflow with functionality specific to the genomic-medicine-sweden/tomte pipeline
+//
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-validation'
+include { fromSamplesheet           } from 'plugin/nf-validation'
+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 { logColours                } from '../../nf-core/utils_nfcore_pipeline'
+include { getWorkflowVersion        } 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 = gmsTomteHatLogo2(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
+    .fromSamplesheet("input")
+    .tap { ch_original_input }
+    .map { meta, fastq_1, fastq_2 -> meta.id }
+    .reduce([:]) { counts, sample -> // get counts of each sample in the samplesheet - for groupTuple
+        counts[sample] = (counts[sample] ?: 0) + 1
+        counts
+    }
+    .combine ( ch_original_input )
+    .map { counts, meta, fastq_1, fastq_2 ->
+        if (!fastq_2) {
+            return [ meta + [ single_end:true, fq_pairs:counts[meta.id] ], [ fastq_1 ] ]
+        } else {
+            return [ meta + [ single_end:false, fq_pairs:counts[meta.id] ], [ fastq_1, fastq_2 ] ]
+        }
+    }
+    .tap { ch_input_counts }
+    .map { meta, fastqs -> fastqs }
+    .reduce([:]) { counts, fastqs -> // get number of fastq sets in the run - for creating unique ID:s
+        counts[fastqs] = counts.size() + 1
+        return counts
+    }
+    .combine( ch_input_counts )
+    .map { lineno, meta, fastqs -> // append line number to sample id for unique set ids
+        new_meta = meta + [id:meta.id+"_id"+lineno[fastqs]]
+        return [ new_meta, fastqs ]
+    }
+    .tap { ch_samplesheet } // Output, the rest is just for validation
+    .map { meta, fastqs ->
+        return [ meta.sample, groupKey( meta + [id:meta.sample], meta.fq_pairs ), fastqs ]
+    }
+    .groupTuple()
+    .map {
+        validateInputSamplesheet(it)
+    }
+
+    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() {
+    def citation_text = [
+            "Tools used in the workflow included:",
+            "BCFtools (Danecek et al. 2021),",
+            "DROP (Yépez et al. 2021),",
+            params.switch_vep ? "EnsemblVEP (McLaren et al. 2016)," : "",
+            "fastp (Chen et al. 2018),",
+            "FastQC (Andrews 2010),",
+            params.switch_drop_as ? "FRASER (Mertes et al 2021)," : "",
+            "GATK (McKenna et al. 2010),",
+            params.switch_stringtie ? "GFFCompare (Pertea et al. 2020), StringTie (Pertea et al. 2015)," : "",
+            "MultiQC (Ewels et al. 2016),",
+            params.switch_drop_ae ? "OUTRIDER (Brechtmann et al. 2018)," : "",
+            "SAMtools (Danecek et al. 2021),",
+            "Salmon (Patro et al. 2017),",
+            "STAR (Dobin et al. 2012),",
+            params.switch_build_tracks ? "UCSC tools (Kent et al. 2010)" : "",
+            "."
+        ].join(' ').trim()
+
+    return citation_text
+}
+
+def toolBibliographyText() {
+    def reference_text = [
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+            params.switch_drop_ae ? "<li>Brechtmann F, Mertes C, Matusevičiūtė A, et al. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. The American Journal of Human Genetics. 12 2018;103:907-917. doi:10.1016/J.AJHG.2018.10.025</li>" : "",
+            "<li>Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England). 9 2018;34:i884-i890. doi:10.1093/BIOINFORMATICS/BTY560</li>",
+            "<li>Dale R, Grüning B, Sjödin A, et al. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature methods. 7 2018;15:475-476. doi:10.1038/S41592-018-0046-7</li>",
+            "<li>Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 1 2021;10:1-4. doi:10.1093/GIGASCIENCE/GIAB008</li>",
+            "<li>Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 10 2012;29:15-21. doi:10.1093/bioinformatics/bts635</li>",
+            "<li>Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics (Oxford, England). 10 2016;32:3047-3048. doi:10.1093/BIOINFORMATICS/BTW354</li>",
+            "<li>Ewels PA, Peltzer A, Fillinger S, et al. The nf-core framework for community-curated bioinformatics pipelines. Nature biotechnology. 3 2020;38:276-278. doi:10.1038/S41587-020-0439-X</li>",
+            params.switch_build_tracks ? "<li>Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 9 2010;26:2204-2207. doi:10.1093/BIOINFORMATICS/BTQ351</li>" : "",
+            "<li>Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PloS one. 5 2017;12. doi:10.1371/JOURNAL.PONE.0177459</li>",
+            "<li>Leprevost FDV, Grüning BA, Aflitos SA, et al. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England). 8 2017;33:2580-2582. doi:10.1093/BIOINFORMATICS/BTX192</li>",
+            "<li>McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research. 9 2010;20:1297-1303. doi:10.1101/GR.107524.110</li>",
+            params.switch_vep ? "<li>McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome biology. 6 2016;17. doi:10.1186/S13059-016-0974-4</li>" : "",
+            "<li>MerkelDirk. Docker. Linux Journal. Published online 3 2014. doi:10.5555/2600239.2600241</li>",
+            params.switch_drop_as ? "<li>Mertes C, Scheller IF, Yépez VA, et al. Detection of aberrant splicing events in RNA-seq data using FRASER. Nature Communications 2021 12:1. 1 2021;12:1-13. doi:10.1038/s41467-020-20573-7</li>" : "",
+            "<li>Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nature methods. 2017;14:417-419. doi:10.1038/NMETH.4197</li>",
+            params.switch_stringtie ? "<li>Pertea M, Pertea G. GFF Utilities: GffRead and GffCompare. F1000Research. 9 2020;9:304. doi:10.12688/F1000RESEARCH.23297.1</li>" : "",
+            params.switch_stringtie ? "<li>Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnology. 2015;33:290-295. doi:10.1038/NBT.3122</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"] = 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()
+}
+
+    //
+    // GMS tomte logo (WIP)
+    //
+def gmsTomteLogo(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}
+        ${colors.blue}   _____ __  __  _____            _                  _${colors.reset}
+        ${colors.blue}  / ____|  \\/  |/ ____|          | |                | |${colors.reset}
+        ${colors.blue} | |  __| \\  / | (___    ______  | |_ ___  _ __ ___ | |_ ___${colors.reset}
+        ${colors.blue} | | |_ | |\\/| |\\___ \\  |______| | __/ _ \\| '_ ` _ \\| __/ _ \\${colors.reset}
+        ${colors.blue} | |__| | |  | |____) |          | || (_) | | | | | | ||  __/${colors.reset}
+        ${colors.blue}  \\_____|_|  |_|_____/            \\__\\___/|_| |_| |_|\\__\\___|${colors.reset}
+
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
+
+def gmsTomteHatLogo(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}
+        ${colors.red}                                                                     @++@${colors.reset}
+        ${colors.blue}   _____ __  __  _____            _                  _              ${colors.red}@    @${colors.reset}
+        ${colors.blue}  / ____|  \\/  |/ ____|          | |                | |            ${colors.red}@      @@${colors.reset}
+        ${colors.blue} | |  __| \\  / | (___    ______  | |_ ___  _ __ ___ | |_ ___      ${colors.red}@       @${colors.white}(+)${colors.reset}
+        ${colors.blue} | | |_ | |\\/| |\\___ \\  |______| | __/ _ \\| '_ ` _ \\| __/ _ \\    ${colors.red}@        @${colors.reset}
+        ${colors.blue} | |__| | |  | |____) |          | || (_) | | | | | | ||  __/    ${colors.red}@         @${colors.reset}
+        ${colors.blue}  \\_____|_|  |_|_____/            \\__\\___/|_| |_| |_|\\__\\___|    ${colors.red}@         @${colors.reset}
+        ${colors.white}                                                                 @===${colors.yellow}(@)${colors.white}===@${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
+
+def gmsTomteHatLogo2(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}                 ${colors.red}_${colors.reset}
+        ${colors.red}                                                                     /  \\${colors.reset}
+        ${colors.blue}   _____ __  __  _____            _                  _              ${colors.red}/     \\${colors.reset}
+        ${colors.blue}  / ____|  \\/  |/ ____|          | |                | |            ${colors.red}/      |\\${colors.reset}
+        ${colors.blue} | |  __| \\  / | (___    ______  | |_ ___  _ __ ___ | |_ ___      ${colors.red}/       |${colors.white}(+)${colors.reset}
+        ${colors.blue} | | |_ | |\\/| |\\___ \\  |______| | __/ _ \\| '_ ` _ \\| __/ _ \\    ${colors.red}|        \\${colors.reset}
+        ${colors.blue} | |__| | |  | |____) |          | || (_) | | | | | | ||  __/    ${colors.red}|         |${colors.reset}
+        ${colors.blue}  \\_____|_|  |_|_____/            \\__\\___/|_| |_| |_|\\__\\___|    ${colors.red}|_________|${colors.reset}
+        ${colors.white}                                                                 {_________}${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
new file mode 100644
index 00000000..ac31f28f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -0,0 +1,126 @@
+//
+// Subworkflow with functionality that may be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NEXTFLOW_PIPELINE {
+
+    take:
+    print_version        // boolean: print version
+    dump_parameters      // boolean: dump parameters
+    outdir               //    path: base directory used to publish pipeline results
+    check_conda_channels // boolean: check conda channels
+
+    main:
+
+    //
+    // Print workflow version and exit on --version
+    //
+    if (print_version) {
+        log.info "${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 00000000..e5c3a0a8
--- /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 00000000..68718e4f
--- /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 00000000..846287c4
--- /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"
+    }
+}
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 00000000..ca964ce8
--- /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 00000000..d0a926bf
--- /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 00000000..f8476112
--- /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 00000000..a8b55d6f
--- /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 00000000..d08d2434
--- /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 00000000..1dc317f8
--- /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 00000000..facbdcfd
--- /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"
+    }
+}
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 00000000..8940d32d
--- /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 00000000..84ee1e1d
--- /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"
+    }
+}
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 00000000..d0a926bf
--- /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 00000000..ac8523c9
--- /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 00000000..2585b65d
--- /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-validation'
+include { paramsSummaryLog   } from 'plugin/nf-validation'
+include { validateParameters } from 'plugin/nf-validation'
+
+/*
+========================================================================================
+    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 00000000..3d4a6b04
--- /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 00000000..5784a33f
--- /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 00000000..7626c1c9
--- /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 00000000..60b1cfff
--- /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/test_data/drop_data/mock_gene_panel.tsv b/test_data/drop_data/mock_gene_panel.tsv
index b55a6e2d..f92b140b 100644
--- a/test_data/drop_data/mock_gene_panel.tsv
+++ b/test_data/drop_data/mock_gene_panel.tsv
@@ -1,44 +1,44 @@
-##genome_build=37
-##gene_panel=MOCK,version=1.0,updated_at=2023-09-01,display_name=MOCK
-##contig=1
-##contig=2
-##contig=3
-##contig=4
-##contig=5
-##contig=6
-##contig=7
-##contig=8
-##contig=9
-##contig=10
-##contig=11
-##contig=12
-##contig=13
-##contig=14
-##contig=15
-##contig=16
-##contig=17
-##contig=18
-##contig=19
-##contig=20
-##contig=21
-##contig=22
-##contig=X
-##contig=Y
-#chromosome	gene_start	gene_stop	hgnc_id	hgnc_symbol
-21	19641433	19775970	9490	TMPRSS15
-21	23807352	23811387	16756	MAPK6P2
-21	27011594	27089874	14686	JAM2
-21	31691450	31692607	33760	KRTAP26-1
-21	37757689	37789125	1911	CHAF1B
-21	33974120	33984918	1301	CFAP298
-21	34949859	34960990	2993	DONSON
-21	42688661	42729654	1253	FAM3B
-21	44263190	44299693	12756	WDR4
-21	44473301	44496487	1550	CBS
-21	44473301	44496055	51829	CBSL
-21	44589141	44592913	2388	CRYAA
-21	44834398	44847002	11142	SIK1
-21	45161367	45182180	8819	PDXK
-21	46720160	46725172	16621	LINC00315
-21	47401684	47424962	2211	COL6A1
-21	47518033	47552763	2212	COL6A2
\ No newline at end of file
+##genome_build=37
+##gene_panel=MOCK,version=1.0,updated_at=2023-09-01,display_name=MOCK
+##contig=1
+##contig=2
+##contig=3
+##contig=4
+##contig=5
+##contig=6
+##contig=7
+##contig=8
+##contig=9
+##contig=10
+##contig=11
+##contig=12
+##contig=13
+##contig=14
+##contig=15
+##contig=16
+##contig=17
+##contig=18
+##contig=19
+##contig=20
+##contig=21
+##contig=22
+##contig=X
+##contig=Y
+#chromosome	gene_start	gene_stop	hgnc_id	hgnc_symbol
+21	19641433	19775970	9490	TMPRSS15
+21	23807352	23811387	16756	MAPK6P2
+21	27011594	27089874	14686	JAM2
+21	31691450	31692607	33760	KRTAP26-1
+21	37757689	37789125	1911	CHAF1B
+21	33974120	33984918	1301	CFAP298
+21	34949859	34960990	2993	DONSON
+21	42688661	42729654	1253	FAM3B
+21	44263190	44299693	12756	WDR4
+21	44473301	44496487	1550	CBS
+21	44473301	44496055	51829	CBSL
+21	44589141	44592913	2388	CRYAA
+21	44834398	44847002	11142	SIK1
+21	45161367	45182180	8819	PDXK
+21	46720160	46725172	16621	LINC00315
+21	47401684	47424962	2211	COL6A1
+21	47518033	47552763	2212	COL6A2
diff --git a/test_data/drop_data/sampleAnnotation.tsv b/test_data/drop_data/sampleAnnotation.tsv
index 9f2cfe0b..c4a31bbf 100644
--- a/test_data/drop_data/sampleAnnotation.tsv
+++ b/test_data/drop_data/sampleAnnotation.tsv
@@ -1,51 +1,51 @@
-RNA_ID	RNA_BAM_FILE	DNA_VCF_FILE	DNA_ID	DROP_GROUP	PAIRED_END	COUNT_MODE	COUNT_OVERLAPS	STRAND	SPLICE_COUNTS_DIR	HPO_TERMS	GENE_COUNTS_FILE	GENE_ANNOTATION	GENOME
-R32621	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R23611	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R97979	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R73084	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R34104	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R18431	NA	NA	NA	fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R83610	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0014	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R17262	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R82158	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R41887	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0019	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0020	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R82971	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R31640	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R98710	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R95723	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R55237	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0021	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0022	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0023	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0024	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R64948	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R68565	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R62478	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R20700	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R39139	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R28319	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R61100	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R74382	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0025	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R36014	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R74287	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0026	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R24289	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R58118	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R97605	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R85592	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R12355	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0027	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0028	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R34834	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R43173	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R31569	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R78859	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0029	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R92616	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0030	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R0031	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
-R79450	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
\ No newline at end of file
+RNA_ID	RNA_BAM_FILE	DNA_VCF_FILE	DNA_ID	DROP_GROUP	PAIRED_END	COUNT_MODE	COUNT_OVERLAPS	STRAND	SPLICE_COUNTS_DIR	HPO_TERMS	GENE_COUNTS_FILE	GENE_ANNOTATION	GENOME
+R32621	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R23611	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R97979	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R73084	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R34104	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R18431	NA	NA	NA	fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R83610	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0014	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R17262	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R82158	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R41887	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0019	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0020	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R82971	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R31640	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R98710	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R95723	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R55237	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0021	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0022	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0023	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0024	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R64948	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R68565	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R62478	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R20700	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R39139	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R28319	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R61100	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R74382	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0025	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R36014	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R74287	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0026	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R24289	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R58118	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R97605	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R85592	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R12355	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0027	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0028	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R34834	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R43173	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R31569	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R78859	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0029	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R92616	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0030	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R0031	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
+R79450	NA	NA	NA	outrider, fraser	TRUE	IntersectionStrict	TRUE	reverse	drop_data	NA	drop_data/geneCounts.tsv	grch37_chr21	NA
diff --git a/test_data/samplesheet_chr21.csv b/test_data/samplesheet_chr21.csv
index 0e5e5d02..c7a52e0b 100644
--- a/test_data/samplesheet_chr21.csv
+++ b/test_data/samplesheet_chr21.csv
@@ -1,3 +1,3 @@
 case,sample,fastq_1,fastq_2,strandedness
 finequagga,ACC5963A1,https://github.com/genomic-medicine-sweden/tomte/raw/master/test_data/ACC5963A1_sub_1.fastq.gz,https://github.com/genomic-medicine-sweden/tomte/raw/master/test_data/ACC5963A1_sub_2.fastq.gz,reverse
-sharpparrot,ACC5963A2,https://github.com/genomic-medicine-sweden/tomte/raw/master/test_data/ACC5963A2_sub_1.fastq.gz,https://github.com/genomic-medicine-sweden/tomte/raw/master/test_data/ACC5963A2_sub_2.fastq.gz,reverse
+finequagga,ACC5963A2,https://github.com/genomic-medicine-sweden/tomte/raw/master/test_data/ACC5963A2_sub_1.fastq.gz,https://github.com/genomic-medicine-sweden/tomte/raw/master/test_data/ACC5963A2_sub_2.fastq.gz,reverse
diff --git a/test_data/subsample.bed b/test_data/subsample.bed
index b51d4e12..06465854 100644
--- a/test_data/subsample.bed
+++ b/test_data/subsample.bed
@@ -1 +1 @@
-chr21	25880535	26171128
\ No newline at end of file
+chr21	25880535	26171128
diff --git a/workflows/tomte.nf b/workflows/tomte.nf
index 13cc1e9d..1b9d3472 100644
--- a/workflows/tomte.nf
+++ b/workflows/tomte.nf
@@ -1,64 +1,18 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    PRINT PARAMS SUMMARY
+    IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.gmsLogo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-def summary_params = paramsSummaryMap(workflow)
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-WorkflowTomte.initialise(params, log)
-
-// TODO nf-core: change this to use the plugin nf-validation
-// Check input path parameters to see if they exist
-def checkPathParamList = [
-    params.input,
-    params.multiqc_config,
-    params.fasta,
-    params.fai,
-    params.sequence_dict,
-    params.star_index,
-    params.salmon_index,
-    params.transcript_fasta,
-    params.gtf,
-    params.reference_drop_annot_file,
-    params.reference_drop_splice_folder,
-    params.reference_drop_count_file,
-    params.gene_panel_clinical_filter,
-    params.subsample_bed,
-    params.vep_filters,
-    params.vep_cache
-]
-
-for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    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 LOCAL MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+//
+// SUBWORKFLOW: nf-core
+//
+include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 
 //
 // SUBWORKFLOW: local
 //
-include { CHECK_INPUT             } from '../subworkflows/local/input_check'
 include { PREPARE_REFERENCES      } from '../subworkflows/local/prepare_references'
 include { ALIGNMENT               } from '../subworkflows/local/alignment'
 include { BAM_QC                  } from '../subworkflows/local/bam_qc'
@@ -67,27 +21,18 @@ include { CALL_VARIANTS           } from '../subworkflows/local/call_variants'
 include { ALLELE_SPECIFIC_CALLING } from '../subworkflows/local/allele_specific_calling'
 include { ANNOTATE_SNV            } from '../subworkflows/local/annotate_snv'
 include { IGV_TRACKS              } from '../subworkflows/local/igv_tracks'
+include { methodsDescriptionText  } from '../subworkflows/local/utils_nfcore_tomte_pipeline'
 
 //
-// MODULE: local
-//
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// SUBWORKFLOW: nf-core/subworkflows
+// MODULE: nf-core
 //
 
 //
-// MODULE: Installed directly from nf-core/modules
+// MODULE: local
 //
-include { FASTQC                      } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { FASTQC                 } from '../modules/nf-core/fastqc/main'
+include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+include { paramsSummaryMap       } from 'plugin/nf-validation'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -95,21 +40,18 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// Info required for completion email and summary
-def multiqc_report = []
-
 workflow TOMTE {
 
-    ch_versions = Channel.empty()
+    take:
+    ch_samplesheet // channel: samplesheet read in from --input
 
-    // Initialize input channels
-    if (params.input) {
-        ch_input = Channel.fromPath(params.input)
-        CHECK_INPUT (ch_input)
-        ch_versions = ch_versions.mix(CHECK_INPUT.out.versions)
-    } else {
-        exit 1, 'Input samplesheet not specified!'
-    }
+    main:
+
+    ch_versions      = Channel.empty()
+    ch_multiqc_files = Channel.empty()
+
+    ch_samples   = ch_samplesheet.map { meta, fastqs -> meta }
+    ch_case_info = ch_samples.toList().map { create_case_channel(it) }
 
     ch_vep_cache_unprocessed      = params.vep_cache                    ? Channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()
                                                                         : Channel.value([[],[]])
@@ -125,6 +67,22 @@ workflow TOMTE {
                                                                         : Channel.empty()
     ch_gene_panel_clinical_filter = params.gene_panel_clinical_filter   ? Channel.fromPath(params.gene_panel_clinical_filter).collect()
                                                                         : Channel.empty()
+    ch_vep_extra_files_unsplit    = params.vep_plugin_files             ? Channel.fromPath(params.vep_plugin_files).collect()
+                                                                        : Channel.value([])
+    ch_platform                   = params.platform.collect()
+
+    // Read and store paths in the vep_plugin_files file
+    ch_vep_extra_files_unsplit.splitCsv ( header:true )
+        .map { row ->
+            f = file(row.vep_files[0])
+            if(f.isFile() || f.isDirectory()){
+                return [f]
+            } else {
+                error("\nVep database file ${f} does not exist.")
+            }
+        }
+        .collect()
+        .set {ch_vep_extra_files}
 
     PREPARE_REFERENCES(
         params.fasta,
@@ -135,54 +93,37 @@ workflow TOMTE {
         params.transcript_fasta,
         params.salmon_index
     ).set { ch_references }
-    ch_versions = ch_versions.mix(PREPARE_REFERENCES.out.versions)
 
     // Gather built indices or get them from the params
-    ch_chrom_sizes           = ch_references.chrom_sizes
-    ch_sequence_dict         = params.sequence_dict           ? Channel.fromPath(params.sequence_dict).collect()
-                                                              : ( ch_references.sequence_dict            ?: Channel.empty() )
-    ch_subsample_bed         = params.subsample_bed           ? Channel.fromPath(params.subsample_bed).collect()
-                                                              : Channel.empty()
-    ch_vep_cache             = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") )  ? ch_references.vep_resources
-                                                                : ( params.vep_cache  ? Channel.fromPath(params.vep_cache).collect() : Channel.value([]) )
-    //
-    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
-    //
-    // INPUT_CHECK (
-    //    file(params.input)
-    // )
-    // ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
-    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
-    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
-    // ! There is currently no tooling to help you write a sample sheet schema
-
-    //
-    // MODULE: Run FastQC
-    //
+    ch_chrom_sizes      = ch_references.chrom_sizes
+    ch_sequence_dict    = params.sequence_dict          ? Channel.fromPath(params.sequence_dict).collect()
+                                                        : ( ch_references.sequence_dict            ?: Channel.empty() )
+    ch_subsample_bed    = params.subsample_bed          ? Channel.fromPath(params.subsample_bed).collect()
+                                                        : Channel.empty()
+    ch_vep_cache        = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") )  ? ch_references.vep_resources
+                                                        : ( params.vep_cache  ? Channel.fromPath(params.vep_cache).collect() : Channel.value([]) )
 
     FASTQC (
-        CHECK_INPUT.out.reads
+        ch_samplesheet
     )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
-
-    // Alignment
     ALIGNMENT(
-        CHECK_INPUT.out.reads,
+        ch_samplesheet,
         ch_references.star_index,
         ch_references.gtf,
-        params.platform,
+        ch_platform,
         params.subsample_bed,
         params.seed_frac,
         params.num_reads,
-        params.subsample_region_switch,
-        params.downsample_switch,
+        params.switch_subsample_region,
+        params.switch_downsample,
         ch_references.salmon_index,
         ch_references.fasta_meta
-    ).set {ch_alignment}
+    ).set { ch_alignment }
     ch_versions = ch_versions.mix(ALIGNMENT.out.versions)
 
-    // BAM QC
     BAM_QC(
         ch_alignment.bam,
         ch_references.fasta_no_meta,
@@ -191,7 +132,6 @@ workflow TOMTE {
     )
     ch_versions = ch_versions.mix(BAM_QC.out.versions)
 
-    // Analyse transcripts
     ANALYSE_TRANSCRIPTS(
         ch_alignment.bam_bai,
         ch_alignment.bam_ds_bai,
@@ -207,11 +147,11 @@ workflow TOMTE {
         params.drop_padjcutoff_ae,
         params.drop_padjcutoff_as,
         params.drop_zscorecutoff,
-        ch_gene_panel_clinical_filter
+        ch_gene_panel_clinical_filter,
+        ch_case_info
     )
     ch_versions = ch_versions.mix(ANALYSE_TRANSCRIPTS.out.versions)
 
-    // Call variants
     CALL_VARIANTS(
         ch_alignment.bam_bai,
         ch_references.fasta_no_meta,
@@ -221,14 +161,14 @@ workflow TOMTE {
     )
     ch_versions = ch_versions.mix(CALL_VARIANTS.out.versions)
 
-
     ALLELE_SPECIFIC_CALLING(
         CALL_VARIANTS.out.vcf_tbi,
         ch_alignment.bam_bai,
         ch_references.fasta_no_meta,
         ch_references.fai_no_meta,
         ch_references.sequence_dict,
-        ch_references.interval_list
+        ch_references.interval_list,
+        ch_case_info
     )
     ch_versions = ch_versions.mix(ALLELE_SPECIFIC_CALLING.out.versions)
 
@@ -237,7 +177,8 @@ workflow TOMTE {
         params.genome,
         params.vep_cache_version,
         ch_vep_cache,
-        ch_references.fasta_no_meta,
+        ch_references.fasta_meta,
+        ch_vep_extra_files,
     )
     ch_versions = ch_versions.mix(ANNOTATE_SNV.out.versions)
 
@@ -246,33 +187,39 @@ workflow TOMTE {
         ch_chrom_sizes,
         ch_alignment.spl_junc
     )
+    ch_versions = ch_versions.mix(IGV_TRACKS.out.versions)
 
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
+    //
+    // Collate and save software versions
+    //
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'tomte_software_mqc_versions.yml', sort: true, newLine: true)
+        .set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    workflow_summary    = WorkflowTomte.paramsSummaryMultiqc(workflow, summary_params)
-    ch_workflow_summary = Channel.value(workflow_summary)
-
-    methods_description    = WorkflowTomte.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
-    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_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ALIGNMENT.out.fastp_report.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ALIGNMENT.out.star_log_final.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ALIGNMENT.out.gene_counts.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ALIGNMENT.out.salmon_info.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(BAM_QC.out.metrics.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ANALYSE_TRANSCRIPTS.out.stats_gtf.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(CALL_VARIANTS.out.stats.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ANNOTATE_SNV.out.report.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
+    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    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))
+    ch_multiqc_files                      = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ALIGNMENT.out.fastp_report.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ALIGNMENT.out.star_log_final.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ALIGNMENT.out.gene_counts.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ALIGNMENT.out.salmon_info.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(BAM_QC.out.metrics_general_rna.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(BAM_QC.out.metrics_insert_size.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ANALYSE_TRANSCRIPTS.out.stats_gtf.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(CALL_VARIANTS.out.stats.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ANNOTATE_SNV.out.report.collect{it[1]}.ifEmpty([]))
 
     MULTIQC (
         ch_multiqc_files.collect(),
@@ -280,24 +227,32 @@ workflow TOMTE {
         ch_multiqc_custom_config.toList(),
         ch_multiqc_logo.toList()
     )
-    multiqc_report = MULTIQC.out.report.toList()
+
+    emit:
+    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    multiqc_report = Channel.empty()
+    versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    COMPLETION EMAIL AND SUMMARY
+    FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
-    }
-    NfcoreTemplate.dump_parameters(workflow, params)
-    NfcoreTemplate.summary(workflow, params, log)
-    if (params.hook_url) {
-        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
+// Function to get a list of metadata (e.g. case id) for the case [ meta ]
+def create_case_channel(List rows) {
+    def case_info = [:]
+    def probands = []
+
+    for (item in rows) {
+        probands.add(item.sample)
     }
+
+    case_info.probands = probands.unique()
+    case_info.id = rows[0].case
+
+    return case_info
 }
 
 /*